changeElement.py

usage: changeElement.py [-h] [-o OUTFILE]
                        [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                        -e target=element [-b] [-c [N]]
                        [-g {point,linear_1,linear_2,bent_2_tetrahedral,bent_2_planar,trigonal_planar,bent_3_tetrahedral,t_shaped,tetrahedral,sawhorse,seesaw,square_planar,trigonal_pyramidal,trigonal_bipyramidal,square_pyramidal,pentagonal,hexagonal,trigonal_prismatic,pentagonal_pyramidal,octahedral,capped_octahedral,hexagonal_pyramidal,pentagonal_bipyramidal,capped_trigonal_prismatic,heptagonal,hexagonal_bipyramidal,heptagonal_pyramidal,octagonal,square_antiprismatic,trigonal_dodecahedral,capped_cube,biaugmented_trigonal_prismatic,cubic,elongated_trigonal_bipyramidal,capped_square_antiprismatic,enneagonal,heptagonal_bipyramidal,hula-hoop,triangular_cupola,tridiminished_icosahedral,muffin,octagonal_pyramidal,tricapped_trigonal_prismatic}]
                        [input file [input file ...]]

change an element and/or adjust the VSEPR geometry

positional arguments:
  input file            a coordinate file

optional arguments:
  -h, --help            show this help message and exit
  -o OUTFILE, --output OUTFILE
                        output destination
                        $INFILE will be replaced with the name of the input file
                        Default: stdout
  -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
  -e target=element, --element target=element
                        element to change into
  -b, --fix-bonds       adjust bond lengths for the new element
  -c [N], --change-hydrogens [N]
                        change the number of hydrogens by the specified amount
                        Specify nothing to automatically determine how many hydrogens
                        to add or remove. If nothing is specified, the new geometry will
                        also be determined automatically.
  -g {point,linear_1,linear_2,bent_2_tetrahedral,bent_2_planar,trigonal_planar,bent_3_tetrahedral,t_shaped,tetrahedral,sawhorse,seesaw,square_planar,trigonal_pyramidal,trigonal_bipyramidal,square_pyramidal,pentagonal,hexagonal,trigonal_prismatic,pentagonal_pyramidal,octahedral,capped_octahedral,hexagonal_pyramidal,pentagonal_bipyramidal,capped_trigonal_prismatic,heptagonal,hexagonal_bipyramidal,heptagonal_pyramidal,octagonal,square_antiprismatic,trigonal_dodecahedral,capped_cube,biaugmented_trigonal_prismatic,cubic,elongated_trigonal_bipyramidal,capped_square_antiprismatic,enneagonal,heptagonal_bipyramidal,hula-hoop,triangular_cupola,tridiminished_icosahedral,muffin,octagonal_pyramidal,tricapped_trigonal_prismatic}, --geometry {point,linear_1,linear_2,bent_2_tetrahedral,bent_2_planar,trigonal_planar,bent_3_tetrahedral,t_shaped,tetrahedral,sawhorse,seesaw,square_planar,trigonal_pyramidal,trigonal_bipyramidal,square_pyramidal,pentagonal,hexagonal,trigonal_prismatic,pentagonal_pyramidal,octahedral,capped_octahedral,hexagonal_pyramidal,pentagonal_bipyramidal,capped_trigonal_prismatic,heptagonal,hexagonal_bipyramidal,heptagonal_pyramidal,octagonal,square_antiprismatic,trigonal_dodecahedral,capped_cube,biaugmented_trigonal_prismatic,cubic,elongated_trigonal_bipyramidal,capped_square_antiprismatic,enneagonal,heptagonal_bipyramidal,hula-hoop,triangular_cupola,tridiminished_icosahedral,muffin,octagonal_pyramidal,tricapped_trigonal_prismatic}
                        specify the geometry to use with the new element
                        if the argument is not supplied, the geometry will remain the same as
                        the previous element's, unless necessitated by an increase in hydrogens