This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Chemfiles.Atom, and Selection.
Note that the integrates with the AtomsBase ecosystem via appropriate conversion routines. See AtomsBase integration for more details.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
Chemfiles is integrated with the AtomsBase by means of appropriate convert methods as well as respective constructors, which are listed below. Note that these conversion routines copy data unlike the majority of functionality in Chemfiles.
If your main interest is in reading structural data from disk, have a look at AtomsIO. This package provides a uniform interface for reading structural data and exposing them in an AtomsBase-compatible way. Under the hood the package employs a number of parser packages (including Chemfiles) to support reading / writing a wide range of file formats.
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
Get the Atom at the given index of the topology without creating a copy.
Warning
This function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.25 on Thursday 17 August 2023. Using Julia version 1.6.7.
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+var documenterSearchIndex = {"docs":
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By default this creates a copy so as to be safe. To not create a copy, use @view frame[index].\n\nSee also Base.view(frame::Frame, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame, Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.view-Tuple{Frame, Integer}","page":"Frame","title":"Base.view","text":"view(frame::Frame, index::Integer) -> Chemfiles.Atom\n\n\nGet the Atom at the given index of the frame without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. 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The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Vector{String}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. 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The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue, Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue, Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Vector{UInt64}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Vector{String}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue, String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(\n topology::Topology,\n index::Integer\n) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(\n residue::Residue,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/atomsbase/#AtomsBase-integration","page":"AtomsBase integration","title":"AtomsBase integration","text":"","category":"section"},{"location":"reference/atomsbase/","page":"AtomsBase integration","title":"AtomsBase integration","text":"Chemfiles is integrated with the AtomsBase by means of appropriate convert methods as well as respective constructors, which are listed below. Note that these conversion routines copy data unlike the majority of functionality in Chemfiles.","category":"page"},{"location":"reference/atomsbase/","page":"AtomsBase integration","title":"AtomsBase integration","text":"If your main interest is in reading structural data from disk, have a look at AtomsIO. This package provides a uniform interface for reading structural data and exposing them in an AtomsBase-compatible way. Under the hood the package employs a number of parser packages (including Chemfiles) to support reading / writing a wide range of file formats.","category":"page"},{"location":"reference/atomsbase/","page":"AtomsBase integration","title":"AtomsBase integration","text":"Modules = [Chemfiles, Base, AtomsBase]\nPages = [\"atomsbase.jl\"]","category":"page"},{"location":"reference/atomsbase/#AtomsBase.AbstractSystem-Tuple{Frame}","page":"AtomsBase integration","title":"AtomsBase.AbstractSystem","text":"Construct an AtomsBase AbstractSystem from a Chemfiles Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atomsbase/#AtomsBase.FlexibleSystem-Tuple{Frame}","page":"AtomsBase integration","title":"AtomsBase.FlexibleSystem","text":"Construct an AtomsBase FlexibleSystem from a Chemfiles Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atomsbase/#Base.convert-Tuple{Type{AbstractSystem}, Frame}","page":"AtomsBase integration","title":"Base.convert","text":"convert(\n _::Type{AbstractSystem},\n frame::Frame\n) -> FlexibleSystem\n\n\nConvert a Chemfiles Frame to an AtomsBase AbstractSystem\n\n\n\n\n\n","category":"method"},{"location":"reference/atomsbase/#Base.convert-Tuple{Type{FlexibleSystem}, Frame}","page":"AtomsBase integration","title":"Base.convert","text":"convert(\n _::Type{FlexibleSystem},\n frame::Frame\n) -> FlexibleSystem\n\n\nConvert a Chemfiles Frame to an AtomsBase FlexibleSystem\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Vector{Float64}) -> UnitCell\nUnitCell(\n lengths::Vector{Float64},\n angles::Vector{Float64}\n) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Matrix{Float64}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Matrix{Float64}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Matrix{Float64}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Vector{Float64})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Vector{Float64})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell, CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(\n cell::UnitCell,\n vector::Vector{Float64}\n) -> Vector{Float64}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles:\n\nChemfiles.UnknownBond: when the bond order is not specified\nChemfiles.SingleBond: for single bonds\nChemfiles.DoubleBond: for double bonds\nChemfiles.TripleBond: for triple bonds\nChemfiles.QuadrupleBond: for quadruple bonds (present in some metals)\nChemfiles.QuintupletBond: for qintuplet bonds (present in some metals)\nChemfiles.AmideBond: for amide bonds\nChemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.getindex-Tuple{Topology, Integer}","page":"Topology","title":"Base.getindex","text":"getindex(\n topology::Topology,\n index::Integer\n) -> Chemfiles.Atom\n\n\nGet the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].\n\nSee also Base.view(topology::Topology, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology, Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.view-Tuple{Topology, Integer}","page":"Topology","title":"Base.view","text":"view(topology::Topology, index::Integer) -> Chemfiles.Atom\n\n\nGet the Atom at the given index of the topology without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology, Chemfiles.Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Chemfiles.Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology, Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Matrix{UInt64}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology, Residue, Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(\n topology::Topology,\n first::Residue,\n second::Residue\n) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(\n topology::Topology,\n i::Integer,\n j::Integer\n) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(\n topology::Topology\n) -> Vector{Chemfiles.BondOrder}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Matrix{UInt64}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Matrix{UInt64}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Matrix{UInt64}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_atom!-Tuple{Topology, Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_bond!-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection, Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Vector{Any}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Trajectory","page":"Trajectory","title":"Trajectory","text":"","category":"section"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Trajectory","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory","page":"Trajectory","title":"Chemfiles.Trajectory","text":"A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Modules = [Chemfiles]\nPages = [\"Trajectory.jl\"]","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory-2","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(path::AbstractString) -> Trajectory\nTrajectory(path::AbstractString, mode::Char) -> Trajectory\nTrajectory(\n path::AbstractString,\n mode::Char,\n format::AbstractString\n) -> Trajectory\n\n\nOpens the trajectory file at the given path.\n\nThe opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/#Chemfiles.Trajectory-Tuple{Function, Vararg{Any, N} where N}","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(f::Function, args...) -> Any\n\n\nApply the function f to the result of Trajectory(args...) and close the resulting trajectory upon completion, similar to open(f, args...).\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.close-Tuple{Trajectory}","page":"Trajectory","title":"Base.close","text":"close(trajectory::Trajectory)\n\n\nClose a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read!-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Vector{UInt8}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.write-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(\n format::AbstractString,\n data::Union{Nothing, AbstractString, Vector{UInt8}}\n) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. 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Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step!-Tuple{Trajectory, Integer, Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(\n trajectory::Trajectory,\n step::Integer,\n frame::Frame\n)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step-Tuple{Trajectory, Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_cell!-Tuple{Trajectory, UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(\n trajectory::Trajectory,\n path::AbstractString,\n format::AbstractString\n)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory, Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Chemfiles.Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Chemfiles.Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Chemfiles.Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Chemfiles.Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#AtomsBase.atomic_number-Tuple{Chemfiles.Atom}","page":"Atom","title":"AtomsBase.atomic_number","text":"atomic_number(atom::Chemfiles.Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Chemfiles.Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Chemfiles.Atom) -> Chemfiles.Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Chemfiles.Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Chemfiles.Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Chemfiles.Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Chemfiles.Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Chemfiles.Atom) -> Vector{String}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Chemfiles.Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Chemfiles.Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Chemfiles.Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Chemfiles.Atom, String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Chemfiles.Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Chemfiles.Atom, Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Chemfiles.Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Chemfiles.Atom, Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Chemfiles.Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Chemfiles.Atom, String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Chemfiles.Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Chemfiles.Atom, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(\n atom::Chemfiles.Atom,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Chemfiles.Atom, String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Chemfiles.Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Chemfiles.Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Chemfiles.Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Chemfiles.Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String: Name of the format\nextension::Union{Nothing, String}: Extension associated with the format, or nothing if there is no extension associated.\ndescription::String: Extended user-facing description of the format\nreference::String: URL pointing to the format definition/reference\nread::Bool: Is reading files in this format implemented?\nwrite::Bool: Is writing files in this format implemented?\nmemory::Bool: Does this format support in-memory IO?\npositions::Bool: Does this format support storing atomic positions?\nvelocities::Bool: Does this format support storing atomic velocities?\nunit_cell::Bool: Does this format support storing unit cell information?\natoms::Bool: Does this format support storing atom names or types?\nbonds::Bool: Does this format support storing bonds between atoms?\nresidues::Bool: Does this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Vector{Chemfiles.FormatMetadata}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Chemfiles.Atom, and Selection.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Note that the integrates with the AtomsBase ecosystem via appropriate conversion routines. See AtomsBase integration for more details.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n \"reference/atomsbase.md\"\n]","category":"page"}]
+}
diff --git a/latest/tutorials/index.html b/latest/tutorials/index.html
new file mode 100644
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--- /dev/null
+++ b/latest/tutorials/index.html
@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 1:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Chemfiles.Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell([10.0, 10.0, 10.0]))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.25 on Thursday 17 August 2023. Using Julia version 1.6.7.
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new file mode 100644
index 0000000..15dc682
--- /dev/null
+++ b/v0.10.0/assets/documenter.js
@@ -0,0 +1,264 @@
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+////////////////////////////////////////////////////////////////////////////////
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+// Modal settings dialog
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+ });
+});
+
+})
+////////////////////////////////////////////////////////////////////////////////
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+ var L0 = e.width();
+ if(L0 > L) {
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+ e.css('font-size', L * h0 / L0);
+ // TODO: make sure it survives resizes?
+ }
+ }
+ // call once and then register events
+ resize();
+ $(window).resize(resize);
+ $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
+$(document).ready(function() {
+ var sidebar = $("#documenter .docs-menu").get(0);
+ var active = $("#documenter .docs-menu .is-active").get(0);
+ if(typeof active !== 'undefined') {
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+function set_theme(theme) {
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+ // Store the theme in localStorage
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+ window.localStorage.setItem("documenter-theme", theme);
+ } else {
+ console.error("Browser does not support window.localStorage");
+ }
+}
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+// Theme picker setup
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+ // onchange callback
+ $('#documenter-themepicker').change(function themepick_callback(ev){
+ var themename = $('#documenter-themepicker option:selected').attr('value');
+ set_theme(themename);
+ });
+
+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
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+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
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+ })
+ }
+ }
+})
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+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
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+$(document).ready(function() {
+ var version_selector = $("#documenter .docs-version-selector");
+ var version_selector_select = $("#documenter .docs-version-selector select");
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+ window.location.href = target_href;
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+ // add the current version to the selector based on siteinfo.js, but only if the selector is empty
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+ var option = $("");
+ version_selector_select.append(option);
+ }
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+ var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
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+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
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+ var option = $("");
+ version_selector_select.append(option);
+ } else {
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+ option.value = version_url;
+ option.disabled = false;
+ }
+ });
+ }
+
+ // only show the version selector if the selector has been populated
+ if (version_selector_select.children("option").length > 0) {
+ version_selector.toggleClass("visible");
+ }
+})
+
+})
diff --git a/v0.10.0/assets/search.js b/v0.10.0/assets/search.js
new file mode 100644
index 0000000..71ebd87
--- /dev/null
+++ b/v0.10.0/assets/search.js
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+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.6/lunr.min',
+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.15/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
+ m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+ uri = {},
+ i = 14;
+
+ while (i--) uri[o.key[i]] = m[i] || "";
+
+ uri[o.q.name] = {};
+ uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+ if ($1) uri[o.q.name][$1] = $2;
+ });
+
+ return uri;
+ };
+ parseUri.options = {
+ strictMode: false,
+ key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+ q: {
+ name: "queryKey",
+ parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+ },
+ parser: {
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+
+ $("#search-form").submit(function(e) {
+ e.preventDefault()
+ })
+
+ // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+ // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
+ // ideally we'd just filter the original list but it's not available as a variable
+ lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
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+ 'him',
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+ 'how',
+ 'however',
+ 'i',
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+ 'into',
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+ 'its',
+ 'just',
+ 'least',
+ 'like',
+ 'likely',
+ 'may',
+ 'me',
+ 'might',
+ 'most',
+ 'must',
+ 'my',
+ 'neither',
+ 'no',
+ 'nor',
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+ 'of',
+ 'off',
+ 'often',
+ 'on',
+ 'or',
+ 'other',
+ 'our',
+ 'own',
+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
+ 'so',
+ 'some',
+ 'than',
+ 'that',
+ 'the',
+ 'their',
+ 'them',
+ 'then',
+ 'there',
+ 'these',
+ 'they',
+ 'this',
+ 'tis',
+ 'to',
+ 'too',
+ 'twas',
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+ 'was',
+ 'we',
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+ 'what',
+ 'when',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+ ])
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+ // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+ // would not find anything if searching for "add!", only for the entire qualification
+ lunr.tokenizer.separator = /[\s\-\.]+/
+
+ // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+ lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+ })
+ }
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+ lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
+ lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
+
+ var index = lunr(function () {
+ this.ref('location')
+ this.field('title',{boost: 100})
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+ })
+ var store = {}
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+ documenterSearchIndex['docs'].forEach(function(e) {
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+ })
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+ $(function(){
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+ searchinfo = $('#documenter-search-info');
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+ tokens.forEach(function (t) {
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+ fields: ["title"],
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+ usePipeline: true,
+ editDistance: 0,
+ wildcard: lunr.Query.wildcard.NONE
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+ boost: 10,
+ usePipeline: true,
+ editDistance: 2,
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+ })
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+ if (data.category != "page"){
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This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl on Sunday 14 February 2021. Using Julia version 1.5.3.
