--- name: "babel" section: "1" platform: "linux" package: "openbabel" version: "2.4.1+dfsg-3" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/babel" --- # babel(1) a converter for chemistry and molecular modeling data files ## NAME **babel**, **obabel** – a converter for chemistry and molecular modeling data files ## SYNOPSIS **babel** \[**-H** *help-options*\] **babel** \[*OPTIONS*\] \[**-i** *input-type*\] *infile* \[**-o** *output-type*\] *outfile* **obabel** \[**-H** *help-options*\] **obabel** \[*OPTIONS*\] \[**-i** *input-type* \| **-**: "*SMILES-string*"\] *infile* \[**-o** *output-type*\] **-O** *outfile* ## DESCRIPTION **babel** is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas. **obabel** and **babel** are slightly different. The first is closer to the normal Unix convention for commandline programs and more flexible when the user needs to specify parameter values on options. With **babel** this only works when the option is the last on the line; with **obabel** no such restriction applies. It further has a shortcut for entering SMILES strings, which can be used in place of an input file. Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages \<**http://openbabel.org/**\>. ## OPTIONS If only input and output files are given, Open Babel will guess the file type from the filename extension. - **-**: "*SMILES-string*" Enter SMILES string and use it in place of an input file. The SMILES string should be enclosed in quotation marks. More than one can be used, and a molecule title can be included if enclosed in quotes. - **-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\** 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 - **-O** *outfile* Specify the output file. This option applies to **obabel** only. - **-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 ## FILE FORMATS 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 \[Write-only\] ## FORMAT OPTIONS 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\\ \ e.g., -Hcml ## EXAMPLES 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 ``` ## SEE ALSO [obenergy(1)](/obenergy/1.md), [obfit(1)](/obfit/1.md), [obgrep(1)](/obgrep/1.md), [obminimize(1)](/obminimize/1.md), [obprop(1)](/obprop/1.md), [obrotate(1)](/obrotate/1.md), [obrotamer(1)](/obrotamer/1.md). The web pages for Open Babel can be found at: \<**http://openbabel.org/**\> ## AUTHORS 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 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. \ Some portions Copyright (C) 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.