removeFragment.py

usage: removeFragment.py [-h]
                         [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                         [-o output destination] -t TARGET [-k AVOID] [-a]
                         [input file [input file ...]]

remove a fragment from a molecule

positional arguments:
  input file            a coordinate file

optional arguments:
  -h, --help            show this help message and exit
  -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 output destination
                        output destination
                        $INFILE will be replaced with the name of the input file
                        Default: stdout
  -t TARGET, --targets TARGET
                        fragment atom connected to the rest of the molecule (1-indexed)
  -k AVOID, --keep-group AVOID
                        atom on the molecule that is connected to the fragment being removed
                        Default: longest fragment
  -a, --add-hydrogen    add hydrogen to cap where the fragment was removed