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cgit.tcl
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cgit.tcl
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#!/usr/bin/tclsh
# +-------+
# | CG-it |
# +-------+
# CG-it, a VMD package to simplify creating coarse grained SDK
# topologies.
# Copyright (c) 2013 by Chris MacDermaid <[email protected]>
# and Giacomo Fiorin <[email protected]>
#(Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
#(DeVane) Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
## None of this will work without topotools.
package require topotools
## This package makes extensive use of some Tcl 8.5 features.
package require Tcl 8.5
namespace eval ::CGit:: {
namespace export CGit
variable version 1.1
## Valid cgit commands
variable validcmd {readtop readparam reanalyzemol setbonds
setangles setdihedrals setimpropers reset clear readlammpsdata writelammpsdata
writelammpsparam writesdktopo writetop setbondparam setangleparam
setpairparam deletebondparam deleteangleparam deletepairparam getbondparam
getangleparam getpairparam readmap map maptrajectory maptraj
printmap setparam deleteparam getparam printparam printmaptable
printmap solvate help commands topo2map}
## Parameter Files loaded by default
variable param_files {param_sdk.dat}
## Parameter array
#variable params
#array set params {}
#array unset params *
#Parameter Dictionary
variable params ""
## Store interface variables
variable sys
array unset sys
## Atom Mappings and Topologies
variable map ""
## Test map internal consistency on loading?
variable maptest 0
## Show the title and citation info?
variable showtitle 0
## Locations of additional data files
variable datadir $env(CGITDIR)
## Make some utility commands accessable
namespace export map map_trajectory
## Return error codes
set sys(OK) 0
set sys(ERROR) -1
}
# +----------------+
# | Global command |
# +----------------+
proc CGit { args } {
eval ::CGit::CGit $args
}
proc CGit::title {} {
variable version
cgCon -info "CG-it Version $version "
cgCon -info "Loading from: [info script] "
cgCon -info "Please Cite: "
}
proc CGit::usage {} {
set groups(1) "common flags:"
set commands(1) {\
{ {-molid} {<num>|top} {molecule id (default: 'top')}}\
{ {-sel} {<selection>} {atom selection function or text (default: 'all')}}\
}
set groups(2) ""
set commands(2) {\
{ {help} {} {prints this message}}\
}
set groups(3) "Topologies and Parameters:"
set commands(3) {\
{ {readtop} {<filename>} {read topology file}}\
{ {readparam} {<filename>} {read parameter file}}\
{ {writetop} {[<filename>]} {write legacy SDK topology for specified selection}}\
{ {topo2map} {<topfile> [<mapfile>]} {convert legacy SDK topology to map}}\
{ {printparam} {} {print to screen all currently loaded parameters}}\
{ {clear} {<maps> <params> <both>} {clear the all maps, params or both}}\
{ {reset} {} {clear loaded parameters and topologies, reload defaults}}\
{ {} {} {}}\
{ {(set|delete)bondparam} {<type1> <type2>} {re/set bond parameters for specified atom types}}\
{ {} {<k> <r_bond>} {}}\
{ {(set|delete)angleparam} {<type1> <type2> <type3>} {re/set angle parameters for specified atom types}}\
{ {} {<k> <theta>} {}}\
{ {(set|delete)pairparam} {<type1> <type2> <lj_type>} {re/set pair parameters for specified atom types}}\
{ {} {<epsilon> <sigma>} {}}\
{ {} {} {}}\
{ {get(bond|angle|pair)param} {} {print specified parameters. Wildcard '*' returns }}\
{ {} {<type1> <type2> [<type3> <type4>]} {all types: e.g. 'cg getbondparam PH *'}}\
}
set groups(4) "CG mappings:"
set commands(4) {\
{ {readmap} {<filename>} {read an SDK map file}}\
{ {map} {} {perfrom a CG mapping}}\
