minimize_ob

Included in psico This command or function is available from psico, which is a PyMOL extension.
Module	psico.minimizing

minimize_ob does energy minimization with Open Babel.

Installation

minimize_ob is available from the psico package and requires Open Babel.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c openbabel openbabel 

Usage

minimize_ob [ selection [, state [, ff [, nsteps [, conv [, cutoff [, cut_vdw [, cut_elec [, name ]]]]]]]]]

Arguments

• selection = str: atom selection {default: enabled}
• state = int: object state {default: -1}
• ff = GAFF|MMFF94s|MMFF94|UFF|Ghemical: force field {default: UFF}
• nsteps = int: number of steps {default: 500}

Example

# load a 2D structure from PubChem
load https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/135398633/record/SDF/?record_type=2d, gtp, format=sdf

# minimize structure to get 3D conformation
import psico.minimizing
minimize_ob

See Also

• minimize_rdkit
• optimize
• clean