openbabel

Chemical toolbox utilities (cli)

Description

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

* Hydrogen addition and deletion

* Support for Molecular Mechanics

* Support for SMARTS molecular matching syntax

* Automatic feature perception (rings, bonds, hybridization, aromaticity)

* Flexible atom typer and perception of multiple bonds from atomic coordinates

* Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

* obabel: Convert between various chemical file formats

* obenergy: Calculate the energy for a molecule

* obminimize: Optimize the geometry, minimize the energy for a molecule

* obgrep: Molecular search program using SMARTS pattern

* obgen: Generate 3D coordinates for a molecule

* obprop: Print standard molecular properties

* obfit: Superimpose two molecules based on a pattern

* obrotamer: Generate conformer/rotamer coordinates

* obconformer: Generate low-energy conformers

* obchiral: Print molecular chirality information

* obrotate: Rotate dihedral angle of molecules in batch mode

* obprobe: Create electrostatic probe grid

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Homepage

http://openbabel.sourceforge.net

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