rmsdAlign.py

usage: rmsdAlign.py [-h]
                    [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                    [-r REF] [-it targets] [-rt targets] [-v | -csv]
                    [-d {comma,semicolon,tab,space}] [-s] [-n] [-o OUTFILE]
                    [input file [input file ...]]

align structure to reference

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
  -r REF, --reference REF
                        reference structure
  -it targets, --input-targets targets
                        target atoms on input (1-indexed)
                        comma (,) and/or hyphen (-) separated list
                        hyphens denote a range of atoms
                        commas separate individual atoms or ranges
                        Default: whole structure
  -rt targets, --ref-targets targets
                        target atoms on reference (1-indexed)
  -s, --sort            sort atoms
  -n, --non-hydrogen    ignore hydrogen atoms

output options:
  -v, --value           print RMSD only
  -csv, --comma-seperated
                        print output in CSV format
  -d {comma,semicolon,tab,space}, --delimiter {comma,semicolon,tab,space}
                        CSV delimiter
  -o OUTFILE, --output OUTFILE
                        output destination
                        $INFILE will be replaced with the name of the input file
                        Default: stdout