usage: coneAngle.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] [-m {Tolman,Exact}]
[-r {umn,bondi}] [-b]
[input file [input file ...]]
calculate ligand cone angles
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
-m {Tolman,Exact}, --method {Tolman,Exact}
cone angle type
Tolman: Tolman's method for unsymmetric mono- and bidentate ligands
see J. Am. Chem. Soc. 1974, 96, 1, 53–60 (DOI:
10.1021/ja00808a009)
Exact: (Default) Allen's method for an all-encompassing cone
see Bilbrey, J.A., Kazez, A.H., Locklin, J. and Allen, W.D.
(2013), Exact ligand cone angles. J. Comput. Chem., 34:
1189-1197. (DOI: 10.1002/jcc.23217)
-r {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
-b, --cone-bild print Chimera/ChimeraX bild file containing cones