substitute.py

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

replace an atom or substituent with another

positional arguments:
  input file            a coordinate file

optional arguments:
  -h, --help            show this help message and exit
  -ls, --list           list available substituents
  -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, --substitute n=substituent
                        substitution instructions
                        n is the 1-indexed position of the starting position of the
                        substituent you are replacing
                        a substituent name prefixed by iupac: or smiles: (e.g. iupac:acetyl
                        or smiles:O=[N.]=O) will create the substituent from the
                        corresponding identifier
  -m, --minimize        rotate substituents to try to minimize LJ energy
  -o output destination, --output output destination
                        output destination
                        $INFILE will be replaced with the name of the input file
                        Default: stdout