diff --git a/v0.10.0/search_index.js b/v0.10.0/search_index.js
new file mode 100644
index 0000000..afa56f2
--- /dev/null
+++ b/v0.10.0/search_index.js
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+var documenterSearchIndex = {"docs":
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In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"We start by opening the two trajectories we will need","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"And we create a Selection object to filter the atoms we want to remove.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"Finally, we can write the cleaned frame to the output file, and start the next iteration.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"The whole program look like this:","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials.html","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"reference/trajectory.html#Trajectory","page":"Trajectory","title":"Trajectory","text":"","category":"section"},{"location":"reference/trajectory.html","page":"Trajectory","title":"Trajectory","text":"Trajectory","category":"page"},{"location":"reference/trajectory.html#Chemfiles.Trajectory","page":"Trajectory","title":"Chemfiles.Trajectory","text":"A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory.html","page":"Trajectory","title":"Trajectory","text":"Modules = [Chemfiles]\nPages = [\"Trajectory.jl\"]","category":"page"},{"location":"reference/trajectory.html#Chemfiles.Trajectory-2","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(path::AbstractString) -> Trajectory\nTrajectory(path::AbstractString, mode::Char) -> Trajectory\nTrajectory(path::AbstractString, mode::Char, format::AbstractString) -> Trajectory\n\n\nOpens the trajectory file at the given path.\n\nThe opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory.html#Chemfiles.Trajectory-Tuple{Function,Vararg{Any,N} where N}","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(f::Function, args::Vararg{Any,N} where N) -> Any\n\n\nApply the function f to the result of Trajectory(args...) and close the resulting trajectory upon completion, similar to open(f, args...).\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.close-Tuple{Trajectory}","page":"Trajectory","title":"Base.close","text":"close(trajectory::Trajectory)\n\n\nClose a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.read!-Tuple{Trajectory,Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Array{UInt8,1}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Base.write-Tuple{Trajectory,Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(format::AbstractString, data::Union{Nothing, AbstractString, Array{UInt8,1}}) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory.html#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Chemfiles.read_step!-Tuple{Trajectory,Integer,Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(trajectory::Trajectory, step::Integer, frame::Frame)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Chemfiles.read_step-Tuple{Trajectory,Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Chemfiles.set_cell!-Tuple{Trajectory,UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(trajectory::Trajectory, path::AbstractString, format::AbstractString)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory.html#Chemfiles.set_topology!-Tuple{Trajectory,Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory.html","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory.html#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame.html#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame.html","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame.html#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame.html","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame.html#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.angle-Tuple{Frame,Integer,Integer,Integer}","page":"Frame","title":"Base.angle","text":"angle(frame::Frame, i::Integer, j::Integer, k::Integer) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.resize!-Tuple{Frame,Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(frame::Frame, atom::Atom, position::Array{Float64,1})\nadd_atom!(frame::Frame, atom::Atom, position::Array{Float64,1}, velocity::Array{Float64,1})\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame.html#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order::Any)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame.html#Chemfiles.add_residue!-Tuple{Frame,Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.dihedral-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.distance-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Array{String,1}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.out_of_plane-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.property-Tuple{Frame,String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.remove_atom!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.remove_bond!-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.set_cell!-Tuple{Frame,UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.set_property!-Tuple{Frame,String,Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value::Any)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.set_step!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.set_topology!-Tuple{Frame,Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame.html#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom.html","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom.html#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom.html","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom.html#Chemfiles.Atom-Tuple{Frame,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.Atom-Tuple{Topology,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Array{String,1}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.property-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.set_charge!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge::Any)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.set_mass!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass::Any)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.set_name!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.set_property!-Tuple{Atom,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(atom::Atom, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.set_type!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom.html#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc.html#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc.html","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc.html#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String\nName of the format\nextension::Union{Nothing, String}\nExtension associated with the format, or nothing if there is no extension associated.\ndescription::String\nExtended user-facing description of the format\nreference::String\nURL pointing to the format definition/reference\nread::Bool\nIs reading files in this format implemented?\nwrite::Bool\nIs writing files in this format implemented?\nmemory::Bool\nDoes this format support in-memory IO?\npositions::Bool\nDoes this format support storing atomic positions?\nvelocities::Bool\nDoes this format support storing atomic velocities?\nunit_cell::Bool\nDoes this format support storing unit cell information?\natoms::Bool\nDoes this format support storing atom names or types?\nbonds::Bool\nDoes this format support storing bonds between atoms?\nresidues::Bool\nDoes this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc.html#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc.html#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc.html#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Array{Chemfiles.FormatMetadata,1}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc.html#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc.html#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell.html","page":"UnitCell","title":"UnitCell","text":"UnitCell\nCellShape","category":"page"},{"location":"reference/cell.html#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell.html#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell.html","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell.html#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Array{Float64,1}) -> UnitCell\nUnitCell(lengths::Array{Float64,1}, angles::Array{Float64,1}) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell.html#Chemfiles.UnitCell-Tuple{Array{Float64,2}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Array{Float64,2}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Array{Float64,2}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.set_angles!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Array{Float64,1})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.set_lengths!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Array{Float64,1})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.set_shape!-Tuple{UnitCell,CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell.html#Chemfiles.wrap!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(cell::UnitCell, vector::Array{Float64,1}) -> Array{Float64,1}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue.html","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue.html#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue.html","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue.html#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id::Any) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue.html#Chemfiles.Residue-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Base.contains-Tuple{Residue,Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.add_atom!-Tuple{Residue,Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Array{UInt64,1}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Array{String,1}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.property-Tuple{Residue,String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.residue_for_atom-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(topology::Topology, index::Integer) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue.html#Chemfiles.set_property!-Tuple{Residue,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(residue::Residue, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection.html#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection.html","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection.html#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection.html","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection.html#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection.html#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection.html#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection.html#Chemfiles.evaluate-Tuple{Selection,Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Array{Any,1}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection.html#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology.html","page":"Topology","title":"Topology","text":"Topology\nChemfiles.BondOrder","category":"page"},{"location":"reference/topology.html#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology.html#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology.html","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology.html#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Base.resize!-Tuple{Topology,Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.add_atom!-Tuple{Topology,Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order::Any)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology.html#Chemfiles.add_residue!-Tuple{Topology,Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Array{UInt64,2}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.are_linked-Tuple{Topology,Residue,Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(topology::Topology, first::Residue, second::Residue) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.bond_order-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(topology::Topology, i::Integer, j::Integer) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(topology::Topology) -> Array{Chemfiles.BondOrder,1}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Array{UInt64,2}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Array{UInt64,2}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Array{UInt64,2}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.remove_atom!-Tuple{Topology,Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology.html#Chemfiles.remove_bond!-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"index.html#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.","category":"page"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"index.html#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"index.html#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"index.html","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n]","category":"page"}]
+}
diff --git a/v0.10.0/tutorials.html b/v0.10.0/tutorials.html
new file mode 100644
index 0000000..dec9781
--- /dev/null
+++ b/v0.10.0/tutorials.html
@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 0:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell(10, 10, 10))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl on Sunday 14 February 2021. Using Julia version 1.5.3.
diff --git a/v0.10.1/assets/documenter.js b/v0.10.1/assets/documenter.js
new file mode 100644
index 0000000..6d0b785
--- /dev/null
+++ b/v0.10.1/assets/documenter.js
@@ -0,0 +1,264 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/languages/julia.min',
+ 'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min',
+ 'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min',
+ 'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/contrib/auto-render.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ 'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min',
+ 'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/katex.min',
+ 'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/highlight.min',
+ 'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/languages/julia-repl.min',
+ },
+ shim: {
+ "highlight-julia": {
+ "deps": [
+ "highlight"
+ ]
+ },
+ "katex-auto-render": {
+ "deps": [
+ "katex"
+ ]
+ },
+ "headroom-jquery": {
+ "deps": [
+ "jquery",
+ "headroom"
+ ]
+ },
+ "highlight-julia-repl": {
+ "deps": [
+ "highlight"
+ ]
+ }
+}
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) {
+$(document).ready(function() {
+ renderMathInElement(
+ document.body,
+ {
+ "delimiters": [
+ {
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+ "right": "$",
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+ "right": "$$",
+ "display": true
+ },
+ {
+ "left": "\\[",
+ "right": "\\]",
+ "display": true
+ }
+ ]
+}
+
+ );
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) {
+$(document).ready(function() {
+ hljs.highlightAll();
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) {
+
+// Manages the top navigation bar (hides it when the user starts scrolling down on the
+// mobile).
+window.Headroom = Headroom; // work around buggy module loading?
+$(document).ready(function() {
+ $('#documenter .docs-navbar').headroom({
+ "tolerance": {"up": 10, "down": 10},
+ });
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Modal settings dialog
+$(document).ready(function() {
+ var settings = $('#documenter-settings');
+ $('#documenter-settings-button').click(function(){
+ settings.toggleClass('is-active');
+ });
+ // Close the dialog if X is clicked
+ $('#documenter-settings button.delete').click(function(){
+ settings.removeClass('is-active');
+ });
+ // Close dialog if ESC is pressed
+ $(document).keyup(function(e) {
+ if (e.keyCode == 27) settings.removeClass('is-active');
+ });
+});
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Manages the showing and hiding of the sidebar.
+$(document).ready(function() {
+ var sidebar = $("#documenter > .docs-sidebar");
+ var sidebar_button = $("#documenter-sidebar-button")
+ sidebar_button.click(function(ev) {
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+ sidebar.toggleClass('visible');
+ if (sidebar.hasClass('visible')) {
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+ $("#documenter .docs-menu a.is-active").focus();
+ }
+ });
+ $("#documenter > .docs-main").bind('click', function(ev) {
+ if ($(ev.target).is(sidebar_button)) {
+ return;
+ }
+ if (sidebar.hasClass('visible')) {
+ sidebar.removeClass('visible');
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+ });
+})
+
+// Resizes the package name / sitename in the sidebar if it is too wide.
+// Inspired by: https://github.com/davatron5000/FitText.js
+$(document).ready(function() {
+ e = $("#documenter .docs-autofit");
+ function resize() {
+ var L = parseInt(e.css('max-width'), 10);
+ var L0 = e.width();
+ if(L0 > L) {
+ var h0 = parseInt(e.css('font-size'), 10);
+ e.css('font-size', L * h0 / L0);
+ // TODO: make sure it survives resizes?
+ }
+ }
+ // call once and then register events
+ resize();
+ $(window).resize(resize);
+ $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
+$(document).ready(function() {
+ var sidebar = $("#documenter .docs-menu").get(0);
+ var active = $("#documenter .docs-menu .is-active").get(0);
+ if(typeof active !== 'undefined') {
+ sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+function set_theme(theme) {
+ var active = null;
+ var disabled = [];
+ for (var i = 0; i < document.styleSheets.length; i++) {
+ var ss = document.styleSheets[i];
+ var themename = ss.ownerNode.getAttribute("data-theme-name");
+ if(themename === null) continue; // ignore non-theme stylesheets
+ // Find the active theme
+ if(themename === theme) active = ss;
+ else disabled.push(ss);
+ }
+ if(active !== null) {
+ active.disabled = false;
+ if(active.ownerNode.getAttribute("data-theme-primary") === null) {
+ document.getElementsByTagName('html')[0].className = "theme--" + theme;
+ } else {
+ document.getElementsByTagName('html')[0].className = "";
+ }
+ disabled.forEach(function(ss){
+ ss.disabled = true;
+ });
+ }
+
+ // Store the theme in localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ window.localStorage.setItem("documenter-theme", theme);
+ } else {
+ console.error("Browser does not support window.localStorage");
+ }
+}
+
+// Theme picker setup
+$(document).ready(function() {
+ // onchange callback
+ $('#documenter-themepicker').change(function themepick_callback(ev){
+ var themename = $('#documenter-themepicker option:selected').attr('value');
+ set_theme(themename);
+ });
+
+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = (e.value === theme);
+ })
+ } else {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = $("html").hasClass(`theme--${e.value}`);
+ })
+ }
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+$(document).ready(function() {
+ var version_selector = $("#documenter .docs-version-selector");
+ var version_selector_select = $("#documenter .docs-version-selector select");
+
+ version_selector_select.change(function(x) {
+ target_href = version_selector_select.children("option:selected").get(0).value;
+ window.location.href = target_href;
+ });
+
+ // add the current version to the selector based on siteinfo.js, but only if the selector is empty
+ if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
+ var option = $("");
+ version_selector_select.append(option);
+ }
+
+ if (typeof DOC_VERSIONS !== 'undefined') {
+ var existing_versions = version_selector_select.children("option");
+ var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+ DOC_VERSIONS.forEach(function(each) {
+ var version_url = documenterBaseURL + "/../" + each;
+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
+ if (existing_id == -1) {
+ var option = $("");
+ version_selector_select.append(option);
+ } else {
+ var option = existing_versions[existing_id];
+ option.value = version_url;
+ option.disabled = false;
+ }
+ });
+ }
+
+ // only show the version selector if the selector has been populated
+ if (version_selector_select.children("option").length > 0) {
+ version_selector.toggleClass("visible");
+ }
+})
+
+})
diff --git a/v0.10.1/assets/search.js b/v0.10.1/assets/search.js
new file mode 100644
index 0000000..1a51454
--- /dev/null
+++ b/v0.10.1/assets/search.js
@@ -0,0 +1,251 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min',
+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
+ m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+ uri = {},
+ i = 14;
+
+ while (i--) uri[o.key[i]] = m[i] || "";
+
+ uri[o.q.name] = {};
+ uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+ if ($1) uri[o.q.name][$1] = $2;
+ });
+
+ return uri;
+ };
+ parseUri.options = {
+ strictMode: false,
+ key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+ q: {
+ name: "queryKey",
+ parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+ },
+ parser: {
+ strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
+ loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
+ }
+ };
+
+ $("#search-form").submit(function(e) {
+ e.preventDefault()
+ })
+
+ // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+ // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
+ // ideally we'd just filter the original list but it's not available as a variable
+ lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
+ 'almost',
+ 'also',
+ 'am',
+ 'among',
+ 'an',
+ 'and',
+ 'are',
+ 'as',
+ 'at',
+ 'be',
+ 'because',
+ 'been',
+ 'but',
+ 'by',
+ 'can',
+ 'cannot',
+ 'could',
+ 'dear',
+ 'did',
+ 'does',
+ 'either',
+ 'ever',
+ 'every',
+ 'from',
+ 'got',
+ 'had',
+ 'has',
+ 'have',
+ 'he',
+ 'her',
+ 'hers',
+ 'him',
+ 'his',
+ 'how',
+ 'however',
+ 'i',
+ 'if',
+ 'into',
+ 'it',
+ 'its',
+ 'just',
+ 'least',
+ 'like',
+ 'likely',
+ 'may',
+ 'me',
+ 'might',
+ 'most',
+ 'must',
+ 'my',
+ 'neither',
+ 'no',
+ 'nor',
+ 'not',
+ 'of',
+ 'off',
+ 'often',
+ 'on',
+ 'or',
+ 'other',
+ 'our',
+ 'own',
+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
+ 'so',
+ 'some',
+ 'than',
+ 'that',
+ 'the',
+ 'their',
+ 'them',
+ 'then',
+ 'there',
+ 'these',
+ 'they',
+ 'this',
+ 'tis',
+ 'to',
+ 'too',
+ 'twas',
+ 'us',
+ 'wants',
+ 'was',
+ 'we',
+ 'were',
+ 'what',
+ 'when',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+ ])
+
+ // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+ // would not find anything if searching for "add!", only for the entire qualification
+ lunr.tokenizer.separator = /[\s\-\.]+/
+
+ // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+ lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+ })
+ }
+
+ lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
+ lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
+
+ var index = lunr(function () {
+ this.ref('location')
+ this.field('title',{boost: 100})
+ this.field('text')
+ documenterSearchIndex['docs'].forEach(function(e) {
+ this.add(e)
+ }, this)
+ })
+ var store = {}
+
+ documenterSearchIndex['docs'].forEach(function(e) {
+ store[e.location] = {title: e.title, category: e.category, page: e.page}
+ })
+
+ $(function(){
+ searchresults = $('#documenter-search-results');
+ searchinfo = $('#documenter-search-info');
+ searchbox = $('#documenter-search-query');
+ function update_search(querystring) {
+ tokens = lunr.tokenizer(querystring)
+ results = index.query(function (q) {
+ tokens.forEach(function (t) {
+ q.term(t.toString(), {
+ fields: ["title"],
+ boost: 100,
+ usePipeline: true,
+ editDistance: 0,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ q.term(t.toString(), {
+ fields: ["title"],
+ boost: 10,
+ usePipeline: true,
+ editDistance: 2,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ q.term(t.toString(), {
+ fields: ["text"],
+ boost: 1,
+ usePipeline: true,
+ editDistance: 0,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ })
+ })
+ searchinfo.text("Number of results: " + results.length)
+ searchresults.empty()
+ results.forEach(function(result) {
+ data = store[result.ref]
+ link = $(''+data.title+'')
+ link.attr('href', documenterBaseURL+'/'+result.ref)
+ if (data.category != "page"){
+ cat = $('('+data.category+', '+data.page+')')
+ } else {
+ cat = $('('+data.category+')')
+ }
+ li = $('
This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.4 on Friday 23 July 2021. Using Julia version 1.5.4.
