usage: solidAngle.py [-h] [-o OUTFILE]
[-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
[-k KEY_ATOMS] [-c CENTER]
[-p {110,194,302,590,974,1454,2030,2702,5810}] [-sca]
[-vdw {umn,bondi}]
[input file [input file ...]]
print ligand solid angle
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
-k KEY_ATOMS, --key-atoms KEY_ATOMS
indices of ligand coordinating atoms you are calculating
the cone angle of (1-indexed)
-c CENTER, --center CENTER
index of complex's center atom (1-indexed)
Default: transition metals
-p {110,194,302,590,974,1454,2030,2702,5810}, --points {110,194,302,590,974,1454,2030,2702,5810}
number of angular points for integration
lower values are faster, but at the cost of accuracy
Default: 5810
-sca, --solid-cone-angle
print solid ligand cone angles instead of solid angles
-vdw {umn,bondi}, --vdw-radii {umn,bondi}
VDW radii to use in calculation
umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812
(DOI: 10.1021/jp8111556)
transition metals are crystal radii from Batsanov, S.S. Van der Waals
Radii of Elements. Inorganic Materials 37, 871–885 (2001).
(DOI: 10.1023/A:1011625728803)
bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)
Default: umn