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babel

a converter for chemistry and molecular modeling data files

- Transpile a specified input file and output to stdout:
babel [path/to/file]

- Transpile a specified input file and output to a specific file:
babel [path/to/input_file] --out-file [path/to/output_file]

- Transpile the input file every time it is changed:
babel [path/to/input_file] --watch

- Transpile a whole directory of files:
babel [path/to/input_directory]

- Ignore specified comma-separated files in a directory:
babel [path/to/input_directory] --ignore [ignored_files]

- Transpile and output as minified JavaScript:
babel [path/to/input_file] --minified

- Choose a set of presets for output formatting:
babel [path/to/input_file] --presets [presets]

- Output all available options:
babel --help

babel [-H help-options]

babel [OPTIONS] [-i input-type] infile [-o output-type] outfile

Babel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.

Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages <http://openbabel.org/>.

If only input and ouput files are given, Open Babel will guess the file type from the filename extension.

 -a options
Format-specific input options. See -H format-ID for options allowed by a particular format

--addtotitle Append text to the current molecule title

--addformula Append the molecular formula after the current molecule title

-b' Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O

-c' Center atomic coordinates at (0,0,0)

-C' Combine molecules in first file with others having the same name

-e' Continue after errors

-d' Delete Hydrogens

---errorlevel 2 Filter the level of errors and warnings displayed: 1 = critical errors only 2 = include warnings too (default) 3 = include informational messages too 4 = include "audit log" messages of changes to data 5 = include debugging messages too

-f # For multiple entry input, start import with molecule # as the first entry

-F' Output the available fingerprint types

-h' Add hydrogens

-H' Output usage information

-H format-ID Output formatting information and options for format specified

-Hall Output formatting information and options for all formats

-i<format-ID> Specifies input format, see below for the available formats

-j'

--join Join all input molecules into a single output molecule entry

-k' Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian)

-m' Produce multiple output files, to allow: - Splitting one input file - put each molecule into consecutively numbered output files - Batch conversion - convert each of multiple input files into a specified output format

-l # For multiple entry input, stop import with molecule # as the last entry

-o format-ID Specifies output format, see below for the available formats

-p' Add Hydrogens appropriate for pH (use transforms in phmodel.txt)

--property Add or replace a property (e.g., in an MDL SD file)

-s SMARTS Convert only molecules matching the SMARTS pattern specified

--separate Separate disconnected fragments into individual molecular records

-t' All input files describe a single molecule

--title title Add or replace molecular title

-x options Format-specific output options. See -H format-ID for options allowed by a particular format

-v SMARTS Convert only molecules NOT matching SMARTS pattern specified

-V' Output version number and exit

-z' Compress the output with gzip

The following formats are currently supported by Open Babel:

