minimize_ob
|
Included in psico | |
| Module | psico.minimizing |
|---|---|
minimize_ob does energy minimization with Open Babel.
Installation
[edit]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
[edit]minimize_ob [ selection [, state [, ff [, nsteps [, conv [, cutoff [, cut_vdw [, cut_elec [, name ]]]]]]]]]
Arguments
[edit]- 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
[edit]# 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