closeRing.py

usage: closeRing.py [-h] [-o output destination] [-ls]
                    [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                    [-r atom1 atom2 ring] [-m] [-f]
                    [input file [input file ...]]

close rings on a geometry

positional arguments:
  input file            a coordinate file

optional arguments:
  -h, --help            show this help message and exit
  -o output destination, --output output destination
                        output destination
                        $INFILE will be replaced with the name of the input file
                        Default: stdout
  -ls, --list           list available rings
  -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
  -r atom1 atom2 ring, --ring atom1 atom2 ring
                        substitution instructions
                        atom1 and atom2 specify the position to add the new ring
  -m, --minimize        try to minimize structure difference
  -f, --flip-rings      also try swapping target order when minimizing