{ {maptraj} {[<start> <end> <skip>]} {perfrom a CG mapping of a trajectory}}\
{ {printmap} {<resname>} {print out mapping information for specified}}\
{ {} {} {residue name (default 'all')}}\
}
set groups(5) "Molecule Preparation:"
set commands(5) {\
{ {set(bonds|angles|dihedrals|impropers)} {} {Apply bonding/angle connectivities specified from}}\
{ {} {} {topologies/maps to selected atoms.}}\
{ {reanalyzemol} {} {Apply [<mass> <charge> <index> <type> <all> <none>] properties}}\
{ {} {} {from topologies to selected atoms and retype}}\
{ {} {} {[<bonds> <angles> <dihedrals> <impropers>] (default 'all bonds angles')}}\
{ {solvate} {[<distance> <filename>]} {Solvate selected atoms in a solvent box according}}\
{ {} {} {to pbc cell size with a minimum <distance> (default '3')}}\
{ {} {} {angstroms from the solute. <filename> specifies a pdb file}}\
{ {} {} {for a orthorhombic solvent box.}}\
}
set groups(6) "LAMMPS:"
set commands(6) {\
{ {writelammpsdata} {<filename> <atomstyle>} {Write out a data file suitable for use with lammps}}\
{ {writelammpsparam} {<filename>} {Write out a lammps SDK 'parameter' file containing}}\
{ {} {(cpu|gpu|both)} {forcefield parameters required by the system. Compatible}}\
{ {} {} {options for simulating with <cpu> <gpu> or <both> are provided}}\
{ {} {(geometric|arithmetic|lb)} {Generate missing LJ parameters with geometric,}}\
{ {} {} {arithmetic, or Lorentz-Berthelot rules}}\
}
cgCon -info "usage: cg <command> \[args...\] <flags>"
cgCon -info "Note: by default, cgit works on all atoms in the top molecule"
cgCon -info ""
## Print out each group
foreach g {2 1 3 4 5 6} {
cgCon -info $groups($g)
foreach cmd $commands($g) {cgCon -info [format " %-15s %-25s %-25s" {*}$cmd]}
cgCon -info ""
}
}
# +---------------------------------------------------+
# | Parse arguments, set defaults, execute directives |
# +---------------------------------------------------+
proc CGit::CGit { args } {
variable validcmd
set molid -1
set seltxt all
set selmol -1
set localsel 1
set cmd {}
set sel {}
set newargs {}
for {set i 0} {$i < [llength $args]} {incr i} {
set arg [lindex $args $i]
if {[string match -?* $arg]} {
set val [lindex $args [expr $i+1]]
switch -- $arg {
-molid {
if {[catch {molinfo $val get name} res]} {
cgCon -err "Invalid -molid argument '$val': $res"
return
}
set molid $val
if {[string equal $molid "top"]} {
set molid [molinfo top]
}
incr i
}
-sel {
# check if the argument to -sel is a valid atomselect command
if {([info commands $val] != "") && ([string equal -length 10 $val atomselect])} {
set localsel 0
set selmol [$val molid]
set sel $val
} else {
set localsel 1
set seltxt $val
}
incr i
}
-- break
default {
#cgCon -info "default: $arg"
lappend newargs $arg
}
}
} else {
lappend newargs $arg
}
}
if {$molid < 0} {
set molid $selmol
}
if {$molid < 0} {
set molid [molinfo top]
}
set retval ""
if {[llength $newargs] > 0} {
set cmd [lindex $newargs 0]
set newargs [lrange $newargs 1 end]
} else {
set newargs {}
set cmd help
}
if {[lsearch -exact -ascii $validcmd $cmd] < 0} {
cgCon -err "Unknown command '$cmd'"
usage
return
}
if { ![string equal $cmd help] && $molid >= 0 } {
if {($selmol >= 0) && ($selmol != $molid)} {
cgCon -err "Molid from selection '$selmol' does not match -molid argument '$molid'"
return
}
if {$localsel} {
# need to create a selection
if {[catch {atomselect $molid $seltxt} sel]} {
cgCon -err "Problem with atom selection using '$seltxt': $sel"
return
}
}
}
switch -- $cmd {
readtop {
if {[llength $newargs] < 1} {
cgCon -err "cgit 'readtop' requires a file to read from"
usage
return
}
## Convert legacy top to map on the fly
readTopo {*}$newargs