diff --git a/v0.10.1/search_index.js b/v0.10.1/search_index.js
new file mode 100644
index 0000000..e49e46f
--- /dev/null
+++ b/v0.10.1/search_index.js
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+var documenterSearchIndex = {"docs":
+[{"location":"tutorials/#Tutorials","page":"Tutorials","title":"Tutorials","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)","category":"page"},{"location":"tutorials/#Read-a-single-frame","page":"Tutorials","title":"Read a single frame","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"In this tutorials we will read a frame from a trajectory, and print the indexes of all the atom in the half-space x < 5.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We start by using the Chemfiles package to bring in scope the needed functions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Then we open a Trajectory and read the first frame:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"And finally we can print our results","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"The whole code looks like this","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"For more information about reading frame in a trajectory, see the following functions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"read_step to directly read a given step.\nset_cell!(::Trajectory) and set_topology!(::Trajectory) to specify an unit cell or a topology for all frames in a trajectory.","category":"page"},{"location":"tutorials/#Generating-a-structure","page":"Tutorials","title":"Generating a structure","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can then set the atomic positions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Finally, we can set the UnitCell associated with this frame.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Wrapping everything up, the whole code looks like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/#Using-selections","page":"Tutorials","title":"Using selections","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We start by opening the two trajectories we will need","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"And we create a Selection object to filter the atoms we want to remove.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Finally, we can write the cleaned frame to the output file, and start the next iteration.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"The whole program look like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"reference/trajectory/#Trajectory","page":"Trajectory","title":"Trajectory","text":"","category":"section"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Trajectory","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory","page":"Trajectory","title":"Chemfiles.Trajectory","text":"A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Modules = [Chemfiles]\nPages = [\"Trajectory.jl\"]","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory-2","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(path::AbstractString) -> Trajectory\nTrajectory(path::AbstractString, mode::Char) -> Trajectory\nTrajectory(path::AbstractString, mode::Char, format::AbstractString) -> Trajectory\n\n\nOpens the trajectory file at the given path.\n\nThe opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/#Chemfiles.Trajectory-Tuple{Function,Vararg{Any,N} where N}","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(f::Function, args...) -> Any\n\n\nApply the function f to the result of Trajectory(args...) and close the resulting trajectory upon completion, similar to open(f, args...).\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.close-Tuple{Trajectory}","page":"Trajectory","title":"Base.close","text":"close(trajectory::Trajectory)\n\n\nClose a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read!-Tuple{Trajectory,Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Array{UInt8,1}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.write-Tuple{Trajectory,Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(format::AbstractString, data::Union{Nothing, AbstractString, Array{UInt8,1}}) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step!-Tuple{Trajectory,Integer,Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(trajectory::Trajectory, step::Integer, frame::Frame)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step-Tuple{Trajectory,Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_cell!-Tuple{Trajectory,UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(trajectory::Trajectory, path::AbstractString, format::AbstractString)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory,Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame/#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame/#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.angle-Tuple{Frame,Integer,Integer,Integer}","page":"Frame","title":"Base.angle","text":"angle(frame::Frame, i::Integer, j::Integer, k::Integer) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame,Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(frame::Frame, atom::Atom, position::Array{Float64,1})\nadd_atom!(frame::Frame, atom::Atom, position::Array{Float64,1}, velocity::Array{Float64,1})\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame,Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Array{String,1}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame,String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame,UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame,String,Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame,Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Array{String,1}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(atom::Atom, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String\nName of the format\nextension::Union{Nothing, String}\nExtension associated with the format, or nothing if there is no extension associated.\ndescription::String\nExtended user-facing description of the format\nreference::String\nURL pointing to the format definition/reference\nread::Bool\nIs reading files in this format implemented?\nwrite::Bool\nIs writing files in this format implemented?\nmemory::Bool\nDoes this format support in-memory IO?\npositions::Bool\nDoes this format support storing atomic positions?\nvelocities::Bool\nDoes this format support storing atomic velocities?\nunit_cell::Bool\nDoes this format support storing unit cell information?\natoms::Bool\nDoes this format support storing atom names or types?\nbonds::Bool\nDoes this format support storing bonds between atoms?\nresidues::Bool\nDoes this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Array{Chemfiles.FormatMetadata,1}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell\nCellShape","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Array{Float64,1}) -> UnitCell\nUnitCell(lengths::Array{Float64,1}, angles::Array{Float64,1}) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Array{Float64,2}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Array{Float64,2}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Array{Float64,2}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Array{Float64,1})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Array{Float64,1})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell,CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(cell::UnitCell, vector::Array{Float64,1}) -> Array{Float64,1}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue,Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue,Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Array{UInt64,1}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Array{String,1}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue,String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(topology::Topology, index::Integer) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(residue::Residue, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection,Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Array{Any,1}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology\nChemfiles.BondOrder","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology,Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology,Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology,Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Array{UInt64,2}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology,Residue,Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(topology::Topology, first::Residue, second::Residue) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(topology::Topology, i::Integer, j::Integer) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(topology::Topology) -> 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Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Array{UInt64,2}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Array{UInt64,2}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_atom!-Tuple{Topology,Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_bond!-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n]","category":"page"}]
+}
diff --git a/v0.10.1/tutorials/index.html b/v0.10.1/tutorials/index.html
new file mode 100644
index 0000000..0121074
--- /dev/null
+++ b/v0.10.1/tutorials/index.html
@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 0:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell(10, 10, 10))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.4 on Friday 23 July 2021. Using Julia version 1.5.4.
diff --git a/v0.10.2/assets/documenter.js b/v0.10.2/assets/documenter.js
new file mode 100644
index 0000000..6d0b785
--- /dev/null
+++ b/v0.10.2/assets/documenter.js
@@ -0,0 +1,264 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/languages/julia.min',
+ 'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min',
+ 'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min',
+ 'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/contrib/auto-render.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ 'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min',
+ 'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/katex.min',
+ 'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/highlight.min',
+ 'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.0.1/languages/julia-repl.min',
+ },
+ shim: {
+ "highlight-julia": {
+ "deps": [
+ "highlight"
+ ]
+ },
+ "katex-auto-render": {
+ "deps": [
+ "katex"
+ ]
+ },
+ "headroom-jquery": {
+ "deps": [
+ "jquery",
+ "headroom"
+ ]
+ },
+ "highlight-julia-repl": {
+ "deps": [
+ "highlight"
+ ]
+ }
+}
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) {
+$(document).ready(function() {
+ renderMathInElement(
+ document.body,
+ {
+ "delimiters": [
+ {
+ "left": "$",
+ "right": "$",
+ "display": false
+ },
+ {
+ "left": "$$",
+ "right": "$$",
+ "display": true
+ },
+ {
+ "left": "\\[",
+ "right": "\\]",
+ "display": true
+ }
+ ]
+}
+
+ );
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) {
+$(document).ready(function() {
+ hljs.highlightAll();
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) {
+
+// Manages the top navigation bar (hides it when the user starts scrolling down on the
+// mobile).
+window.Headroom = Headroom; // work around buggy module loading?
+$(document).ready(function() {
+ $('#documenter .docs-navbar').headroom({
+ "tolerance": {"up": 10, "down": 10},
+ });
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Modal settings dialog
+$(document).ready(function() {
+ var settings = $('#documenter-settings');
+ $('#documenter-settings-button').click(function(){
+ settings.toggleClass('is-active');
+ });
+ // Close the dialog if X is clicked
+ $('#documenter-settings button.delete').click(function(){
+ settings.removeClass('is-active');
+ });
+ // Close dialog if ESC is pressed
+ $(document).keyup(function(e) {
+ if (e.keyCode == 27) settings.removeClass('is-active');
+ });
+});
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Manages the showing and hiding of the sidebar.
+$(document).ready(function() {
+ var sidebar = $("#documenter > .docs-sidebar");
+ var sidebar_button = $("#documenter-sidebar-button")
+ sidebar_button.click(function(ev) {
+ ev.preventDefault();
+ sidebar.toggleClass('visible');
+ if (sidebar.hasClass('visible')) {
+ // Makes sure that the current menu item is visible in the sidebar.
+ $("#documenter .docs-menu a.is-active").focus();
+ }
+ });
+ $("#documenter > .docs-main").bind('click', function(ev) {
+ if ($(ev.target).is(sidebar_button)) {
+ return;
+ }
+ if (sidebar.hasClass('visible')) {
+ sidebar.removeClass('visible');
+ }
+ });
+})
+
+// Resizes the package name / sitename in the sidebar if it is too wide.
+// Inspired by: https://github.com/davatron5000/FitText.js
+$(document).ready(function() {
+ e = $("#documenter .docs-autofit");
+ function resize() {
+ var L = parseInt(e.css('max-width'), 10);
+ var L0 = e.width();
+ if(L0 > L) {
+ var h0 = parseInt(e.css('font-size'), 10);
+ e.css('font-size', L * h0 / L0);
+ // TODO: make sure it survives resizes?
+ }
+ }
+ // call once and then register events
+ resize();
+ $(window).resize(resize);
+ $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
+$(document).ready(function() {
+ var sidebar = $("#documenter .docs-menu").get(0);
+ var active = $("#documenter .docs-menu .is-active").get(0);
+ if(typeof active !== 'undefined') {
+ sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+function set_theme(theme) {
+ var active = null;
+ var disabled = [];
+ for (var i = 0; i < document.styleSheets.length; i++) {
+ var ss = document.styleSheets[i];
+ var themename = ss.ownerNode.getAttribute("data-theme-name");
+ if(themename === null) continue; // ignore non-theme stylesheets
+ // Find the active theme
+ if(themename === theme) active = ss;
+ else disabled.push(ss);
+ }
+ if(active !== null) {
+ active.disabled = false;
+ if(active.ownerNode.getAttribute("data-theme-primary") === null) {
+ document.getElementsByTagName('html')[0].className = "theme--" + theme;
+ } else {
+ document.getElementsByTagName('html')[0].className = "";
+ }
+ disabled.forEach(function(ss){
+ ss.disabled = true;
+ });
+ }
+
+ // Store the theme in localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ window.localStorage.setItem("documenter-theme", theme);
+ } else {
+ console.error("Browser does not support window.localStorage");
+ }
+}
+
+// Theme picker setup
+$(document).ready(function() {
+ // onchange callback
+ $('#documenter-themepicker').change(function themepick_callback(ev){
+ var themename = $('#documenter-themepicker option:selected').attr('value');
+ set_theme(themename);
+ });
+
+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = (e.value === theme);
+ })
+ } else {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = $("html").hasClass(`theme--${e.value}`);
+ })
+ }
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+$(document).ready(function() {
+ var version_selector = $("#documenter .docs-version-selector");
+ var version_selector_select = $("#documenter .docs-version-selector select");
+
+ version_selector_select.change(function(x) {
+ target_href = version_selector_select.children("option:selected").get(0).value;
+ window.location.href = target_href;
+ });
+
+ // add the current version to the selector based on siteinfo.js, but only if the selector is empty
+ if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
+ var option = $("");
+ version_selector_select.append(option);
+ }
+
+ if (typeof DOC_VERSIONS !== 'undefined') {
+ var existing_versions = version_selector_select.children("option");
+ var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+ DOC_VERSIONS.forEach(function(each) {
+ var version_url = documenterBaseURL + "/../" + each;
+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
+ if (existing_id == -1) {
+ var option = $("");
+ version_selector_select.append(option);
+ } else {
+ var option = existing_versions[existing_id];
+ option.value = version_url;
+ option.disabled = false;
+ }
+ });
+ }
+
+ // only show the version selector if the selector has been populated
+ if (version_selector_select.children("option").length > 0) {
+ version_selector.toggleClass("visible");
+ }
+})
+
+})
diff --git a/v0.10.2/assets/search.js b/v0.10.2/assets/search.js
new file mode 100644
index 0000000..1a51454
--- /dev/null
+++ b/v0.10.2/assets/search.js
@@ -0,0 +1,251 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min',
+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
+ m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+ uri = {},
+ i = 14;
+
+ while (i--) uri[o.key[i]] = m[i] || "";
+
+ uri[o.q.name] = {};
+ uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+ if ($1) uri[o.q.name][$1] = $2;
+ });
+
+ return uri;
+ };
+ parseUri.options = {
+ strictMode: false,
+ key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+ q: {
+ name: "queryKey",
+ parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+ },
+ parser: {
+ strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
+ loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
+ }
+ };
+
+ $("#search-form").submit(function(e) {
+ e.preventDefault()
+ })
+
+ // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+ // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
+ // ideally we'd just filter the original list but it's not available as a variable
+ lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
+ 'almost',
+ 'also',
+ 'am',
+ 'among',
+ 'an',
+ 'and',
+ 'are',
+ 'as',
+ 'at',
+ 'be',
+ 'because',
+ 'been',
+ 'but',
+ 'by',
+ 'can',
+ 'cannot',
+ 'could',
+ 'dear',
+ 'did',
+ 'does',
+ 'either',
+ 'ever',
+ 'every',
+ 'from',
+ 'got',
+ 'had',
+ 'has',
+ 'have',
+ 'he',
+ 'her',
+ 'hers',
+ 'him',
+ 'his',
+ 'how',
+ 'however',
+ 'i',
+ 'if',
+ 'into',
+ 'it',
+ 'its',
+ 'just',
+ 'least',
+ 'like',
+ 'likely',
+ 'may',
+ 'me',
+ 'might',
+ 'most',
+ 'must',
+ 'my',
+ 'neither',
+ 'no',
+ 'nor',
+ 'not',
+ 'of',
+ 'off',
+ 'often',
+ 'on',
+ 'or',
+ 'other',
+ 'our',
+ 'own',
+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
+ 'so',
+ 'some',
+ 'than',
+ 'that',
+ 'the',
+ 'their',
+ 'them',
+ 'then',
+ 'there',
+ 'these',
+ 'they',
+ 'this',
+ 'tis',
+ 'to',
+ 'too',
+ 'twas',
+ 'us',
+ 'wants',
+ 'was',
+ 'we',
+ 'were',
+ 'what',
+ 'when',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+ ])
+
+ // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+ // would not find anything if searching for "add!", only for the entire qualification
+ lunr.tokenizer.separator = /[\s\-\.]+/
+
+ // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+ lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+ })
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This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.10 on Monday 29 November 2021. Using Julia version 1.5.4.
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This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(frame::Frame, atom::Atom, position::Array{Float64,1})\nadd_atom!(frame::Frame, atom::Atom, position::Array{Float64,1}, velocity::Array{Float64,1})\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame,Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Array{String,1}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame,Integer,Integer,Integer,Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(frame::Frame, i::Integer, j::Integer, k::Integer, m::Integer) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame,String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame,Integer,Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame,UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame,String,Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame,Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame,Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology,Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Array{String,1}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom,Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(atom::Atom, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom,String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String\nName of the format\nextension::Union{Nothing, String}\nExtension associated with the format, or nothing if there is no extension associated.\ndescription::String\nExtended user-facing description of the format\nreference::String\nURL pointing to the format definition/reference\nread::Bool\nIs reading files in this format implemented?\nwrite::Bool\nIs writing files in this format implemented?\nmemory::Bool\nDoes this format support in-memory IO?\npositions::Bool\nDoes this format support storing atomic positions?\nvelocities::Bool\nDoes this format support storing atomic velocities?\nunit_cell::Bool\nDoes this format support storing unit cell information?\natoms::Bool\nDoes this format support storing atom names or types?\nbonds::Bool\nDoes this format support storing bonds between atoms?\nresidues::Bool\nDoes this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Array{Chemfiles.FormatMetadata,1}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell\nCellShape","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Array{Float64,1}) -> UnitCell\nUnitCell(lengths::Array{Float64,1}, angles::Array{Float64,1}) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Array{Float64,2}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Array{Float64,2}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Array{Float64,1}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Array{Float64,2}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Array{Float64,1})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Array{Float64,1})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell,CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell,Array{Float64,1}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(cell::UnitCell, vector::Array{Float64,1}) -> Array{Float64,1}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue,Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue,Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Array{UInt64,1}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Array{String,1}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue,String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology,Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(topology::Topology, index::Integer) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue,String,Union{Bool, Float64, Array{Float64,1}, String}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(residue::Residue, name::String, value::Union{Bool, Float64, Array{Float64,1}, String})\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection,Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Array{Any,1}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology\nChemfiles.BondOrder","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles: - Chemfiles.UnknownBond: when the bond order is not specified - Chemfiles.SingleBond: for single bonds - Chemfiles.DoubleBond: for double bonds - Chemfiles.TripleBond: for triple bonds - Chemfiles.QuadrupleBond: for quadruple bonds (present in some metals) - Chemfiles.QuintupletBond: for qintuplet bonds (present in some metals) - Chemfiles.AmideBond: for amide bonds - Chemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology,Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology,Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology,Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Array{UInt64,2}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology,Residue,Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(topology::Topology, first::Residue, second::Residue) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(topology::Topology, i::Integer, j::Integer) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(topology::Topology) -> Array{Chemfiles.BondOrder,1}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Array{UInt64,2}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Array{UInt64,2}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Array{UInt64,2}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_atom!-Tuple{Topology,Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_bond!-Tuple{Topology,Integer,Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n]","category":"page"}]
+}
diff --git a/v0.10.2/tutorials/index.html b/v0.10.2/tutorials/index.html
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+++ b/v0.10.2/tutorials/index.html
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+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 0:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell(10, 10, 10))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.10 on Monday 29 November 2021. Using Julia version 1.5.4.
