OpenBabel is a program designed to interconvert a number of file formats currently used in molecular modeling software. It is distributed by sourceforge.net This is the replacement for the older version of babel that was installed on icebox.

• Version: Version 2.0.2
• Machines: All clusters of arches metacluster
• Location: /uufs/arches/sys/openbabel
• To Use: babel -i < input-type > < infile > -o < output-type > < outfile >

If babel is not found:

source /uufs/arches/sys/openbabel/etc/babel.csh

If you use it often you can add this line to your .tcshrc file.

Conversion options:

• -f <#> Start import at molecule # specified
• -l <#> End import at molecule # specified
• -t All input files describe a single molecule
• -e Continue with next object after error, if possible
• -z Compress the output with gzip
• -H Outputs this help text
• -Hxxx (xxx is file format ID e.g. -Hcml) gives format info
• -Hall Outputs details of all formats
• -V Outputs version number
• -F Outputs the available fingerprint types
• -m Produces multiple output files, to allow: Splitting: e.g. babel infile.mol new.smi -m puts each molecule into new1.smi new2.smi etc Batch conversion: e.g. babel *.mol -osmi -m converts each input file to a .smi file

Additional options for conversion of molecules:

• -c Center coordinates
• -d Delete hydrogens
• -h Add hydrogens
• -p Add hydrogens appropriate for pH
• -j Join all input molecules into a single output molecule
• -s"smarts" Convert only molecules matching SMARTS:
• -v"smarts" Convert only molecules NOT matching SMARTS:

File formats recognized by OpenBabel:

• alc -- Alchemy format
• 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]
• car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
• ccc -- CCC format [Read-only]
• cht -- Chemtool format [Write-only]
• 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 diagram format (2D)
• 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
• 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 -- FastSearching
• g03 -- Gaussian98/03 Output [Read-only]
• g98 -- Gaussian98/03 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]
• gpr -- Ghemical format
• gr96 -- GROMOS96 format [Write-only]
• hin -- HyperChem HIN format
• inchi -- InChI format [Write-only]
• inp -- GAMESS Input [Write-only]
• ins -- ShelX format [Read-only]
• jin -- Jaguar input format [Write-only]
• jout -- Jaguar output format [Read-only]
• k -- Compares first molecule to others using InChI. [Write-only]
• mdl -- MDL MOL format
• mmd -- MacroModel format
• mmod -- MacroModel format
• mol -- MDL MOL format
• mol2 -- Sybyl Mol2 format
• mopcrt -- MOPAC Cartesian format
• mopout -- MOPAC Output format [Read-only]
• 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
• test -- Test format [Write-only]
• 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]

See further specific info and options using -H, e.g. -Hcml