Electrostatics
flat.electrostatics
Module for computing electrostatic properties.
- flat.electrostatics.get_vacuum_esp(selection, mode=2, cutoff=10.0, *, _self=cmd)
- DESCRIPTION
Calculate vacuum electrostatic potential map.
Available calculation modes:
0: coulomb, no cutoff
1: coulomb_neutral map, no cutoff
2: coulomb_local, cutoff
- USAGE
get_vacuum_esp selection [, mode [, border ]]
- ARGUMENTS
- selectionstr, optional
Atom selection.
- mode = int, default = 2
Calculation mode (see above).
- cutofffloat, default = 10.0
Calculation cutoff value.
- SOURCE
From PSICO (c) 2012 Thomas Holder
- flat.electrostatics.set_charges_and_radii(obj_name, quiet=1, *, _self=cmd)
- DESCRIPTION
Assign atom VdW radii, formal, and partial charges using AMBER99 force-field. Function has it’s own fair share of problems. Use with caution!
- USAGE
set_charges_and_radii obj_name
- ARGUMENTS
- obj_namestr
Molecular object name.
- flat.electrostatics.sum_formal_charges(selection='all', quiet=1, *, _self=cmd)
- DESCRIPTION
Get sum of formal charges for selection.
- USAGE
sum_formal_charges [ selection ]
- ARGUMENTS
- selectionstr, optional
Atom selection.
- RETURNS
- : int
Sum of formal charges.
- flat.electrostatics.sum_partial_charges(selection='(all)', quiet=1, *, _self=cmd)
- DESCRIPTION
Get sum of partial charges for selection
- USAGE
sum_partial_charges [ selection ]
- ARGUMENTS
- selectionstr, optional
Atom selection.
- RETURNS
- : float
Sum of partial charges.