findAtoms.py

usage: findAtoms.py [-h]
                    [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
                    [-o OUTFILE] [-d {comma,semicolon,tab,space}]
                    [-e ELEMENTS] [-n NDX] [-bf BONDS NUM] [-wb BONDS NDX]
                    [-bt NDX] [-pd X Y Z R] [-ad NDX R] [-tm] [-mg] [-v SHAPE]
                    [-nb NUM_NEIGHBORS] [-ct THIS_NDX THAN_NDX] [-c]
                    [-f FRAGMENTS] [-or] [-i]
                    [input file [input file ...]]

find atoms matching a description and return the list of indices

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 OUTFILE, --output OUTFILE
                        output destination
                        Default: stdout
  -d {comma,semicolon,tab,space}, --delimiter {comma,semicolon,tab,space}
                        delimiter for output atom indices
  -e ELEMENTS, --element ELEMENTS
                        element symbol
  -n NDX, --index NDX   1-index position of atoms in the input file
                        may hyphen separated to denote a range
                        ranges and individual indices may be comma-separated
  -bf BONDS NUM, --bonds-from BONDS NUM
                        find atoms BONDS (integer) bonds away from atom NDX
  -wb BONDS NDX, --within-bonds BONDS NDX
                        find atoms within BONDS (integer) bonds from atom NDX
  -bt NDX, --bonded-to NDX
                        find atoms bonded to atom NDX
  -pd X Y Z R, --point-distance X Y Z R
                        find atoms within R Angstroms of (X, Y, Z)
  -ad NDX R, --atom-distance NDX R
                        find atoms within R Angstroms of atom NDX
  -tm, --transition-metal
                        find any elements in the d-block, up to the Actinides
  -mg, --main-group     find any main group element (including H)
  -v SHAPE, --vsepr SHAPE
                        find atoms with the specified VSEPR shape
                        shape can be:
                        linear_1, linear_2, bent_2_planar, bent_2_tetrahedral,
                        trigonal_planar, bent_3_tetrahedral,
                        t_shaped, tetrahedral, sawhorse, square_planar,
                        trigonal_bipyriamidal, square_pyramidal,
                        octahedral
  -nb NUM_NEIGHBORS, --number-of-bonds NUM_NEIGHBORS
                        find atoms with the specified number of bonds
  -ct THIS_NDX THAN_NDX, --closer-to THIS_NDX THAN_NDX
                        atoms that are fewer bonds from THIS_NDX than THAN_NDX
  -c, --chiral-center   find chiral centers
  -f FRAGMENTS, --fragment FRAGMENTS
                        fragments containing the specified atoms

match method (Default is atoms matching all):
  -or, --match-any      find atoms matching any of the given descriptions
  -i, --invert          invert match results