usage: findAtoms.py [-h] [-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,pdb,pdbqt,cif,mmcif,crest,xtb,sqmout,47,31,qout}] [-o OUTFILE] [-d {comma,semicolon,tab,space}] [-xyz] [-a]
[-e ELEMENTS] [-n NDX] [-bf BONDS NUM] [-wb BONDS NDX] [-bt NDX] [-pd X Y Z R] [-ad NDX R] [-tm] [-mg] [-dum] [-v SHAPE] [-nb NUM_NEIGHBORS] [-ct THIS_NDX THAN_NDX]
[-c] [-f FRAGMENTS] [-or] [-i]
[input file ...]
find atoms matching a description and return the list of indices
positional arguments:
input file a coordinate file
options:
-h, --help show this help message and exit
-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,pdb,pdbqt,cif,mmcif,crest,xtb,sqmout,47,31,qout}, --input-format {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,pdb,pdbqt,cif,mmcif,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
-xyz, --xyz-format print atoms in XYZ format
-a, --append append output data to file (default is to overwrite)
atom matching criteria:
-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)
-dum, --dummy-atoms find dummy atoms
-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