psico.minimizing

3. Thomas Holder, Schrodinger Inc.

Functions

clean_ob(selection[, present, state, fix, ...])	Replacement for pymol.computing._clean, using openbabel.
get_fixed_indices(selection, state, _self)
load_or_update(molstr, name, sele, state, _self)
minimize_ob([selection, state, ff, nsteps, ...])	Emergy minimization with openbabel
minimize_rdkit([selection, state, ff, ...])	Emergy minimization with RDKit
randomize_coords_if_collapsed(selection, state)	If all coordinates are the same (collapsed into one point), then randomize them.

psico.minimizing.clean_ob(selection, present='', state=-1, fix='', restrain='', method='mmff', save_undo=1, message=None, _self=...)

Replacement for pymol.computing._clean, using openbabel.

Side effects: clears “fix” flag if “present” argument is given.

import pymol.computing import psico.minimizing pymol.computing._clean = psico.minimizing.clean_ob

See Also

minimize_ob

psico.minimizing.get_fixed_indices(selection, state, _self)

psico.minimizing.load_or_update(molstr, name, sele, state, _self)

psico.minimizing.minimize_ob(selection='enabled', state=-1, ff='UFF', nsteps=500, conv=0.0001, cutoff=0, cut_vdw=6.0, cut_elec=8.0, name='', quiet=1, _self=...)

Emergy minimization with openbabel

Supports fixed atoms (flag fix)

Arguments

selection = str: atom selection

state = int: object state {default: -1}

ff = GAFF|MMFF94s|MMFF94|UFF|Ghemical: force field {default: UFF}

nsteps = int: number of steps {default: 500}

psico.minimizing.minimize_rdkit(selection='enabled', state=-1, ff='MMFF94', nsteps=200, name='', quiet=1, _self=...)

Emergy minimization with RDKit

Supports fixed atoms (flag fix)

Arguments

selection = str: atom selection

state = int: object state {default: -1}

ff = MMFF94s|MMFF94|UFF: force field {default: MMFF94}

nsteps = int: number of steps {default: 200}

psico.minimizing.randomize_coords_if_collapsed(selection, state, fancy=True, _self=...)

If all coordinates are the same (collapsed into one point), then randomize them.

Parameters:

fancy (bool) – Arrange atoms in a circle (this works better for openbabel)