diff --git a/v0.10.3/assets/documenter.js b/v0.10.3/assets/documenter.js
new file mode 100644
index 0000000..6adfbbb
--- /dev/null
+++ b/v0.10.3/assets/documenter.js
@@ -0,0 +1,331 @@
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+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) {
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+ el.select();
+ document.execCommand("copy");
+
+ resolve();
+ } catch (err) {
+ reject(err);
+ } finally {
+ document.body.removeChild(el);
+ }
+ });
+ }
+}
+
+if (document.readyState === "loading") {
+ document.addEventListener("DOMContentLoaded", addCopyButtonCallbacks);
+} else {
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+}
+
+})
+////////////////////////////////////////////////////////////////////////////////
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+
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+ });
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+function set_theme(theme) {
+ var active = null;
+ var disabled = [];
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+ // Store the theme in localStorage
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+ } else {
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+ }
+}
+
+// Theme picker setup
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+ $('#documenter-themepicker').change(function themepick_callback(ev){
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+ set_theme(themename);
+ });
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+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
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+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = (e.value === theme);
+ })
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+$(document).ready(function() {
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+ }
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+ if (typeof DOC_VERSIONS !== 'undefined') {
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+ var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+ DOC_VERSIONS.forEach(function(each) {
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+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
+ if (existing_id == -1) {
+ var option = $("");
+ version_selector_select.append(option);
+ } else {
+ var option = existing_versions[existing_id];
+ option.value = version_url;
+ option.disabled = false;
+ }
+ });
+ }
+
+ // only show the version selector if the selector has been populated
+ if (version_selector_select.children("option").length > 0) {
+ version_selector.toggleClass("visible");
+ }
+})
+
+})
diff --git a/v0.10.3/assets/search.js b/v0.10.3/assets/search.js
new file mode 100644
index 0000000..c133f74
--- /dev/null
+++ b/v0.10.3/assets/search.js
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+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min',
+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
+ m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+ uri = {},
+ i = 14;
+
+ while (i--) uri[o.key[i]] = m[i] || "";
+
+ uri[o.q.name] = {};
+ uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
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+ });
+
+ return uri;
+ };
+ parseUri.options = {
+ strictMode: false,
+ key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+ q: {
+ name: "queryKey",
+ parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+ },
+ parser: {
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+ }
+ };
+
+ $("#search-form").submit(function(e) {
+ e.preventDefault()
+ })
+
+ // list below is the lunr 2.1.3 list minus the intersect with names(Base)
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+ // ideally we'd just filter the original list but it's not available as a variable
+ lunr.stopWordFilter = lunr.generateStopWordFilter([
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+ 'able',
+ 'about',
+ 'across',
+ 'after',
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+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
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+ 'what',
+ 'when',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+ ])
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+ // would not find anything if searching for "add!", only for the entire qualification
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+
+ // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+ lunr.trimmer = function (token) {
+ return token.update(function (s) {
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+ lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
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+ })
+ var store = {}
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+ documenterSearchIndex['docs'].forEach(function(e) {
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+ })
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+ $(function(){
+ searchresults = $('#documenter-search-results');
+ searchinfo = $('#documenter-search-info');
+ searchbox = $('#documenter-search-query');
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+ sidebar = $('.docs-sidebar');
+ function update_search(querystring) {
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+ results = index.query(function (q) {
+ tokens.forEach(function (t) {
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This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
view(topology::Topology, index::Integer) -> Atom
+
Get the Atom at the given index of the topology without creating a copy.
Warning
This function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.23 on Saturday 27 August 2022. Using Julia version 1.6.7.
diff --git a/v0.10.3/build/search_index.js b/v0.10.3/build/search_index.js
new file mode 100644
index 0000000..ec8bdd1
--- /dev/null
+++ b/v0.10.3/build/search_index.js
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For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Wrapping everything up, the whole code looks like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/#Using-selections","page":"Tutorials","title":"Using selections","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We start by opening the two trajectories we will need","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"And we create a Selection object to filter the atoms we want to remove.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Finally, we can write the cleaned frame to the output file, and start the next iteration.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"The whole program look like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"reference/trajectory/#Trajectory","page":"Trajectory","title":"Trajectory","text":"","category":"section"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Trajectory","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory","page":"Trajectory","title":"Chemfiles.Trajectory","text":"A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Modules = [Chemfiles]\nPages = [\"Trajectory.jl\"]","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory-2","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(path::AbstractString) -> Trajectory\nTrajectory(path::AbstractString, mode::Char) -> Trajectory\nTrajectory(\n path::AbstractString,\n mode::Char,\n format::AbstractString\n) -> Trajectory\n\n\nOpens the trajectory file at the given path.\n\nThe opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/#Chemfiles.Trajectory-Tuple{Function, Vararg{Any, N} where N}","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(f::Function, args...) -> Any\n\n\nApply the function f to the result of Trajectory(args...) and close the resulting trajectory upon completion, similar to open(f, args...).\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.close-Tuple{Trajectory}","page":"Trajectory","title":"Base.close","text":"close(trajectory::Trajectory)\n\n\nClose a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read!-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Vector{UInt8}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.write-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(\n format::AbstractString,\n data::Union{Nothing, AbstractString, Vector{UInt8}}\n) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step!-Tuple{Trajectory, Integer, Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(\n trajectory::Trajectory,\n step::Integer,\n frame::Frame\n)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step-Tuple{Trajectory, Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_cell!-Tuple{Trajectory, UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(\n trajectory::Trajectory,\n path::AbstractString,\n format::AbstractString\n)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory, Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame/#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame/#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.angle-Tuple{Frame, Integer, Integer, Integer}","page":"Frame","title":"Base.angle","text":"angle(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer\n) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.getindex-Tuple{Frame, Integer}","page":"Frame","title":"Base.getindex","text":"getindex(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame. By default this creates a copy so as to be safe. To not create a copy, use @view frame[index].\n\nSee also Base.view(frame::Frame, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame, Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.view-Tuple{Frame, Integer}","page":"Frame","title":"Base.view","text":"view(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. Whith code like this:frame = Frame()\nresize!(frame, 3)\n\natom = @view frame[0]\nresize!(frame, 4)atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64}\n)\nadd_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64},\n velocity::Vector{Float64}\n)\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame, Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Vector{String}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame, String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame, UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame, String, Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame, Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Vector{String}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(\n atom::Atom,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String\nName of the format\nextension::Union{Nothing, String}\nExtension associated with the format, or nothing if there is no extension associated.\ndescription::String\nExtended user-facing description of the format\nreference::String\nURL pointing to the format definition/reference\nread::Bool\nIs reading files in this format implemented?\nwrite::Bool\nIs writing files in this format implemented?\nmemory::Bool\nDoes this format support in-memory IO?\npositions::Bool\nDoes this format support storing atomic positions?\nvelocities::Bool\nDoes this format support storing atomic velocities?\nunit_cell::Bool\nDoes this format support storing unit cell information?\natoms::Bool\nDoes this format support storing atom names or types?\nbonds::Bool\nDoes this format support storing bonds between atoms?\nresidues::Bool\nDoes this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Vector{Chemfiles.FormatMetadata}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Vector{Float64}) -> UnitCell\nUnitCell(\n lengths::Vector{Float64},\n angles::Vector{Float64}\n) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Matrix{Float64}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Matrix{Float64}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Matrix{Float64}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Vector{Float64})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Vector{Float64})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell, CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(\n cell::UnitCell,\n vector::Vector{Float64}\n) -> Vector{Float64}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue, Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue, Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Vector{UInt64}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Vector{String}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue, String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(\n topology::Topology,\n index::Integer\n) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(\n residue::Residue,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection, Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Vector{Any}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles:\n\nChemfiles.UnknownBond: when the bond order is not specified\nChemfiles.SingleBond: for single bonds\nChemfiles.DoubleBond: for double bonds\nChemfiles.TripleBond: for triple bonds\nChemfiles.QuadrupleBond: for quadruple bonds (present in some metals)\nChemfiles.QuintupletBond: for qintuplet bonds (present in some metals)\nChemfiles.AmideBond: for amide bonds\nChemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.getindex-Tuple{Topology, Integer}","page":"Topology","title":"Base.getindex","text":"getindex(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].\n\nSee also Base.view(topology::Topology, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology, Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.view-Tuple{Topology, Integer}","page":"Topology","title":"Base.view","text":"view(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology, Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology, Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Matrix{UInt64}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology, Residue, Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(\n topology::Topology,\n first::Residue,\n second::Residue\n) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(\n topology::Topology,\n i::Integer,\n j::Integer\n) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(\n topology::Topology\n) -> Vector{Chemfiles.BondOrder}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Matrix{UInt64}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Matrix{UInt64}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Matrix{UInt64}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the 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diff --git a/v0.10.3/build/tutorials/index.html b/v0.10.3/build/tutorials/index.html
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@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 1:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell([10.0, 10.0, 10.0]))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.23 on Saturday 27 August 2022. Using Julia version 1.6.7.
diff --git a/v0.10.3/index.html b/v0.10.3/index.html
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@@ -0,0 +1,5 @@
+
+Julia interface to chemfiles · Chemfiles.jl
This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
view(topology::Topology, index::Integer) -> Atom
+
Get the Atom at the given index of the topology without creating a copy.
Warning
This function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.23 on Saturday 27 August 2022. Using Julia version 1.6.7.
diff --git a/v0.10.3/search_index.js b/v0.10.3/search_index.js
new file mode 100644
index 0000000..ec8bdd1
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Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read!-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Vector{UInt8}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.write-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(\n format::AbstractString,\n data::Union{Nothing, AbstractString, Vector{UInt8}}\n) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step!-Tuple{Trajectory, Integer, Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(\n trajectory::Trajectory,\n step::Integer,\n frame::Frame\n)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step-Tuple{Trajectory, Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_cell!-Tuple{Trajectory, UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(\n trajectory::Trajectory,\n path::AbstractString,\n format::AbstractString\n)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory, Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame/#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame/#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.angle-Tuple{Frame, Integer, Integer, Integer}","page":"Frame","title":"Base.angle","text":"angle(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer\n) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.getindex-Tuple{Frame, Integer}","page":"Frame","title":"Base.getindex","text":"getindex(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame. By default this creates a copy so as to be safe. To not create a copy, use @view frame[index].\n\nSee also Base.view(frame::Frame, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame, Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.view-Tuple{Frame, Integer}","page":"Frame","title":"Base.view","text":"view(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. Whith code like this:frame = Frame()\nresize!(frame, 3)\n\natom = @view frame[0]\nresize!(frame, 4)atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64}\n)\nadd_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64},\n velocity::Vector{Float64}\n)\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame, Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Vector{String}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame, String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame, UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame, String, Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame, Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Vector{String}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(\n atom::Atom,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String\nName of the format\nextension::Union{Nothing, String}\nExtension associated with the format, or nothing if there is no extension associated.\ndescription::String\nExtended user-facing description of the format\nreference::String\nURL pointing to the format definition/reference\nread::Bool\nIs reading files in this format implemented?\nwrite::Bool\nIs writing files in this format implemented?\nmemory::Bool\nDoes this format support in-memory IO?\npositions::Bool\nDoes this format support storing atomic positions?\nvelocities::Bool\nDoes this format support storing atomic velocities?\nunit_cell::Bool\nDoes this format support storing unit cell information?\natoms::Bool\nDoes this format support storing atom names or types?\nbonds::Bool\nDoes this format support storing bonds between atoms?\nresidues::Bool\nDoes this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Vector{Chemfiles.FormatMetadata}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Vector{Float64}) -> UnitCell\nUnitCell(\n lengths::Vector{Float64},\n angles::Vector{Float64}\n) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Matrix{Float64}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Matrix{Float64}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Matrix{Float64}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Vector{Float64})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Vector{Float64})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell, CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(\n cell::UnitCell,\n vector::Vector{Float64}\n) -> Vector{Float64}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue, Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue, Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Vector{UInt64}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Vector{String}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue, String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(\n topology::Topology,\n index::Integer\n) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(\n residue::Residue,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection, Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Vector{Any}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles:\n\nChemfiles.UnknownBond: when the bond order is not specified\nChemfiles.SingleBond: for single bonds\nChemfiles.DoubleBond: for double bonds\nChemfiles.TripleBond: for triple bonds\nChemfiles.QuadrupleBond: for quadruple bonds (present in some metals)\nChemfiles.QuintupletBond: for qintuplet bonds (present in some metals)\nChemfiles.AmideBond: for amide bonds\nChemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.getindex-Tuple{Topology, Integer}","page":"Topology","title":"Base.getindex","text":"getindex(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].\n\nSee also Base.view(topology::Topology, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology, Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.view-Tuple{Topology, Integer}","page":"Topology","title":"Base.view","text":"view(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology, Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology, Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Matrix{UInt64}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology, Residue, Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(\n topology::Topology,\n first::Residue,\n second::Residue\n) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(\n topology::Topology,\n i::Integer,\n j::Integer\n) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(\n topology::Topology\n) -> Vector{Chemfiles.BondOrder}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Matrix{UInt64}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Matrix{UInt64}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Matrix{UInt64}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_atom!-Tuple{Topology, Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_bond!-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n]","category":"page"}]
+}
diff --git a/v0.10.3/tutorials/index.html b/v0.10.3/tutorials/index.html
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+++ b/v0.10.3/tutorials/index.html
@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 1:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell([10.0, 10.0, 10.0]))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.23 on Saturday 27 August 2022. Using Julia version 1.6.7.
diff --git a/v0.10.31/assets/documenter.js b/v0.10.31/assets/documenter.js
new file mode 100644
index 0000000..6adfbbb
--- /dev/null
+++ b/v0.10.31/assets/documenter.js
@@ -0,0 +1,331 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'highlight-julia': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia.min',
+ 'headroom': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/headroom.min',
+ 'jqueryui': 'https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min',
+ 'katex-auto-render': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/contrib/auto-render.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ 'headroom-jquery': 'https://cdnjs.cloudflare.com/ajax/libs/headroom/0.12.0/jQuery.headroom.min',
+ 'katex': 'https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min',
+ 'highlight': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/highlight.min',
+ 'highlight-julia-repl': 'https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.5.1/languages/julia-repl.min',
+ },
+ shim: {
+ "highlight-julia": {
+ "deps": [
+ "highlight"
+ ]
+ },
+ "katex-auto-render": {
+ "deps": [
+ "katex"
+ ]
+ },
+ "headroom-jquery": {
+ "deps": [
+ "jquery",
+ "headroom"
+ ]
+ },
+ "highlight-julia-repl": {
+ "deps": [
+ "highlight"
+ ]
+ }
+}
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'katex', 'katex-auto-render'], function($, katex, renderMathInElement) {
+$(document).ready(function() {
+ renderMathInElement(
+ document.body,
+ {
+ "delimiters": [
+ {
+ "left": "$",
+ "right": "$",
+ "display": false
+ },
+ {
+ "left": "$$",
+ "right": "$$",
+ "display": true
+ },
+ {
+ "left": "\\[",
+ "right": "\\]",
+ "display": true
+ }
+ ]
+}
+
+ );
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'highlight', 'highlight-julia', 'highlight-julia-repl'], function($) {
+$(document).ready(function() {
+ hljs.highlightAll();
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require([], function() {
+function addCopyButtonCallbacks() {
+ for (const el of document.getElementsByTagName("pre")) {
+ const button = document.createElement("button");
+ button.classList.add("copy-button", "fas", "fa-copy");
+ el.appendChild(button);
+
+ const success = function () {
+ button.classList.add("success", "fa-check");
+ button.classList.remove("fa-copy");
+ };
+
+ const failure = function () {
+ button.classList.add("error", "fa-times");
+ button.classList.remove("fa-copy");
+ };
+
+ button.addEventListener("click", function () {
+ copyToClipboard(el.innerText).then(success, failure);
+
+ setTimeout(function () {
+ button.classList.add("fa-copy");
+ button.classList.remove("success", "fa-check", "fa-times");
+ }, 5000);
+ });
+ }
+}
+
+function copyToClipboard(text) {
+ // clipboard API is only available in secure contexts
+ if (window.navigator && window.navigator.clipboard) {
+ return window.navigator.clipboard.writeText(text);
+ } else {
+ return new Promise(function (resolve, reject) {
+ try {
+ const el = document.createElement("textarea");
+ el.textContent = text;
+ el.style.position = "fixed";
+ el.style.opacity = 0;
+ document.body.appendChild(el);
+ el.select();
+ document.execCommand("copy");
+
+ resolve();
+ } catch (err) {
+ reject(err);
+ } finally {
+ document.body.removeChild(el);
+ }
+ });
+ }
+}
+
+if (document.readyState === "loading") {
+ document.addEventListener("DOMContentLoaded", addCopyButtonCallbacks);
+} else {
+ addCopyButtonCallbacks();
+}
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'headroom', 'headroom-jquery'], function($, Headroom) {
+
+// Manages the top navigation bar (hides it when the user starts scrolling down on the
+// mobile).
