usage: makeConf.py [-h] [-ls] [-i]
[-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
[-s (n=substituent|substituent name)] [-rc] [-sc]
[-o output destination]
[input file [input file ...]]
generate rotamers for substituents using a hierarchical method
positional arguments:
input file a coordinate file
optional arguments:
-h, --help show this help message and exit
-ls, --list list available substituents
-i, --info list information on substituents to be generated
-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
-s (n=substituent|substituent name), --substituent (n=substituent|substituent name)
substituents to rotate
n is the 1-indexed position of the starting position of the
substituent you are rotating
if only a substituent name is specified, all substituents with
that name will be rotated
Default: rotate any detected substituents
-rc, --remove-clash if atoms are too close together, wiggle the
substituents to remove the clash
-sc, --skip-clash do not print structures with atoms that are
too close together or for which substituent
clashing could not be resolved with '--remove-clash'
-o output destination, --output-destination output destination
output destination
$i in the filename will be replaced with conformer number
if a directory is given, default is "conformer-$i.xyz" in that directory
$INFILE will be replaced with the name of the input file
Default: stdout