bond.py

usage: bond.py [-h]
               [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
               [-o output destination] [-m atom1 atom2]
               [-c atom1 atom2 increment] [-s atom1 atom2 distance]
               [input file [input file ...]]

measure or modify distance between atoms

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
  -m atom1 atom2, --measure atom1 atom2
                        measure and print distance between atoms (1-indexed)
  -c atom1 atom2 increment, --change atom1 atom2 increment
                        change distance by the amount specified
  -s atom1 atom2 distance, --set atom1 atom2 distance
                        set distance to the amount specified