+window.Headroom = Headroom; // work around buggy module loading?
+$(document).ready(function() {
+ $('#documenter .docs-navbar').headroom({
+ "tolerance": {"up": 10, "down": 10},
+ });
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Modal settings dialog
+$(document).ready(function() {
+ var settings = $('#documenter-settings');
+ $('#documenter-settings-button').click(function(){
+ settings.toggleClass('is-active');
+ });
+ // Close the dialog if X is clicked
+ $('#documenter-settings button.delete').click(function(){
+ settings.removeClass('is-active');
+ });
+ // Close dialog if ESC is pressed
+ $(document).keyup(function(e) {
+ if (e.keyCode == 27) settings.removeClass('is-active');
+ });
+});
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Manages the showing and hiding of the sidebar.
+$(document).ready(function() {
+ var sidebar = $("#documenter > .docs-sidebar");
+ var sidebar_button = $("#documenter-sidebar-button")
+ sidebar_button.click(function(ev) {
+ ev.preventDefault();
+ sidebar.toggleClass('visible');
+ if (sidebar.hasClass('visible')) {
+ // Makes sure that the current menu item is visible in the sidebar.
+ $("#documenter .docs-menu a.is-active").focus();
+ }
+ });
+ $("#documenter > .docs-main").bind('click', function(ev) {
+ if ($(ev.target).is(sidebar_button)) {
+ return;
+ }
+ if (sidebar.hasClass('visible')) {
+ sidebar.removeClass('visible');
+ }
+ });
+})
+
+// Resizes the package name / sitename in the sidebar if it is too wide.
+// Inspired by: https://github.com/davatron5000/FitText.js
+$(document).ready(function() {
+ e = $("#documenter .docs-autofit");
+ function resize() {
+ var L = parseInt(e.css('max-width'), 10);
+ var L0 = e.width();
+ if(L0 > L) {
+ var h0 = parseInt(e.css('font-size'), 10);
+ e.css('font-size', L * h0 / L0);
+ // TODO: make sure it survives resizes?
+ }
+ }
+ // call once and then register events
+ resize();
+ $(window).resize(resize);
+ $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
+$(document).ready(function() {
+ var sidebar = $("#documenter .docs-menu").get(0);
+ var active = $("#documenter .docs-menu .is-active").get(0);
+ if(typeof active !== 'undefined') {
+ sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+function set_theme(theme) {
+ var active = null;
+ var disabled = [];
+ for (var i = 0; i < document.styleSheets.length; i++) {
+ var ss = document.styleSheets[i];
+ var themename = ss.ownerNode.getAttribute("data-theme-name");
+ if(themename === null) continue; // ignore non-theme stylesheets
+ // Find the active theme
+ if(themename === theme) active = ss;
+ else disabled.push(ss);
+ }
+ if(active !== null) {
+ active.disabled = false;
+ if(active.ownerNode.getAttribute("data-theme-primary") === null) {
+ document.getElementsByTagName('html')[0].className = "theme--" + theme;
+ } else {
+ document.getElementsByTagName('html')[0].className = "";
+ }
+ disabled.forEach(function(ss){
+ ss.disabled = true;
+ });
+ }
+
+ // Store the theme in localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ window.localStorage.setItem("documenter-theme", theme);
+ } else {
+ console.error("Browser does not support window.localStorage");
+ }
+}
+
+// Theme picker setup
+$(document).ready(function() {
+ // onchange callback
+ $('#documenter-themepicker').change(function themepick_callback(ev){
+ var themename = $('#documenter-themepicker option:selected').attr('value');
+ set_theme(themename);
+ });
+
+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = (e.value === theme);
+ })
+ } else {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = $("html").hasClass(`theme--${e.value}`);
+ })
+ }
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+$(document).ready(function() {
+ // If the version selector is disabled with DOCUMENTER_VERSION_SELECTOR_DISABLED in the
+ // siteinfo.js file, we just return immediately and not display the version selector.
+ if (typeof DOCUMENTER_VERSION_SELECTOR_DISABLED === 'boolean' && DOCUMENTER_VERSION_SELECTOR_DISABLED) {
+ return;
+ }
+
+ var version_selector = $("#documenter .docs-version-selector");
+ var version_selector_select = $("#documenter .docs-version-selector select");
+
+ version_selector_select.change(function(x) {
+ target_href = version_selector_select.children("option:selected").get(0).value;
+ window.location.href = target_href;
+ });
+
+ // add the current version to the selector based on siteinfo.js, but only if the selector is empty
+ if (typeof DOCUMENTER_CURRENT_VERSION !== 'undefined' && $('#version-selector > option').length == 0) {
+ var option = $("");
+ version_selector_select.append(option);
+ }
+
+ if (typeof DOC_VERSIONS !== 'undefined') {
+ var existing_versions = version_selector_select.children("option");
+ var existing_versions_texts = existing_versions.map(function(i,x){return x.text});
+ DOC_VERSIONS.forEach(function(each) {
+ var version_url = documenterBaseURL + "/../" + each;
+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
+ if (existing_id == -1) {
+ var option = $("");
+ version_selector_select.append(option);
+ } else {
+ var option = existing_versions[existing_id];
+ option.value = version_url;
+ option.disabled = false;
+ }
+ });
+ }
+
+ // only show the version selector if the selector has been populated
+ if (version_selector_select.children("option").length > 0) {
+ version_selector.toggleClass("visible");
+ }
+})
+
+})
diff --git a/v0.10.31/assets/search.js b/v0.10.31/assets/search.js
new file mode 100644
index 0000000..c133f74
--- /dev/null
+++ b/v0.10.31/assets/search.js
@@ -0,0 +1,267 @@
+// Generated by Documenter.jl
+requirejs.config({
+ paths: {
+ 'lunr': 'https://cdnjs.cloudflare.com/ajax/libs/lunr.js/2.3.9/lunr.min',
+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
+ m = o.parser[o.strictMode ? "strict" : "loose"].exec(str),
+ uri = {},
+ i = 14;
+
+ while (i--) uri[o.key[i]] = m[i] || "";
+
+ uri[o.q.name] = {};
+ uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) {
+ if ($1) uri[o.q.name][$1] = $2;
+ });
+
+ return uri;
+ };
+ parseUri.options = {
+ strictMode: false,
+ key: ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"],
+ q: {
+ name: "queryKey",
+ parser: /(?:^|&)([^&=]*)=?([^&]*)/g
+ },
+ parser: {
+ strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/,
+ loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/
+ }
+ };
+
+ $("#search-form").submit(function(e) {
+ e.preventDefault()
+ })
+
+ // list below is the lunr 2.1.3 list minus the intersect with names(Base)
+ // (all, any, get, in, is, only, which) and (do, else, for, let, where, while, with)
+ // ideally we'd just filter the original list but it's not available as a variable
+ lunr.stopWordFilter = lunr.generateStopWordFilter([
+ 'a',
+ 'able',
+ 'about',
+ 'across',
+ 'after',
+ 'almost',
+ 'also',
+ 'am',
+ 'among',
+ 'an',
+ 'and',
+ 'are',
+ 'as',
+ 'at',
+ 'be',
+ 'because',
+ 'been',
+ 'but',
+ 'by',
+ 'can',
+ 'cannot',
+ 'could',
+ 'dear',
+ 'did',
+ 'does',
+ 'either',
+ 'ever',
+ 'every',
+ 'from',
+ 'got',
+ 'had',
+ 'has',
+ 'have',
+ 'he',
+ 'her',
+ 'hers',
+ 'him',
+ 'his',
+ 'how',
+ 'however',
+ 'i',
+ 'if',
+ 'into',
+ 'it',
+ 'its',
+ 'just',
+ 'least',
+ 'like',
+ 'likely',
+ 'may',
+ 'me',
+ 'might',
+ 'most',
+ 'must',
+ 'my',
+ 'neither',
+ 'no',
+ 'nor',
+ 'not',
+ 'of',
+ 'off',
+ 'often',
+ 'on',
+ 'or',
+ 'other',
+ 'our',
+ 'own',
+ 'rather',
+ 'said',
+ 'say',
+ 'says',
+ 'she',
+ 'should',
+ 'since',
+ 'so',
+ 'some',
+ 'than',
+ 'that',
+ 'the',
+ 'their',
+ 'them',
+ 'then',
+ 'there',
+ 'these',
+ 'they',
+ 'this',
+ 'tis',
+ 'to',
+ 'too',
+ 'twas',
+ 'us',
+ 'wants',
+ 'was',
+ 'we',
+ 'were',
+ 'what',
+ 'when',
+ 'who',
+ 'whom',
+ 'why',
+ 'will',
+ 'would',
+ 'yet',
+ 'you',
+ 'your'
+ ])
+
+ // add . as a separator, because otherwise "title": "Documenter.Anchors.add!"
+ // would not find anything if searching for "add!", only for the entire qualification
+ lunr.tokenizer.separator = /[\s\-\.]+/
+
+ // custom trimmer that doesn't strip @ and !, which are used in julia macro and function names
+ lunr.trimmer = function (token) {
+ return token.update(function (s) {
+ return s.replace(/^[^a-zA-Z0-9@!]+/, '').replace(/[^a-zA-Z0-9@!]+$/, '')
+ })
+ }
+
+ lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'juliaStopWordFilter')
+ lunr.Pipeline.registerFunction(lunr.trimmer, 'juliaTrimmer')
+
+ var index = lunr(function () {
+ this.ref('location')
+ this.field('title',{boost: 100})
+ this.field('text')
+ documenterSearchIndex['docs'].forEach(function(e) {
+ this.add(e)
+ }, this)
+ })
+ var store = {}
+
+ documenterSearchIndex['docs'].forEach(function(e) {
+ store[e.location] = {title: e.title, category: e.category, page: e.page}
+ })
+
+ $(function(){
+ searchresults = $('#documenter-search-results');
+ searchinfo = $('#documenter-search-info');
+ searchbox = $('#documenter-search-query');
+ searchform = $('.docs-search');
+ sidebar = $('.docs-sidebar');
+ function update_search(querystring) {
+ tokens = lunr.tokenizer(querystring)
+ results = index.query(function (q) {
+ tokens.forEach(function (t) {
+ q.term(t.toString(), {
+ fields: ["title"],
+ boost: 100,
+ usePipeline: true,
+ editDistance: 0,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ q.term(t.toString(), {
+ fields: ["title"],
+ boost: 10,
+ usePipeline: true,
+ editDistance: 2,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ q.term(t.toString(), {
+ fields: ["text"],
+ boost: 1,
+ usePipeline: true,
+ editDistance: 0,
+ wildcard: lunr.Query.wildcard.NONE
+ })
+ })
+ })
+ searchinfo.text("Number of results: " + results.length)
+ searchresults.empty()
+ results.forEach(function(result) {
+ data = store[result.ref]
+ link = $(''+data.title+'')
+ link.attr('href', documenterBaseURL+'/'+result.ref)
+ if (data.category != "page"){
+ cat = $('('+data.category+', '+data.page+')')
+ } else {
+ cat = $('('+data.category+')')
+ }
+ li = $('
This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
view(topology::Topology, index::Integer) -> Atom
+
Get the Atom at the given index of the topology without creating a copy.
Warning
This function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.24 on Sunday 19 March 2023. Using Julia version 1.6.7.
