changeChirality.py

usage: changeChirality.py [-h] [-ls]
                          [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                          [-o output destination] [-t TARGETS] [-d] [-m]
                          [input file [input file ...]]

change handedness of chiral centers

positional arguments:
  input file            a coordinate file

optional arguments:
  -h, --help            show this help message and exit
  -ls, --list-chiral    list information on detected chiral centers
  -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
  -o output destination, --output-destination output destination
                        output destination
                        $i in the filename will be replaced with a number
                        if a directory is given, default is "diastereomer-$i.xyz" in
                        that directory
                        Default: stdout
  -t TARGETS, --targets TARGETS
                        comma- or hyphen-seperated list of chiral centers to invert (1-indexed)
                        Chiral centers must have at least two fragments not in a ring
                        Detected chiral centers are atoms that:
                            - have > 2 bonds
                            - have a non-planar VSEPR shape
                            - each connected fragment is distinct or is a spiro center
                        Default: change chirality of any detected chiral centers
  -d, --diastereomers   print all diastereomers for selected chiral centers
  -m, --minimize        rotate substituents to mitigate steric clashing