Minimizing
flat.minimizing
Module for relaxing andminimizing molecular objects.
- flat.minimizing.minimize_mm(selection='enabled', state=-1, ff='amber14-all.xml', nsteps=500, name='', quiet=1, *, _self=cmd)
- DESCRIPTION
Energy minimization with OpenMM. Supports fixed atoms (flag fix).
- USAGE
minimize_mm [ selection [, state [, ff [, nsteps [, … ]]]]]
- ARGUMENTS
- selectionstr, optional
Atom selection.
- stateint, default = -1
Object state.
- ffstr, default = ‘amber14-all.xml’
Force-field.
- nstepsint, default = 500
Number of minimization steps.
- flat.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=cmd)
- DESCRIPTION
Energy minimization with OpenBabel. Supports fixed atoms (flag fix).
- USAGE
minimize_ob [ selection [, state [, ff [, nsteps [, … ]]]]]
- ARGUMENTS
- selectionstr
Atom selection.
- stateint, default = -1
Object state.
- ffstr, default = ‘UFF’
Force-field: GAFF, MMFF94s, MMFF94, UFF, Ghemical
- nstepsint, default = 500
Number of minimization steps.
- SOURCE
From PSICO (c) Thomas Holder, Schrodinger Inc.
- flat.minimizing.minimize_rdkit(selection='enabled', state=-1, ff='MMFF94', nsteps=500, name='', quiet=1, *, _self=cmd)
- DESCRIPTION
Energy minimization with RDKit. Supports fixed atoms (flag fix)
- USAGE
minimize_rdkit [ selection [, state [, ff [, nsteps [, … ]]]]]
- ARGUMENTS
- selectionstr
Atom selection.
- stateint, default = -1
Object state.
- ffstr, default = ‘MMFF94’
Force-field: MMFF94s, MMFF94, UFF
- nstepsint, default = 500
Number of minimization steps.
- SOURCE
From PSICO (c) Thomas Holder, Schrodinger Inc.
- flat.minimizing.randomize_coords_if_collapsed(selection, state=-1, fancy=True, _self=cmd)
- DESCRIPTION
If all coordinates are the same (collapsed into one point), then randomize them.
- USAGE
randomize_coords_if_collapsed selection [, state [, fancy ]]
- ARGUMENTS
- selectionstr
Atom selection.
- stateint, default = -1
Object state.
- fancybool, default = True
Arrange atoms in a circle (this works better for openbabel).
- SOURCE
From PSICO (c) Thomas Holder, Schrodinger Inc.