Exchange Mappings

Exchange mappings describe how one molecule can be transformed into another.

Operations

Most exchanges between from_residue and to_residue require a series of operations. An empty object, new_residue is created and operations are applied to this object. The final new_residue has the position of the from_residue and the topology of the to_residue.

Direct Overlay

This action adds atoms from to_residue to new_residue using positions of atoms in from_residue. It is specified in an Alchex JSON file like so:

{
    "method" : "direct_overlay", // Use Direct Overlay method
    "map"    : {
                 "2" : "8", 
                 "3" : "7" // Add atom 8 and 7 of to_residue at position
}                          // of atom 2 and 3 of from_residue respectively.

Fragment Align

This action requires at least three atoms which have already been added to the new_residue.

See Issue#11 regarding support for two reference atoms.

Molecule Align

Simple Bridge

Scale Match Vector