diff --git a/v0.10.31/search_index.js b/v0.10.31/search_index.js
new file mode 100644
index 0000000..5c89bd2
--- /dev/null
+++ b/v0.10.31/search_index.js
@@ -0,0 +1,3 @@
+var documenterSearchIndex = {"docs":
+[{"location":"tutorials/#Tutorials","page":"Tutorials","title":"Tutorials","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)","category":"page"},{"location":"tutorials/#Read-a-single-frame","page":"Tutorials","title":"Read a single frame","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"In this tutorials we will read a frame from a trajectory, and print the indexes of all the atom in the half-space x < 5.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We start by using the Chemfiles package to bring in scope the needed functions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Then we open a Trajectory and read the first frame:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"And finally we can print our results","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"The whole code looks like this","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"For more information about reading frame in a trajectory, see the following functions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"read_step to directly read a given step.\nset_cell!(::Trajectory) and set_topology!(::Trajectory) to specify an unit cell or a topology for all frames in a trajectory.","category":"page"},{"location":"tutorials/#Generating-a-structure","page":"Tutorials","title":"Generating a structure","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We can then set the atomic positions:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Finally, we can set the UnitCell associated with this frame.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Wrapping everything up, the whole code looks like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/#Using-selections","page":"Tutorials","title":"Using selections","text":"","category":"section"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"We start by opening the two trajectories we will need","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"And we create a Selection object to filter the atoms we want to remove.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Finally, we can write the cleaned frame to the output file, and start the next iteration.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"Click here to see the whole program","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"The whole program look like this:","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"tutorials/","page":"Tutorials","title":"Tutorials","text":"","category":"page"},{"location":"reference/trajectory/#Trajectory","page":"Trajectory","title":"Trajectory","text":"","category":"section"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Trajectory","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory","page":"Trajectory","title":"Chemfiles.Trajectory","text":"A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Modules = [Chemfiles]\nPages = [\"Trajectory.jl\"]","category":"page"},{"location":"reference/trajectory/#Chemfiles.Trajectory-2","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(path::AbstractString) -> Trajectory\nTrajectory(path::AbstractString, mode::Char) -> Trajectory\nTrajectory(\n path::AbstractString,\n mode::Char,\n format::AbstractString\n) -> Trajectory\n\n\nOpens the trajectory file at the given path.\n\nThe opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.\n\n\n\n\n\n","category":"type"},{"location":"reference/trajectory/#Chemfiles.Trajectory-Tuple{Function, Vararg{Any, N} where N}","page":"Trajectory","title":"Chemfiles.Trajectory","text":"Trajectory(f::Function, args...) -> Any\n\n\nApply the function f to the result of Trajectory(args...) and close the resulting trajectory upon completion, similar to open(f, args...).\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.close-Tuple{Trajectory}","page":"Trajectory","title":"Base.close","text":"close(trajectory::Trajectory)\n\n\nClose a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.isopen-Tuple{Trajectory}","page":"Trajectory","title":"Base.isopen","text":"isopen(trajectory::Trajectory) -> Bool\n\n\nCheck if the trajectory is open.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.length-Tuple{Trajectory}","page":"Trajectory","title":"Base.length","text":"length(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read!-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.read!","text":"read!(trajectory::Trajectory, frame::Frame)\n\n\nRead the next step of the trajectory data into the preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.read-Tuple{Trajectory}","page":"Trajectory","title":"Base.read","text":"read(trajectory::Trajectory) -> Frame\n\n\nRead the next step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.size-Tuple{Trajectory}","page":"Trajectory","title":"Base.size","text":"size(trajectory::Trajectory) -> UInt64\n\n\nGet the number of steps (the number of frames) in a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.take!-Tuple{Trajectory}","page":"Trajectory","title":"Base.take!","text":"take!(trajectory::Trajectory) -> Vector{UInt8}\n\n\nObtain the memory buffer of a in-memory trajectory writer as a Vector{UInt8}, without copying.\n\nIf more data is written to the trajectory, the buffer is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Base.write-Tuple{Trajectory, Frame}","page":"Trajectory","title":"Base.write","text":"write(trajectory::Trajectory, frame::Frame)\n\n\nWrite the given frame to the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.MemoryTrajectory","page":"Trajectory","title":"Chemfiles.MemoryTrajectory","text":"MemoryTrajectory(format::AbstractString) -> Trajectory\nMemoryTrajectory(\n format::AbstractString,\n data::Union{Nothing, AbstractString, Vector{UInt8}}\n) -> Trajectory\n\n\nOpen a trajectory that read in-memory data as if it were a formatted file.\n\nThe format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.path-Tuple{Trajectory}","page":"Trajectory","title":"Chemfiles.path","text":"path(trajectory::Trajectory) -> String\n\n\nGet the path used to open a trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step!-Tuple{Trajectory, Integer, Frame}","page":"Trajectory","title":"Chemfiles.read_step!","text":"read_step!(\n trajectory::Trajectory,\n step::Integer,\n frame::Frame\n)\n\n\nRead the given step of the trajectory into an preexisting Frame structure.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.read_step-Tuple{Trajectory, Integer}","page":"Trajectory","title":"Chemfiles.read_step","text":"read_step(trajectory::Trajectory, step::Integer) -> Frame\n\n\nRead the given step of the trajectory, and return the corresponding Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_cell!-Tuple{Trajectory, UnitCell}","page":"Trajectory","title":"Chemfiles.set_cell!","text":"set_cell!(trajectory::Trajectory, cell::UnitCell)\n\n\nSet the cell associated with a trajectory. This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(\n trajectory::Trajectory,\n path::AbstractString,\n format::AbstractString\n)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory, Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame/#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame/#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.angle-Tuple{Frame, Integer, Integer, Integer}","page":"Frame","title":"Base.angle","text":"angle(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer\n) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.getindex-Tuple{Frame, Integer}","page":"Frame","title":"Base.getindex","text":"getindex(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame. By default this creates a copy so as to be safe. To not create a copy, use @view frame[index].\n\nSee also Base.view(frame::Frame, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame, Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.view-Tuple{Frame, Integer}","page":"Frame","title":"Base.view","text":"view(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. Whith code like this:frame = Frame()\nresize!(frame, 3)\n\natom = @view frame[0]\nresize!(frame, 4)atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64}\n)\nadd_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64},\n velocity::Vector{Float64}\n)\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame, Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Vector{String}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame, String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame, UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame, String, Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame, Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Vector{String}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(\n atom::Atom,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String: Name of the format\nextension::Union{Nothing, String}: Extension associated with the format, or nothing if there is no extension associated.\ndescription::String: Extended user-facing description of the format\nreference::String: URL pointing to the format definition/reference\nread::Bool: Is reading files in this format implemented?\nwrite::Bool: Is writing files in this format implemented?\nmemory::Bool: Does this format support in-memory IO?\npositions::Bool: Does this format support storing atomic positions?\nvelocities::Bool: Does this format support storing atomic velocities?\nunit_cell::Bool: Does this format support storing unit cell information?\natoms::Bool: Does this format support storing atom names or types?\nbonds::Bool: Does this format support storing bonds between atoms?\nresidues::Bool: Does this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Vector{Chemfiles.FormatMetadata}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Vector{Float64}) -> UnitCell\nUnitCell(\n lengths::Vector{Float64},\n angles::Vector{Float64}\n) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Matrix{Float64}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Matrix{Float64}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Matrix{Float64}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Vector{Float64})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Vector{Float64})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell, CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(\n cell::UnitCell,\n vector::Vector{Float64}\n) -> Vector{Float64}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue, Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue, Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Vector{UInt64}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Vector{String}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue, String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(\n topology::Topology,\n index::Integer\n) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(\n residue::Residue,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection, Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Vector{Any}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles:\n\nChemfiles.UnknownBond: when the bond order is not specified\nChemfiles.SingleBond: for single bonds\nChemfiles.DoubleBond: for double bonds\nChemfiles.TripleBond: for triple bonds\nChemfiles.QuadrupleBond: for quadruple bonds (present in some metals)\nChemfiles.QuintupletBond: for qintuplet bonds (present in some metals)\nChemfiles.AmideBond: for amide bonds\nChemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.getindex-Tuple{Topology, Integer}","page":"Topology","title":"Base.getindex","text":"getindex(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].\n\nSee also Base.view(topology::Topology, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology, Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.view-Tuple{Topology, Integer}","page":"Topology","title":"Base.view","text":"view(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology, Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology, Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in 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between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(\n topology::Topology,\n i::Integer,\n j::Integer\n) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(\n topology::Topology\n) -> Vector{Chemfiles.BondOrder}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Matrix{UInt64}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) 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+}
diff --git a/v0.10.31/tutorials/index.html b/v0.10.31/tutorials/index.html
new file mode 100644
index 0000000..d37b26f
--- /dev/null
+++ b/v0.10.31/tutorials/index.html
@@ -0,0 +1,105 @@
+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 1:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell([10.0, 10.0, 10.0]))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.24 on Sunday 19 March 2023. Using Julia version 1.6.7.
diff --git a/v0.10.40/assets/documenter.js b/v0.10.40/assets/documenter.js
new file mode 100644
index 0000000..6adfbbb
--- /dev/null
+++ b/v0.10.40/assets/documenter.js
@@ -0,0 +1,331 @@
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+ "jquery",
+ "headroom"
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+ button.classList.add("fa-copy");
+ button.classList.remove("success", "fa-check", "fa-times");
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+ return window.navigator.clipboard.writeText(text);
+ } else {
+ return new Promise(function (resolve, reject) {
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+ el.textContent = text;
+ el.style.position = "fixed";
+ el.style.opacity = 0;
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+ $('#documenter .docs-navbar').headroom({
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+ });
+})
+
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+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// Modal settings dialog
+$(document).ready(function() {
+ var settings = $('#documenter-settings');
+ $('#documenter-settings-button').click(function(){
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+////////////////////////////////////////////////////////////////////////////////
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+$(document).ready(function() {
+ var sidebar = $("#documenter > .docs-sidebar");
+ var sidebar_button = $("#documenter-sidebar-button")
+ sidebar_button.click(function(ev) {
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+ }
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+ sidebar.removeClass('visible');
+ }
+ });
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+
+// Resizes the package name / sitename in the sidebar if it is too wide.
+// Inspired by: https://github.com/davatron5000/FitText.js
+$(document).ready(function() {
+ e = $("#documenter .docs-autofit");
+ function resize() {
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+ var L0 = e.width();
+ if(L0 > L) {
+ var h0 = parseInt(e.css('font-size'), 10);
+ e.css('font-size', L * h0 / L0);
+ // TODO: make sure it survives resizes?
+ }
+ }
+ // call once and then register events
+ resize();
+ $(window).resize(resize);
+ $(window).on('orientationchange', resize);
+});
+
+// Scroll the navigation bar to the currently selected menu item
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+ var active = $("#documenter .docs-menu .is-active").get(0);
+ if(typeof active !== 'undefined') {
+ sidebar.scrollTop = active.offsetTop - sidebar.offsetTop - 15;
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+function set_theme(theme) {
+ var active = null;
+ var disabled = [];
+ for (var i = 0; i < document.styleSheets.length; i++) {
+ var ss = document.styleSheets[i];
+ var themename = ss.ownerNode.getAttribute("data-theme-name");
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+ else disabled.push(ss);
+ }
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+ if(active.ownerNode.getAttribute("data-theme-primary") === null) {
+ document.getElementsByTagName('html')[0].className = "theme--" + theme;
+ } else {
+ document.getElementsByTagName('html')[0].className = "";
+ }
+ disabled.forEach(function(ss){
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+ if(typeof(window.localStorage) !== "undefined") {
+ window.localStorage.setItem("documenter-theme", theme);
+ } else {
+ console.error("Browser does not support window.localStorage");
+ }
+}
+
+// Theme picker setup
+$(document).ready(function() {
+ // onchange callback
+ $('#documenter-themepicker').change(function themepick_callback(ev){
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+ set_theme(themename);
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+ // Make sure that the themepicker displays the correct theme when the theme is retrieved
+ // from localStorage
+ if(typeof(window.localStorage) !== "undefined") {
+ var theme = window.localStorage.getItem("documenter-theme");
+ if(theme !== null) {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = (e.value === theme);
+ })
+ } else {
+ $('#documenter-themepicker option').each(function(i,e) {
+ e.selected = $("html").hasClass(`theme--${e.value}`);
+ })
+ }
+ }
+})
+
+})
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery'], function($) {
+
+// update the version selector with info from the siteinfo.js and ../versions.js files
+$(document).ready(function() {
+ // If the version selector is disabled with DOCUMENTER_VERSION_SELECTOR_DISABLED in the
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+ var version_url = documenterBaseURL + "/../" + each;
+ var existing_id = $.inArray(each, existing_versions_texts);
+ // if not already in the version selector, add it as a new option,
+ // otherwise update the old option with the URL and enable it
+ if (existing_id == -1) {
+ var option = $("");
+ version_selector_select.append(option);
+ } else {
+ var option = existing_versions[existing_id];
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+ option.disabled = false;
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+ version_selector.toggleClass("visible");
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diff --git a/v0.10.40/assets/search.js b/v0.10.40/assets/search.js
new file mode 100644
index 0000000..c133f74
--- /dev/null
+++ b/v0.10.40/assets/search.js
@@ -0,0 +1,267 @@
+// Generated by Documenter.jl
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+ paths: {
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+ 'lodash': 'https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min',
+ 'jquery': 'https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.0/jquery.min',
+ }
+});
+////////////////////////////////////////////////////////////////////////////////
+require(['jquery', 'lunr', 'lodash'], function($, lunr, _) {
+
+$(document).ready(function() {
+ // parseUri 1.2.2
+ // (c) Steven Levithan
+ // MIT License
+ function parseUri (str) {
+ var o = parseUri.options,
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+ uri = {},
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+
+ uri[o.q.name] = {};
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This is the documentation for the Julia interface to the chemfiles library.
The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.
Warning
All indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.
This may change in future release to use 1-based indexing, which is more familiar to Julia developers.
You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:
pkg> add Chemfiles
+
+# You may also want to run the test suite with
+pkg> test Chemfiles
A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:
Resize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.
atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).
Add velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.
Get the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
Get the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.
If the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.
By default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.
This function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.
Get the format that chemfiles would use to read a file at the given path.
The format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).
The returned format is represented in a way compatible with the various Trajectory constructors, i.e. "<format name> [/ <compression>]", where compression is optional.
A Selection is used to select a group of atoms. Examples of selections are "name H" and "(x < 45 and name O) or name C". See the full documentation <http://chemfiles.org/chemfiles/latest/selections.html>_ for more information about the selection language.
A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.
Resize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.
If it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.
view(topology::Topology, index::Integer) -> Atom
+
Get the Atom at the given index of the topology without creating a copy.
Warning
This function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.
Check if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.
A Trajectory represents a simulation file on the hard drive. It can read or write one or many Frames to this file. The file format can be automatically determined from the extention, or manually specified. Writing to a Trajectory is buffered, which means that one needs to close() the trajectory and flush the buffer before being able to read the file again.
The opening mode can be 'r' for read, 'w' for write or 'a' for append, and defaults to 'r'. The optional format parameter give a specific file format to use when opening the file.
Close a trajectory. This function flushes any buffer content to the hard drive, and frees the associated memory. Necessary when running on the REPL to finish writing.
Open a trajectory that read in-memory data as if it were a formatted file.
The format of the data is mandatory, and must match one of the known formats. If data is nothing, this function creates a memory writer, the resulting data can be retrieved with buffer. Else, this function creates a memory reader using the given data.
Set the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.
This document was generated with Documenter.jl version 0.27.24 on Wednesday 17 May 2023. Using Julia version 1.6.7.