acr -- Carine ASCI Crystal alc -- Alchemy format arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] bgf -- MSI BGF format box -- Dock 3.5 Box format bs -- Ball and Stick format c3d1 -- Chem3D Cartesian 1 format c3d2 -- Chem3D Cartesian 2 format caccrt -- Cacao Cartesian format cache -- CAChe MolStruct format [Write-only] cacint -- Cacao Internal format [Write-only] can -- Canonical SMILES format car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] ccc -- CCC format [Read-only] cdx -- ChemDraw binary format [Read-only] cdxml -- ChemDraw CDXML format cht -- Chemtool format [Write-only] cif -- Crystallographic Information File cml -- Chemical Markup Language cmlr -- CML Reaction format com -- Gaussian 98/03 Cartesian Input [Write-only] copy -- Copies raw text [Write-only] crk2d -- Chemical Resource Kit 2D diagram format crk3d -- Chemical Resource Kit 3D format csr -- Accelrys/MSI Quanta CSR format [Write-only] cssr -- CSD CSSR format [Write-only] ct -- ChemDraw Connection Table format dmol -- DMol3 coordinates format ent -- Protein Data Bank format fa -- FASTA format [Write-only] fasta -- FASTA format [Write-only] fch -- Gaussian formatted checkpoint file format [Read-only] fchk -- Gaussian formatted checkpoint file format [Read-only] fck -- Gaussian formatted checkpoint file format [Read-only] feat -- Feature format fh -- Fenske-Hall Z-Matrix format [Write-only] fix -- SMILES FIX format [Write-only] fpt -- Fingerprint format [Write-only] fract -- Free Form Fractional format fs -- Open Babel FastSearching database fsa -- FASTA format [Write-only] g03 -- Gaussian 98/03 Output [Read-only] g98 -- Gaussian 98/03 Output [Read-only] gam -- GAMESS Output [Read-only] gamin -- GAMESS Input [Write-only] gamout -- GAMESS Output [Read-only] gau -- Gaussian 98/03 Cartesian Input [Write-only] gjc -- Gaussian 98/03 Cartesian Input [Write-only] gjf -- Gaussian 98/03 Cartesian Input [Write-only] gpr -- Ghemical format gr96 -- GROMOS96 format [Write-only] hin -- HyperChem HIN format inchi -- IUPAC InChI [Write-only] inp -- GAMESS Input [Write-only] ins -- ShelX format [Read-only] jin -- Jaguar input format [Write-only] jout -- Jaguar output format [Read-only] mdl -- MDL MOL format mmd -- MacroModel format mmod -- MacroModel format mol -- MDL MOL format mol2 -- Sybyl Mol2 format molreport -- Open Babel molecule report [Write-only] moo -- MOPAC Output format [Read-only] mop -- MOPAC Cartesian format mopcrt -- MOPAC Cartesian format mopin -- MOPAC Internal mopout -- MOPAC Output format [Read-only] mpc -- MOPAC Cartesian format mpd -- Sybyl descriptor format [Write-only] mpqc -- MPQC output format [Read-only] mpqcin -- MPQC simplified input format [Write-only] nw -- NWChem input format [Write-only] nwo -- NWChem output format [Read-only] pc -- PubChem format [Read-only] pcm -- PCModel format pdb -- Protein Data Bank format pov -- POV-Ray input format [Write-only] pqs -- Parallel Quantum Solutions format prep -- Amber Prep format [Read-only] qcin -- Q-Chem input format [Write-only] qcout -- Q-Chem output format [Read-only] report -- Open Babel report format [Write-only] res -- ShelX format [Read-only] rxn -- MDL RXN format sd -- MDL MOL format sdf -- MDL MOL format smi -- SMILES format sy2 -- Sybyl Mol2 format tdd -- Thermo format test -- Test format [Write-only] therm -- Thermo format tmol -- TurboMole Coordinate format txyz -- Tinker MM2 format [Write-only] unixyz -- UniChem XYZ format vmol -- ViewMol format xed -- XED format [Write-only] xml -- General XML format [Read-only] xyz -- XYZ cartesian coordinates format yob -- YASARA.org YOB format zin -- ZINDO input format [Write-only]

Individual file formats may have additional formatting options.

Input format options are preceded by 'a', e.g. -as

Output format options are preceded by 'x', e.g. -xn

For further specific information and options, use -H<format-type> e.g., -Hcml

Standard conversion:

babel -ixyz ethanol.xyz -opdb ethanol.pdb

Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:

babel -ismi -omol2

Split a multi-molecule file into new1.smi, new2.smi, etc.:

babel infile.mol new.smi -m

obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1), obrotamer(1). The web pages for Open Babel can be found at: <http://openbabel.org/>

A cast of many, including the currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

Copyright © 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright © 2001-2007 by Geoffrey R. Hutchison

This program 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.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Open Babel 2.2 July 4, 2008 Open Babel 2.2

chemtool(1), obchiral(1), obconformer(1), obgen(1), obprobe(1), roundtrip(1)

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