usage: ligandSterimol.py [-h]
[-if {xyz,log,com,gjf,sd,sdf,mol,mol2,out,dat,fchk,crest,xtb,sqmout,47,31,qout}]
-k KEY -c CENTER [-r {bondi,umn}] [-bl] [-al L_VALUE]
[-v] [-o output destination]
[input file [input file ...]]
calculate B1-B5, and L sterimol parameters for ligands - see Verloop, A. and Tipker, J. (1976), Use of linear free energy related and other parameters in the study of fungicidal selectivity. Pestic. Sci., 7: 379-390.
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
-k KEY, --key-atoms KEY
1-indexed position of the ligand's coordinating atoms
-c CENTER, --center-atom CENTER
atom the ligand is coordinated to
-r {bondi,umn}, --radii {bondi,umn}
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: bondi
-bl, --bisect-L L axis will bisect (or analogous for higher denticity
ligands) the L-M-L angle
Default: center to centroid of key atoms
-al L_VALUE, --at-L L_VALUE
get widths at specific L values (comma-separated)
can be used for Sterimol2Vec parameters
Default: use the entire ligand
-v, --vector print Chimera/ChimeraX bild file for vectors instead of parameter values
-o output destination, --output output destination
output destination
Default: stdout