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This cell will be used when reading and writing the file, replacing any unit cell in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/#Chemfiles.set_topology!","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, path::AbstractString)\nset_topology!(\n trajectory::Trajectory,\n path::AbstractString,\n format::AbstractString\n)\n\n\nSet the Topology associated with a trajectory by reading the first frame of the file at path; and extracting the topology of this frame. The optional format parameter can be used to specify the file format.\n\n\n\n\n\n","category":"function"},{"location":"reference/trajectory/#Chemfiles.set_topology!-Tuple{Trajectory, Topology}","page":"Trajectory","title":"Chemfiles.set_topology!","text":"set_topology!(trajectory::Trajectory, topology::Topology)\n\n\nSet the Topology associated with a trajectory. This topology will be used when reading and writing the file, replacing any topology in the file.\n\n\n\n\n\n","category":"method"},{"location":"reference/trajectory/","page":"Trajectory","title":"Trajectory","text":"Chemfiles.DataBuffer","category":"page"},{"location":"reference/trajectory/#Chemfiles.DataBuffer","page":"Trajectory","title":"Chemfiles.DataBuffer","text":"Data (either binary or string) used for in-memory reading of trajectory\n\nDataBuffer = Union{AbstractString,Vector{UInt8},Nothing}\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/#Frame","page":"Frame","title":"Frame","text":"","category":"section"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Frame","category":"page"},{"location":"reference/frame/#Chemfiles.Frame","page":"Frame","title":"Chemfiles.Frame","text":"A Frame holds data for one step of a simulation. As not all formats provide all the types of information, some fields may be initialized to a default value. A Frame may contain the following data:\n\nPositions for all the atoms in the system;\nVelocities for all the atoms in the system;\nThe Topology of the system;\nThe UnitCell of the system.\n\n\n\n\n\n","category":"type"},{"location":"reference/frame/","page":"Frame","title":"Frame","text":"Modules = [Chemfiles]\nPages = [\"Frame.jl\"]","category":"page"},{"location":"reference/frame/#Chemfiles.Frame-Tuple{}","page":"Frame","title":"Chemfiles.Frame","text":"Frame() -> Frame\n\n\nCreate a new empty Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.angle-Tuple{Frame, Integer, Integer, Integer}","page":"Frame","title":"Base.angle","text":"angle(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer\n) -> Float64\n\n\nCalculate the angle made by three atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.deepcopy-Tuple{Frame}","page":"Frame","title":"Base.deepcopy","text":"deepcopy(frame::Frame) -> Frame\n\n\nMake a deep copy of a Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.getindex-Tuple{Frame, Integer}","page":"Frame","title":"Base.getindex","text":"getindex(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame. By default this creates a copy so as to be safe. To not create a copy, use @view frame[index].\n\nSee also Base.view(frame::Frame, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.length-Tuple{Frame}","page":"Frame","title":"Base.length","text":"length(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.resize!-Tuple{Frame, Integer}","page":"Frame","title":"Base.resize!","text":"resize!(frame::Frame, natoms::Integer)\n\n\nResize the positions and the velocities in the frame, to make space for natoms atoms. This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.size-Tuple{Frame}","page":"Frame","title":"Base.size","text":"size(frame::Frame) -> Int64\n\n\nGet the number of atoms in the frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.step-Tuple{Frame}","page":"Frame","title":"Base.step","text":"step(frame::Frame) -> UInt64\n\n\nGet the frame step, i.e. the frame number in the trajectory.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Base.view-Tuple{Frame, Integer}","page":"Frame","title":"Base.view","text":"view(frame::Frame, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the frame without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. Whith code like this:frame = Frame()\nresize!(frame, 3)\n\natom = @view frame[0]\nresize!(frame, 4)atom contains a pointer to memory owned by frame, but this pointer has been invalidated when resizing the frame. Using atom after the second call to resize! might trigger undefined behavior (segmentation fault in the best case, silent data corruption in the worst case).\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_atom!","page":"Frame","title":"Chemfiles.add_atom!","text":"add_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64}\n)\nadd_atom!(\n frame::Frame,\n atom::Atom,\n position::Vector{Float64},\n velocity::Vector{Float64}\n)\n\n\nAdd an atom and the corresponding position and velocity data to a frame.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_bond!","page":"Frame","title":"Chemfiles.add_bond!","text":"add_bond!(frame::Frame, i::Integer, j::Integer)\nadd_bond!(frame::Frame, i::Integer, j::Integer, order)\n\n\nAdd an additional bond to the Frame's Topology.\n\n\n\n\n\n","category":"function"},{"location":"reference/frame/#Chemfiles.add_residue!-Tuple{Frame, Residue}","page":"Frame","title":"Chemfiles.add_residue!","text":"add_residue!(frame::Frame, residue::Residue)\n\n\nAdd a residue to the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.add_velocities!-Tuple{Frame}","page":"Frame","title":"Chemfiles.add_velocities!","text":"add_velocities!(frame::Frame)\n\n\nAdd velocities to this frame. The storage is initialized with the result of size(frame) as the number of atoms. If the frame already has velocities, this does nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.clear_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(frame::Frame)\n\n\nRemove all bonds, angles and dihedral angles from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.dihedral-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.dihedral","text":"dihedral(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the dihedral (torsional) angle made by four unbranched atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.distance-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.distance","text":"distance(frame::Frame, i::Integer, j::Integer) -> Float64\n\n\nCalculate the distance between two atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.guess_bonds!-Tuple{Frame}","page":"Frame","title":"Chemfiles.guess_bonds!","text":"guess_bonds!(frame::Frame)\n\n\nGuess the bonds, angles, and dihedrals in the frame using a distance criteria.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.has_velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.has_velocities","text":"has_velocities(frame::Frame) -> Bool\n\n\nCheck if a frame contains velocity data or not.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.list_properties-Tuple{Frame}","page":"Frame","title":"Chemfiles.list_properties","text":"list_properties(frame::Frame) -> Vector{String}\n\n\nGet the names of all properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.out_of_plane-Tuple{Frame, Integer, Integer, Integer, Integer}","page":"Frame","title":"Chemfiles.out_of_plane","text":"out_of_plane(\n frame::Frame,\n i::Integer,\n j::Integer,\n k::Integer,\n m::Integer\n) -> Float64\n\n\nCalculate the out-of-plane (improper) angle made by four atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.positions-Tuple{Frame}","page":"Frame","title":"Chemfiles.positions","text":"positions(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the positions in a Frame as an array. The positions are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.properties_count-Tuple{Frame}","page":"Frame","title":"Chemfiles.properties_count","text":"properties_count(frame::Frame) -> Int64\n\n\nGet the number of properties associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.property-Tuple{Frame, String}","page":"Frame","title":"Chemfiles.property","text":"property(frame::Frame, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_atom!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.remove_atom!","text":"remove_atom!(frame::Frame, index::Integer)\n\n\nRemove the atom at index from the frame.\n\nThis function modifies all the atoms indexes after index, and invalidates any array obtained using positions or velocities.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.remove_bond!-Tuple{Frame, Integer, Integer}","page":"Frame","title":"Chemfiles.remove_bond!","text":"remove_bond!(frame::Frame, i::Integer, j::Integer)\n\n\nRemove a bond from the Frame's Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_cell!-Tuple{Frame, UnitCell}","page":"Frame","title":"Chemfiles.set_cell!","text":"set_cell!(frame::Frame, cell::UnitCell)\n\n\nSet the cell associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_property!-Tuple{Frame, String, Any}","page":"Frame","title":"Chemfiles.set_property!","text":"set_property!(frame::Frame, name::String, value)\n\n\nSet a named property for the given Frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_step!-Tuple{Frame, Integer}","page":"Frame","title":"Chemfiles.set_step!","text":"set_step!(frame::Frame, step::Integer)\n\n\nSet the frame step to step.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.set_topology!-Tuple{Frame, Topology}","page":"Frame","title":"Chemfiles.set_topology!","text":"set_topology!(frame::Frame, topology::Topology)\n\n\nSet the topology associated with a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/frame/#Chemfiles.velocities-Tuple{Frame}","page":"Frame","title":"Chemfiles.velocities","text":"velocities(frame::Frame) -> Chemfiles.ChemfilesArray\n\n\nGet the velocities in a Frame as an array. The velocities are readable and writable from this array. If the frame is resized (by writing to it, or calling resize!), the array is invalidated.\n\nIf the frame do not have velocity, this function will error. You can use add_velocities! to add velocities to a frame before calling this function.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Atom","page":"Atom","title":"Atom","text":"","category":"section"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Atom","category":"page"},{"location":"reference/atom/#Chemfiles.Atom","page":"Atom","title":"Chemfiles.Atom","text":"An Atom is a particle in the current Frame.\n\nAn atom stores the following atomic properties:\n\natom name\natom type\natom mass\natom charge\n\nThe atom name is usually an unique identifier (\"H1\", \"C_a\") while the atom type will be shared among all particles of the same type: \"H\", \"Ow\", \"CH3\".\n\n\n\n\n\n","category":"type"},{"location":"reference/atom/","page":"Atom","title":"Atom","text":"Modules = [Chemfiles]\nPages = [\"Atom.jl\"]","category":"page"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Frame, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(frame::Frame, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{String}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(name::String) -> Atom\n\n\nCreate an atom with the given name and set the atom type to be the same as name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.Atom-Tuple{Topology, Integer}","page":"Atom","title":"Chemfiles.Atom","text":"Atom(topology::Topology, index::Integer) -> Atom\n\n\nGet a copy of the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.deepcopy-Tuple{Atom}","page":"Atom","title":"Base.deepcopy","text":"deepcopy(atom::Atom) -> Atom\n\n\nMake a deep copy of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Base.fullname-Tuple{Atom}","page":"Atom","title":"Base.fullname","text":"fullname(atom::Atom) -> String\n\n\nGet the full name of an atom from the atom type.\n\nFor example, the full name of an atom with type \"He\" is \"Helium\".\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.atomic_number-Tuple{Atom}","page":"Atom","title":"Chemfiles.atomic_number","text":"atomic_number(atom::Atom) -> UInt64\n\n\nGet the atomic number of an atom from the atom type.\n\nIf the atomic number can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.charge-Tuple{Atom}","page":"Atom","title":"Chemfiles.charge","text":"charge(atom::Atom) -> Float64\n\n\nGet the charge of an atom in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.covalent_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.covalent_radius","text":"covalent_radius(atom::Atom) -> Float64\n\n\nGet the covalent radius of an atom from the atom type.\n\nIf the radius can not be found, returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.list_properties-Tuple{Atom}","page":"Atom","title":"Chemfiles.list_properties","text":"list_properties(atom::Atom) -> Vector{String}\n\n\nGet the names of all properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.mass-Tuple{Atom}","page":"Atom","title":"Chemfiles.mass","text":"mass(atom::Atom) -> Float64\n\n\nGet the mass of an atom in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.name-Tuple{Atom}","page":"Atom","title":"Chemfiles.name","text":"name(atom::Atom) -> String\n\n\nGet the name of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.properties_count-Tuple{Atom}","page":"Atom","title":"Chemfiles.properties_count","text":"properties_count(atom::Atom) -> Int64\n\n\nGet the number of properties associated with an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.property-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.property","text":"property(atom::Atom, name::String) -> Any\n\n\nGet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_charge!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_charge!","text":"set_charge!(atom::Atom, charge)\n\n\nSet the charge of an atom to charge.\n\nThe charge must be in number of the electron charge e.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_mass!-Tuple{Atom, Any}","page":"Atom","title":"Chemfiles.set_mass!","text":"set_mass!(atom::Atom, mass)\n\n\nSet the mass of an atom to mass.\n\nThe mass must be in atomic mass units.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_name!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_name!","text":"set_name!(atom::Atom, name::String)\n\n\nSet the name of an atom to name.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_property!-Tuple{Atom, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Atom","title":"Chemfiles.set_property!","text":"set_property!(\n atom::Atom,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.set_type!-Tuple{Atom, String}","page":"Atom","title":"Chemfiles.set_type!","text":"set_type!(atom::Atom, type::String)\n\n\nSet the type of an atom to type.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.type-Tuple{Atom}","page":"Atom","title":"Chemfiles.type","text":"type(atom::Atom) -> String\n\n\nGet the type of an atom.\n\n\n\n\n\n","category":"method"},{"location":"reference/atom/#Chemfiles.vdw_radius-Tuple{Atom}","page":"Atom","title":"Chemfiles.vdw_radius","text":"vdw_radius(atom::Atom) -> Float64\n\n\nGet the van der Waals radius of an atom from the atom type.\n\nIf the radius can not be found, this function returns 0.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Miscelaneous-functions","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"","category":"section"},{"location":"reference/misc/","page":"Miscelaneous functions","title":"Miscelaneous functions","text":"Modules = [Chemfiles]\nPages = [\"misc.jl\"]\nFilter = name -> !startswith(string(name), \"_\")","category":"page"},{"location":"reference/misc/#Chemfiles.FormatMetadata","page":"Miscelaneous functions","title":"Chemfiles.FormatMetadata","text":"Metadata associated with one of the format Chemfiles can read/write\n\nname::String: Name of the format\nextension::Union{Nothing, String}: Extension associated with the format, or nothing if there is no extension associated.\ndescription::String: Extended user-facing description of the format\nreference::String: URL pointing to the format definition/reference\nread::Bool: Is reading files in this format implemented?\nwrite::Bool: Is writing files in this format implemented?\nmemory::Bool: Does this format support in-memory IO?\npositions::Bool: Does this format support storing atomic positions?\nvelocities::Bool: Does this format support storing atomic velocities?\nunit_cell::Bool: Does this format support storing unit cell information?\natoms::Bool: Does this format support storing atom names or types?\nbonds::Bool: Does this format support storing bonds between atoms?\nresidues::Bool: Does this format support storing residues?\n\n\n\n\n\n","category":"type"},{"location":"reference/misc/#Chemfiles.add_configuration-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.add_configuration","text":"add_configuration(path::String)\n\n\nRead configuration data from the file at path.\n\nBy default, chemfiles reads configuration from any file name .chemfilesrc in the current directory or any parent directory. This function can be used to add data from another configuration file.\n\nThis function will fail if there is no file at path, or if the file is incorectly formatted. Data from the new configuration file will overwrite any existing data.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.clear_errors-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.clear_errors","text":"clear_errors()\n\n\nClear any error messages stored by the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.format_list-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.format_list","text":"format_list() -> Vector{Chemfiles.FormatMetadata}\n\n\nGet the full list of formats supported by Chemfiles, and associated metadata\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.guess_format-Tuple{String}","page":"Miscelaneous functions","title":"Chemfiles.guess_format","text":"guess_format(path::String) -> String\n\n\nGet the format that chemfiles would use to read a file at the given path.\n\nThe format is mostly guessed from the path extension, chemfiles only tries to read the file to distinguish between CIF and mmCIF files. Opening the file using the returned format string might still fail. For example, it will fail if the file is not actually formatted according to the guessed format; or the format/compression combination is not supported (e.g. XTC / GZ will not work since the XTC reader does not support compressed files).\n\nThe returned format is represented in a way compatible with the various Trajectory constructors, i.e. \" [/ ]\", where compression is optional.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.last_error-Tuple{}","page":"Miscelaneous functions","title":"Chemfiles.last_error","text":"last_error() -> String\n\n\nGet the last error message from the chemfiles runtime.\n\n\n\n\n\n","category":"method"},{"location":"reference/misc/#Chemfiles.set_warning_callback-Tuple{Function}","page":"Miscelaneous functions","title":"Chemfiles.set_warning_callback","text":"set_warning_callback(callback::Function)\n\n\nSet the global warning callback to be used for each warning event.\n\nThe callback function must take a String and return nothing.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#UnitCell","page":"UnitCell","title":"UnitCell","text":"","category":"section"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"UnitCell","category":"page"},{"location":"reference/cell/#Chemfiles.UnitCell","page":"UnitCell","title":"Chemfiles.UnitCell","text":"A UnitCell describes the bounding box of a system. It is represented by a 3x3 matrix containing the base vectors a, b and c.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/","page":"UnitCell","title":"UnitCell","text":"Modules = [Chemfiles]\nPages = [\"UnitCell.jl\"]","category":"page"},{"location":"reference/cell/#Chemfiles.CellShape","page":"UnitCell","title":"Chemfiles.CellShape","text":"The possible shape for an unit cell are:\n\nChemfiles.Orthorhombic for unit cells with the three angles are 90°.\nChemfiles.Triclinic for unit cells where the three angles may not be 90°.\nChemfiles.Infinite for unit cells without boundaries.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-2","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(lengths::Vector{Float64}) -> UnitCell\nUnitCell(\n lengths::Vector{Float64},\n angles::Vector{Float64}\n) -> UnitCell\n\n\nCreate an UnitCell from the given lengths and angles.\n\n\n\n\n\n","category":"type"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Frame}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(frame::Frame) -> UnitCell\n\n\nGet a copy of the UnitCell of a frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.UnitCell-Tuple{Matrix{Float64}}","page":"UnitCell","title":"Chemfiles.UnitCell","text":"UnitCell(matrix::Matrix{Float64}) -> UnitCell\n\n\nCreate an UnitCell from the given 3x3 cell matrix.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Base.deepcopy-Tuple{UnitCell}","page":"UnitCell","title":"Base.deepcopy","text":"deepcopy(cell::UnitCell) -> UnitCell\n\n\nMake a deep copy of a cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.angles-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.angles","text":"angles(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell angles in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.lengths-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.lengths","text":"lengths(cell::UnitCell) -> Vector{Float64}\n\n\nGet the three cell lengths in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.matrix-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.matrix","text":"matrix(cell::UnitCell) -> Matrix{Float64}\n\n\nGet the cell matricial representation, i.e. the representation of the three base vectors as:\n\n | a_x b_x c_x |\n | 0 b_y c_y |\n | 0 0 c_z |\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_angles!