usage: mapLigand.py [-h] [-ls [elements:X[,Y...] | name:RegEx]]
[-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
[-l [n[,m...]]=ligand | ligand] [-c CENTER]
[-o output destination]
[input file [input file ...]]
replace a ligand on an organometallic system
positional arguments:
input file a coordinate file
optional arguments:
-h, --help show this help message and exit
-ls [elements:X[,Y...] | name:RegEx], --list [elements:X[,Y...] | name:RegEx]
list available ligands
elements:X[,Y] can be used to only list ligands that coordinate
with the specified elements - must match exactly
name:RegEx can be used to only list ligands with names matching
the supplied regular expression - matches are case-insensitive
-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}, --input-format {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}
file format of input - xyz is assumed if input is stdin
-l [n[,m...]]=ligand | ligand, --ligand [n[,m...]]=ligand | ligand
ligand used to replace the current one
n[,m...] are the 1-indexed positions of the coordinating atoms of the
ligand that is being replaced
if these indices are not provided, they will the guessed
elements:X[,Y] or name:RegEx can be used in place of ligand
to swap ligands matching these criteria (see --list option)
-c CENTER, --center CENTER
catalyst center the ligand is bonded to
Default: any transition metal
-o output destination, --output output destination
output destination
$LIGAND will be replaced with ligand name
$INFILE will be replaced with the name of the input file
Default: stdout