}
topo2map {
if {[llength $newargs] < 1} {
usage
return
}
set out [lindex $newargs 1]
if {$out == ""} {set out stdout}
topo2map [lindex $newargs 0] $out 0
}
writetop -
writesdktopo {
if {$sel == "" || $molid < 0} {return [usage]}
writesdktopo $sel {*}$newargs
}
readparam {
if {[llength $newargs] < 1} {
cgCon -err "cgit 'readparam' requires a file to read from"
usage
return
}
#read_param $newargs
readParam {*}$newargs
}
readlammpsdata {
if {[llength $newargs] < 1} {
cgCon -err "cgit 'readlammpsdata' requires a file to read from as argument"
usage
return
}
set retval [readlammpsdata {*}$newargs]
}
writelammpsdata {
if {[llength $newargs] < 1} {
cgCon -err "cgit 'writelammpsdata' requires a file to write to as argument"
usage
return
}
writelammpsdata $molid {*}$newargs
}
writelammpsparam {
if {[llength $newargs] < 1} {
cgCon -err "cgit 'writelammpsparam' requires a file to write to as argument"
usage
return
}
writelammpsparam $molid {*}$newargs
}
printmap -
printmaptable {map_stats {*}$newargs}
mapread -
readmap {
if {[llength $newargs] < 0} {
cgCon -err "cgit 'readmap' requires a file to read from as argument"
usage
return
}
readTopo{*}$newargs
}
map -
maptraj -
maptrajectory {
if {$sel == "" || $molid < 0} {return [usage]}
set retval [map $sel {*}$newargs]
}
setbond -
setbonds {
if {$sel == "" || $molid < 0} {return [usage]}
set_bonds $sel
}
setangle -
setangles {
if {$sel == "" || $molid < 0} {return [usage]}
set_angles $sel
}
setdihedral -
setdihedrals {
if {$sel == "" || $molid < 0} {return [usage]}
set_dihedrals $sel
}
setimproper -
setimpropers {
if {$sel == "" || $molid < 0} {return [usage]}
set_impropers $sel {*}$newargs
}
reanalyzemol {
if {$sel == "" || $molid < 0} {return [usage]}
reanalyze_mol $sel {*}$newargs
}
reset {reset}
clear {
clear {*}$newargs
}
solvate {
if {$sel == "" || $molid < 0} {return [usage]}
set retval [solvate_box $sel {*}$newargs]
}
setbondparam {set_param bond {*}$newargs}
setangleparam {set_param angle {*}$newargs}
setpairparam {set_param pair {*}$newargs}
setparam {set_param {*}$newargs}
deletebondparam {delete_param bond {*}$newargs}
deleteangleparam {delete_param angle {*}$newargs}
deletepairparam {delete_param pair {*}$newargs}
deleteparam {delete_param {*}$newargs}
getbondparam {set retval [get_param bond {*}$newargs]}
getangleparam {set retval [get_param angle {*}$newargs]}
getpairparam {set retval [get_param pair {*}$newargs]}
getparam {set retval [get_param {*}$newargs]}
printparam {print_param {*}$newargs}
commands {return [join $validcmd]}
help -
default {usage}
}
if {$localsel} {
catch {$sel delete}
}
return $retval
}
# +---------+
# | Helpers |
# +---------+
## A wrapper around cgCon
proc CGit::cgCon {flag str} {
switch -- $flag {
"-error" -
"-err" { vmdcon -err "CG> $str" }
"-warn" { vmdcon -warn "CG> $str" }
"-info" { vmdcon -info "CG> $str" }
default { vmdcon $str}
}
}
# +---------+
# | Startup |
# +---------+
interp alias {} cg {} ::CGit::CGit
package provide cg $::CGit::version
if {$::CGit::showtitle} {::CGit::title}
## Load other cgit files
#source [file join $env(CGITDIR) maps common.tcl]
source [file join $env(CGITDIR) cgit_map.tcl]
source [file join $env(CGITDIR) cgit_partopo.tcl]
source [file join $env(CGITDIR) cgit_traj.tcl]
source [file join $env(CGITDIR) cgit_lammps.tcl]
source [file join $env(CGITDIR) cgit_solvate.tcl]
source [file join $env(CGITDIR) cgit_legacy.tcl]
source [file join $env(CGITDIR) cgit_helpers.tcl]
source [file join $env(CGITDIR) json.tcl]
## C-based routines
catch {load [file join $env(CGITDIR) libcgmap.so]}
## Load the default mappings from maps in $env(CGITDIR)/maps
##::CGit::map_defaults