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_angles!","text":"set_angles!(cell::UnitCell, angles::Vector{Float64})\n\n\nSet the cell angles to the given values. The angles should be in degrees.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_lengths!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.set_lengths!","text":"set_lengths!(cell::UnitCell, lengths::Vector{Float64})\n\n\nSet the cell lengths to the given values. The lengths should be in angstroms.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.set_shape!-Tuple{UnitCell, CellShape}","page":"UnitCell","title":"Chemfiles.set_shape!","text":"set_shape!(cell::UnitCell, shape::CellShape)\n\n\nSet the cell shape to the given shape.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.shape-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.shape","text":"shape(cell::UnitCell) -> CellShape\n\n\nGet the cell shape, as a CellShape value.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.volume-Tuple{UnitCell}","page":"UnitCell","title":"Chemfiles.volume","text":"volume(cell::UnitCell) -> Float64\n\n\nGet the unit cell volume.\n\n\n\n\n\n","category":"method"},{"location":"reference/cell/#Chemfiles.wrap!-Tuple{UnitCell, Vector{Float64}}","page":"UnitCell","title":"Chemfiles.wrap!","text":"wrap!(\n cell::UnitCell,\n vector::Vector{Float64}\n) -> Vector{Float64}\n\n\nWrap a vector in the unit cell.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Residue","page":"Residue","title":"Residue","text":"","category":"section"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Residue","category":"page"},{"location":"reference/residue/#Chemfiles.Residue","page":"Residue","title":"Chemfiles.Residue","text":"A Residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/","page":"Residue","title":"Residue","text":"Modules = [Chemfiles]\nPages = [\"Residue.jl\"]","category":"page"},{"location":"reference/residue/#Chemfiles.Residue-2","page":"Residue","title":"Chemfiles.Residue","text":"Residue(name::String) -> Residue\nResidue(name::String, id) -> Residue\n\n\nCreate a new residue with the given name and optional residue identifier id.\n\n\n\n\n\n","category":"type"},{"location":"reference/residue/#Chemfiles.Residue-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.Residue","text":"Residue(topology::Topology, index::Integer) -> Residue\n\n\nGet a copy of the residue at index from a topology.\n\nThe residue index in the topology is not always the same as the residue identifier.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.contains-Tuple{Residue, Integer}","page":"Residue","title":"Base.contains","text":"contains(residue::Residue, index::Integer) -> Bool\n\n\nCheck if the atom at the given index is in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.deepcopy-Tuple{Residue}","page":"Residue","title":"Base.deepcopy","text":"deepcopy(residue::Residue) -> Residue\n\n\nMake a deep copy of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Base.size-Tuple{Residue}","page":"Residue","title":"Base.size","text":"size(residue::Residue) -> Int64\n\n\nGet the number of atoms in a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.add_atom!-Tuple{Residue, Integer}","page":"Residue","title":"Chemfiles.add_atom!","text":"add_atom!(residue::Residue, index::Integer)\n\n\nAdd the atom at the given index in the residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.atoms-Tuple{Residue}","page":"Residue","title":"Chemfiles.atoms","text":"atoms(residue::Residue) -> Vector{UInt64}\n\n\nGet the atoms in a residue. This function returns a list of indexes.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.id-Tuple{Residue}","page":"Residue","title":"Chemfiles.id","text":"id(residue::Residue) -> Int64\n\n\nGet the identifier of a residue in the initial topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.list_properties-Tuple{Residue}","page":"Residue","title":"Chemfiles.list_properties","text":"list_properties(residue::Residue) -> Vector{String}\n\n\nGet the names of all properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.name-Tuple{Residue}","page":"Residue","title":"Chemfiles.name","text":"name(residue::Residue) -> String\n\n\nGet the name of a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.properties_count-Tuple{Residue}","page":"Residue","title":"Chemfiles.properties_count","text":"properties_count(residue::Residue) -> Int64\n\n\nGet the number of properties associated with a residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.property-Tuple{Residue, String}","page":"Residue","title":"Chemfiles.property","text":"property(residue::Residue, name::String) -> Any\n\n\nGet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.residue_for_atom-Tuple{Topology, Integer}","page":"Residue","title":"Chemfiles.residue_for_atom","text":"residue_for_atom(\n topology::Topology,\n index::Integer\n) -> Union{Nothing, Residue}\n\n\nGet a copy of the residue containing the atom at index in the topology.\n\nThis function will return nothing if the atom is not in a residue, or if the index is bigger than the number of atoms in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/residue/#Chemfiles.set_property!-Tuple{Residue, String, Union{Bool, Float64, String, Vector{Float64}}}","page":"Residue","title":"Chemfiles.set_property!","text":"set_property!(\n residue::Residue,\n name::String,\n value::Union{Bool, Float64, String, Vector{Float64}}\n)\n\n\nSet a named property for the given residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Selection","page":"Selection","title":"Selection","text":"","category":"section"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Selection","category":"page"},{"location":"reference/selection/#Chemfiles.Selection","page":"Selection","title":"Chemfiles.Selection","text":"A Selection is used to select a group of atoms. Examples of selections are \"name H\" and \"(x < 45 and name O) or name C\". See the full documentation _ for more information about the selection language.\n\n\n\n\n\n","category":"type"},{"location":"reference/selection/","page":"Selection","title":"Selection","text":"Modules = [Chemfiles]\nPages = [\"Selection.jl\"]","category":"page"},{"location":"reference/selection/#Chemfiles.Selection-Tuple{AbstractString}","page":"Selection","title":"Chemfiles.Selection","text":"Selection(selection::AbstractString) -> Selection\n\n\nCreate a Selection from a selection string.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.deepcopy-Tuple{Selection}","page":"Selection","title":"Base.deepcopy","text":"deepcopy(selection::Selection) -> Selection\n\n\nMake a deep copy of a selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Base.size-Tuple{Selection}","page":"Selection","title":"Base.size","text":"size(selection::Selection) -> UInt64\n\n\nGet the size of a selection, i.e. the number of atoms we are selecting together.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.evaluate-Tuple{Selection, Frame}","page":"Selection","title":"Chemfiles.evaluate","text":"evaluate(selection::Selection, frame::Frame) -> Vector{Any}\n\n\nEvaluate a selection on a given frame. This function return a list of indexes or tuples of indexes of atoms in the frame matching the selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/selection/#Chemfiles.selection_string-Tuple{Selection}","page":"Selection","title":"Chemfiles.selection_string","text":"selection_string(selection::Selection) -> String\n\n\nGet the selection string used to create a given selection.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Topology","page":"Topology","title":"Topology","text":"","category":"section"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Topology","category":"page"},{"location":"reference/topology/#Chemfiles.Topology","page":"Topology","title":"Chemfiles.Topology","text":"A Topology describes the organisation of the particles in the system: what their names are, how they are bonded together, etc. A Topology is a list of Atoms in the system, together with the list of bonds between the atoms.\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/","page":"Topology","title":"Topology","text":"Modules = [Chemfiles]\nPages = [\"Topology.jl\"]","category":"page"},{"location":"reference/topology/#Chemfiles.BondOrder","page":"Topology","title":"Chemfiles.BondOrder","text":"Possible bond orders in Chemfiles:\n\nChemfiles.UnknownBond: when the bond order is not specified\nChemfiles.SingleBond: for single bonds\nChemfiles.DoubleBond: for double bonds\nChemfiles.TripleBond: for triple bonds\nChemfiles.QuadrupleBond: for quadruple bonds (present in some metals)\nChemfiles.QuintupletBond: for qintuplet bonds (present in some metals)\nChemfiles.AmideBond: for amide bonds\nChemfiles.AromaticBond: for aromatic bonds\n\n\n\n\n\n","category":"type"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{Frame}","page":"Topology","title":"Chemfiles.Topology","text":"Topology(frame::Frame) -> Topology\n\n\nGet a copy of the Topology of the given frame.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.Topology-Tuple{}","page":"Topology","title":"Chemfiles.Topology","text":"Topology() -> Topology\n\n\nCreate an empty Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.deepcopy-Tuple{Topology}","page":"Topology","title":"Base.deepcopy","text":"deepcopy(topology::Topology) -> Topology\n\n\nMake a deep copy of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.getindex-Tuple{Topology, Integer}","page":"Topology","title":"Base.getindex","text":"getindex(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology. By default this creates a copy so as to be safe. To not create a copy, use @view topology[index].\n\nSee also Base.view(topology::Topology, index::Integer)\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.resize!-Tuple{Topology, Integer}","page":"Topology","title":"Base.resize!","text":"resize!(topology::Topology, size::Integer)\n\n\nResize the topology to hold natoms atoms. If the new number of atoms is bigger than the current number, new atoms will be created with an empty name and type.\n\nIf it is lower than the current number of atoms, the last atoms will be removed, together with the associated bonds, angles and dihedrals.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.size-Tuple{Topology}","page":"Topology","title":"Base.size","text":"size(topology::Topology) -> Int64\n\n\nGet the Topology size, i.e. the current number of atoms.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Base.view-Tuple{Topology, Integer}","page":"Topology","title":"Base.view","text":"view(topology::Topology, index::Integer) -> Atom\n\n\nGet the Atom at the given index of the topology without creating a copy.\n\nwarning: Warning\nThis function can lead to unefined behavior when keeping the returned Atom around. See Base.view(frame::Frame, index::Integer) for more information on this issue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_atom!-Tuple{Topology, Atom}","page":"Topology","title":"Chemfiles.add_atom!","text":"add_atom!(topology::Topology, atom::Atom)\n\n\nAdd an atom at the end of a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.add_bond!","page":"Topology","title":"Chemfiles.add_bond!","text":"add_bond!(topology::Topology, i::Integer, j::Integer)\nadd_bond!(topology::Topology, i::Integer, j::Integer, order)\n\n\nAdd a bond between the atoms i and j in the topology, optionaly setting the bond order.\n\n\n\n\n\n","category":"function"},{"location":"reference/topology/#Chemfiles.add_residue!-Tuple{Topology, Residue}","page":"Topology","title":"Chemfiles.add_residue!","text":"add_residue!(topology::Topology, residue::Residue)\n\n\nAdd a copy of residue to this topology.\n\nThe residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles","text":"angles(topology::Topology) -> Matrix{UInt64}\n\n\nGet the angles in the topology, in a 3 x angles_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.angles_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.angles_count","text":"angles_count(topology::Topology) -> Int64\n\n\nGet the number of angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.are_linked-Tuple{Topology, Residue, Residue}","page":"Topology","title":"Chemfiles.are_linked","text":"are_linked(\n topology::Topology,\n first::Residue,\n second::Residue\n) -> Bool\n\n\nCheck if the two residues first and second from the topology are linked together, i.e. if there is a bond between one atom in the first residue and one atom in the second one.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_order-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.bond_order","text":"bond_order(\n topology::Topology,\n i::Integer,\n j::Integer\n) -> Chemfiles.BondOrder\n\n\nGet the BondOrder for the bond between atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bond_orders-Tuple{Topology}","page":"Topology","title":"Chemfiles.bond_orders","text":"bond_orders(\n topology::Topology\n) -> Vector{Chemfiles.BondOrder}\n\n\nGet the BondOrder for all the bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds","text":"bonds(topology::Topology) -> Matrix{UInt64}\n\n\nGet the bonds in the topology, in a 2 x bonds_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.bonds_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.bonds_count","text":"bonds_count(topology::Topology) -> Int64\n\n\nGet the number of bonds in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.clear_bonds!-Tuple{Topology}","page":"Topology","title":"Chemfiles.clear_bonds!","text":"clear_bonds!(topology::Topology)\n\n\nRemove all bonds, angles and dihedral angles from this Topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.count_residues-Tuple{Topology}","page":"Topology","title":"Chemfiles.count_residues","text":"count_residues(topology::Topology) -> Int64\n\n\nGet the number of residues in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals","text":"dihedrals(topology::Topology) -> Matrix{UInt64}\n\n\nGet the dihedral angles in the topology, in a 4 x dihedrals_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.dihedrals_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.dihedrals_count","text":"dihedrals_count(topology::Topology) -> Int64\n\n\nGet the number of dihedral angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers","text":"impropers(topology::Topology) -> Matrix{UInt64}\n\n\nGet the improper angles in the topology, in a 4 x impropers_count(topology) array.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.impropers_count-Tuple{Topology}","page":"Topology","title":"Chemfiles.impropers_count","text":"impropers_count(topology::Topology) -> Int64\n\n\nGet the number of improper angles in the topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_atom!-Tuple{Topology, Integer}","page":"Topology","title":"Chemfiles.remove_atom!","text":"remove_atom!(topology::Topology, index::Integer)\n\n\nRemove the atom at the given index from a topology.\n\n\n\n\n\n","category":"method"},{"location":"reference/topology/#Chemfiles.remove_bond!-Tuple{Topology, Integer, Integer}","page":"Topology","title":"Chemfiles.remove_bond!","text":"remove_bond!(topology::Topology, i::Integer, j::Integer)\n\n\nRemove any existing bond between the atoms i and j in the topology.\n\n\n\n\n\n","category":"method"},{"location":"#Julia-interface-to-chemfiles","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This is the documentation for the Julia interface to the chemfiles library.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"The Julia interface to chemfiles wraps around the C interface providing a Julian API. All the functionalities are in the Chemfiles module, which can be imported by the using Chemfiles expression. The Chemfiles module is built around the main types of chemfiles: Trajectory, Frame, UnitCell, Topology, Residue, Atom, and Selection.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"warning: Warning\nAll indexing in chemfiles is 0-based! That means that the first atom in a frame have the index 0, not 1. This is because no translation is made from the underlying C library.This may change in future release to use 1-based indexing, which is more familiar to Julia developers.","category":"page"},{"location":"#Installation","page":"Julia interface to chemfiles","title":"Installation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"You will need to use a recent version of Julia (Julia >= 1.0), and then you can install the Chemfiles package by running the following at Julia prompt:","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"pkg> add Chemfiles\n\n# You may also want to run the test suite with\npkg> test Chemfiles","category":"page"},{"location":"#User-documentation","page":"Julia interface to chemfiles","title":"User documentation","text":"","category":"section"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"This section contains example of how to use Chemfiles.jl, and the complete interface reference for all the types and functions in chemfiles.","category":"page"},{"location":"","page":"Julia interface to chemfiles","title":"Julia interface to chemfiles","text":"Pages = [\n \"reference/trajectory.md\",\n \"reference/frame.md\",\n \"reference/atom.md\",\n \"reference/cell.md\",\n \"reference/topology.md\",\n \"reference/residue.md\",\n \"reference/selection.md\",\n \"reference/misc.md\",\n]","category":"page"}]
+}
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+
+Tutorials · Chemfiles.jl
This section presents some hand-on tutorials to the chemfiles Julia package. All the code here is under the CC-0 Universal Licence which means that you are free to do whatever you want with it (i.e. it is Public Domain code)
We can now create a list to store the indices of the atoms with x < 5, and get the positions of the atoms in the frame with the positions function
less_than_five = UInt64[]
+pos = positions(frame)
Iterating through the atoms in the frame, we get the ones matching our condition. size(::Frame) gives the number of atoms in the frame, which is also the size of the positions array. This positions array shape is (3, size(frame)).
for i in 1:size(frame)
+ if pos[1, i] < 5
+ push!(less_than_five, i)
+ end
+end
And finally we can print our results
println("Atoms with x < 5: ")
+for i in less_than_five
+ println(" - $i")
+end
Now that we know how to read frames from a trajectory, let's try to create a new structure and write it to a file. As previsouly, we start by using the Chemfiles package
#!/usr/bin/env julia
+using Chemfiles
Everything starts in a Topology. This is the class that defines the atoms and the connectivity in a system. Here, we add three Atom and two bonds to create a water molecule.
We can then create a Frame corresponding to this topology. We resize the frame to ensure that the frame and the topology contains the same number of atoms.
Another possibility is to directly add atoms to the frame. Here we define a second molecule representing carbon dioxyde. add_atom! takes three arguments: the frame, the atom, and the position of the atom.
Finally, we can set the UnitCell associated with this frame.
set_cell!(frame, UnitCell([10.0, 10.0, 10.0]))
Now that our frame is constructed, it is time to write it to a file. For that, we open a trajectory in write ('w') mode, and write to it, using the same syntax as a standard Julia open(...) do ... end block
Trajectory("water-co2.pdb", 'w') do trajectory
+ write(trajectory, frame)
+end
Now that we know how to read and write frame from trajectories, how about we do a bit a filtering? In this tutorial, we will read all the frames from a file, and use selections to filter which atoms we will write back to another file. This example will also show how chemfiles can be used to convert from a file format to another one.
We start by opening the two trajectories we will need
And we create a Selection object to filter the atoms we want to remove.
selection = Selection("name Zn or name N")
Then we can iterate over all the frames in the trajectory, and use the selection to get the list of atoms to remove. The result of evaluate is a list containing the atoms matching the selection.
for frame in trajectory
+ to_remove = evaluate(selection, frame)
In order to remove the atoms from the frame, we need to sort the to_remove list in descending order: removing the atom at index i will shift the index of all the atoms after i. So we start from the end and work toward the start of the frame.
for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
Finally, we can write the cleaned frame to the output file, and start the next iteration.
write(output, frame)
+end
Since we opened the files directly instead of using a do ... end block, we hae to close them to flush all buffers and release file descriptors.
close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
#!/usr/bin/env julia
+using Chemfiles
+
+trajectory = Trajectory("input.arc")
+output = Trajectory("output.pdb", 'w')
+
+selection = Selection("name Zn or name N")
+
+for frame in trajectory
+ to_remove = evaluate(selection, frame)
+ for i in reverse(sort(to_remove))
+ remove_atom!(frame, i)
+ end
+ write(output, frame)
+end
+
+close(trajectory)
+# When running on the REPL, closing the trajectory
+# is required to flush buffered output and finish writing
+close(output)
Settings
This document was generated with Documenter.jl version 0.27.24 on Wednesday 17 May 2023. Using Julia version 1.6.7.