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openbabel

Chemical toolbox utilities (cli)

Variants:
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: * babel: 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

Homepage:
Package version:2.3.1+dfsg-4
Architecture:i386
Distribution:Debian
Filename:openbabel_2.3.1+dfsg-4_i386.deb

/usr/share/doc/openbabel/README.dioxin.pov

Sample POV-Ray Rendering

First convert dioxin.mol2 to the dioxin.inc file:

babel -imol2 dioxin.mol2 -opov dioxin.inc

Then type 

(POV-Ray 3.1)
povray +V +A +D0 +Q9 +W320 +H200 +I dioxin.pov

(POV-Ray 3.5)
povray +V +A +D0 +Q9 +W320 +H200 dioxin.pov

for a demo.



/usr/share/doc/openbabel/README.povray.gz

This file describes the extensions made for generating pictures with babel 
and povray. This extensions are copyrighted by 

Oliver Weichold (weichold@sas.upenn.edu)

and 

Steffen Reith (streit@streit.cc)

This software is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
more»

/usr/share/doc/openbabel/FAQ.html

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Open Babel: Frequently Asked Questions</title>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />

<link rel="top" href="http://openbabel.org/" />
<link rel="stylesheet" href="site.css" type="text
more»

/usr/share/man/man1/babel.1.gz

babel(1)               User's Reference Manual              babel(1)

NAME
     babel, obabel — a 
more»

/usr/share/man/man1/obchiral.1.gz

obchiral(1)            User's Reference Manual           obchiral(1)

NAME
     obchiral — print m
more»

/usr/share/man/man1/obconformer.1.gz

obconformer(1)         User's Reference Manual        obconformer(1)

NAME
     obconformer — gene
more»

/usr/share/man/man1/obenergy.1.gz

obenergy(1)            User's Reference Manual           obenergy(1)

NAME
     obenergy — calcula
more»

/usr/share/man/man1/obfit.1.gz

obfit(1)               User's Reference Manual              obfit(1)

NAME
     obfit — superimpos
more»

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