Open Babel - a converter for molecular modeling data files

babel [-i<input-type>] <infile> [-o<output-type>] <outfile>

Open Babel is a program designed to interconvert a number of file formats currently used in molecular modeling software.

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

-c

Center molecule

-d

Delete hydrogens

-f <number>

Start importing at molecule number specified

-h

Add hydrogens

-hpH

Add hydrogens appropriate for pH

-i

Specifies input format, see below for the available formats

-l <number>

End importing at molecule number specified

-o

Specifies output format, see below for the available formats

Open Babel recognizes the following input formats: alc -- Alchemy file prep -- AMBER PREP file bs -- Ball and Stick file caccrt -- Cacao Cartesian file ccc -- CCC file c3d1 -- Chem3D Cartesian 1 file c3d2 -- Chem3D Cartesian 2 file cml -- Chemical Markup Language file box -- Dock 3.5 Box file dmol -- DMol3 Coordinates file feat -- Feature file gam -- GAMESS Output file gamout -- GAMESS Output file gpr -- Ghemical Project file mm1gp -- Ghemical MM file qm1gp -- Ghemical QM file hin -- Hyperchem HIN file jout -- Jaguar Output file bin -- OpenEye Binary file mmd -- MacroModel file mmod -- MacroModel file out -- MacroModel file dat -- MacroModel file car -- MSI Biosym/Insight II CAR file sdf -- MDL Isis SDF file sd -- MDL Isis SDF file mdl -- MDL Molfile file mol -- MDL Molfile file mopcrt -- MOPAC Cartesian file mopout -- MOPAC Output file mmads -- MMADS file mpqc -- MPQC file bgf -- MSI BGF file nwo -- NWChem Output file pdb -- PDB file ent -- PDB file qcout -- QChem Output file res -- ShelX file smi -- SMILES file mol2 -- Sybyl Mol2 file unixyz -- UniChem XYZ file vmol -- ViewMol file xyz -- XYZ file

The following output formats may be written by Open Babel: alc -- Alchemy file bs -- Ball & Stick file caccrt -- Cacao Cartesian file cacint -- Cacao Internal file cache -- CAChe MolStruct file c3d1 -- Chem3D Cartesian 1 file c3d2 -- Chem3D Cartesian 2 file ct -- ChemDraw Connection Table file cml -- Chemical Markup Language file cssr -- CSD CSSR file box -- Dock 3.5 Box file dmol -- DMol3 Coordinates file feat -- Feature file fh -- Fenske-Hall Z-Matrix file gamin -- GAMESS Input file inp -- GAMESS Input file gcart -- Gaussian Cartesian file gau -- Gaussian Input file gpr -- Ghemical Project file gr96A -- GROMOS96 (A) file gr96N -- GROMOS96 (nm) file hin -- HyperChem HIN file jin -- Jaguar Input file bin -- OpenEye Binary file mmd -- MacroModel file mmod -- MacroModel file out -- MacroModel file dat -- MacroModel file sdf -- MDL Isis SDF file sd -- MDL Isis SDF file mdl -- MDL Molfile file mol -- MDL Molfile file mopcrt -- MOPAC Cartesian file mmads -- MMADS file bgf -- MSI BGF file csr -- MSI Quanta CSR file nw -- NWChem Input file pdb -- PDB file ent -- PDB file pov -- POV-Ray Output file report -- Report file qcin -- QChem Input file smi -- SMILES file fix -- SMILES Fix file mol2 -- Sybyl Mol2 file txyz -- Tinker XYZ file txt -- Titles file unixyz -- UniChem XYZ file vmol -- ViewMol file xed -- XED file xyz -- XYZ file zin -- ZINDO Input file

Open Babel is derived from OElib, written by Matt Stahl, which is a rewrite of the classic babel program. Open Babel is currently maintained by Geoff Hutchison and Michael Banck.