.Dd Oct 10, 2019 .Os "Open Babel" 3.1 .Dt obabel 1 URM .Sh NAME .Nm obabel .Nd "a converter for chemistry and molecular modeling data files" .Sh SYNOPSIS .Nm .Op Fl H Ar help-options .Nm .Op Ar OPTIONS .Op Fl i Ar input-type | Fl : Qo Ar SMILES-string Qc .Ar infile .Op Fl o Ar output-type .Fl O Ar outfile .Sh DESCRIPTION .Nm is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas. .Pp Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages \%<\fBhttp://openbabel.org/\fR>. .Sh OPTIONS If only input and output files are given, Open Babel will guess the file type from the filename extension. .Bl -tag -width flag .It Fl : Qo Ar SMILES-string Qc 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. .It Fl a Ar options Format-specific input options. See .Fl H Ar format-ID for options allowed by a particular format .It Fl -addtotitle Append text to the current molecule title .It Fl -addformula Append the molecular formula after the current molecule title .It Fl b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O .It Fl c Center atomic coordinates at (0,0,0) .It Fl C Combine molecules in first file with others having the same name .It Fl e Continue after errors .It Fl d Delete Hydrogens .It Fl --errorlevel Ar 2 Filter the level of errors and warnings displayed: .br 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 .It Fl f Ar # For multiple entry input, start import with molecule # as the first entry .It Fl F Output the available fingerprint types .It Fl h Add hydrogens .It Fl H Output usage information .It Fl H Ar format-ID Output formatting information and options for format specified .It Fl Hall Output formatting information and options for all formats .It Fl i Specifies input format, see below for the available formats .It Fl j .It Fl -join Join all input molecules into a single output molecule entry .It Fl k Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian) .It Fl m Produce multiple output files, to allow: .Bl -dash -offset indent -compact .It Splitting one input file - put each molecule into consecutively numbered output files .It Batch conversion - convert each of multiple input files into a specified output format .El .It Fl l Ar # For multiple entry input, stop import with molecule # as the last entry .It Fl o Ar format-ID Specifies output format, see below for the available formats .It Fl O Ar outfile Specify the output file. This option applies to .Nm obabel only. .It Fl p Add Hydrogens appropriate for pH (use transforms in phmodel.txt) .It Fl -property Add or replace a property (e.g., in an MDL SD file) .It Fl s Ar SMARTS Convert only molecules matching the SMARTS pattern specified .It Fl -separate Separate disconnected fragments into individual molecular records .It Fl t All input files describe a single molecule .It Fl -title Ar title Add or replace molecular title .It Fl x Ar options Format-specific output options. See .Fl H Ar format-ID for options allowed by a particular format .It Fl v Ar SMARTS Convert only molecules \fBNOT\fP matching SMARTS pattern specified .It Fl V Output version number and exit .It Fl z Compress the output with gzip .El .Sh "FILE FORMATS" The following formats are currently supported by Open Babel: .Bl -item -offset indent -compact .It acr -- Carine ASCI Crystal .It alc -- Alchemy format .It arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] .It bgf -- MSI BGF format .It box -- Dock 3.5 Box format .It bs -- Ball and Stick format .It c3d1 -- Chem3D Cartesian 1 format .It c3d2 -- Chem3D Cartesian 2 format .It caccrt -- Cacao Cartesian format .It cache -- CAChe MolStruct format [Write-only] .It cacint -- Cacao Internal format [Write-only] .It can -- Canonical SMILES format .It car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] .It ccc -- CCC format [Read-only] .It cdx -- ChemDraw binary format [Read-only] .It cdxml -- ChemDraw CDXML format .It cht -- Chemtool format [Write-only] .It cif -- Crystallographic Information File .It cml -- Chemical Markup Language .It cmlr -- CML Reaction format .It com -- Gaussian Cartesian Input [Write-only] .It copy -- Copies raw text [Write-only] .It crk2d -- Chemical Resource Kit 2D diagram format .It crk3d -- Chemical Resource Kit 3D format .It csr -- Accelrys/MSI Quanta CSR format [Write-only] .It cssr -- CSD CSSR format [Write-only] .It ct -- ChemDraw Connection Table format .It dmol -- DMol3 coordinates format .It ent -- Protein Data Bank format .It fa -- FASTA format [Write-only] .It fasta -- FASTA format [Write-only] .It fch -- Gaussian formatted checkpoint file format [Read-only] .It fchk -- Gaussian formatted checkpoint file format [Read-only] .It fck -- Gaussian formatted checkpoint file format [Read-only] .It feat -- Feature format .It fh -- Fenske-Hall Z-Matrix format [Write-only] .It fix -- SMILES FIX format [Write-only] .It fpt -- Fingerprint format [Write-only] .It fract -- Free Form Fractional format .It fs -- Open Babel FastSearching database .It fsa -- FASTA format [Write-only] .It g03 -- Gaussian 98/03 Output [Read-only] .It g98 -- Gaussian 98/03 Output [Read-only] .It gam -- GAMESS Output [Read-only] .It gamin -- GAMESS Input [Write-only] .It gamout -- GAMESS Output [Read-only] .It gau -- Gaussian Cartesian Input [Write-only] .It gjc -- Gaussian Cartesian Input [Write-only] .It gjf -- Gaussian Cartesian Input [Write-only] .It gpr -- Ghemical format .It gr96 -- GROMOS96 format [Write-only] .It gzmat -- Gaussian Z-Matrix Input .It hin -- HyperChem HIN format .It inchi -- IUPAC InChI [Write-only] .It inp -- GAMESS Input [Write-only] .It ins -- ShelX format [Read-only] .It jin -- Jaguar input format [Write-only] .It jout -- Jaguar output format [Read-only] .It mdl -- MDL MOL format .It mmd -- MacroModel format .It mmod -- MacroModel format .It mol -- MDL MOL format .It mol2 -- Sybyl Mol2 format .It molreport -- Open Babel molecule report [Write-only] .It moo -- MOPAC Output format [Read-only] .It mop -- MOPAC Cartesian format .It mopcrt -- MOPAC Cartesian format .It mopin -- MOPAC Internal .It mopout -- MOPAC Output format [Read-only] .It mpc -- MOPAC Cartesian format .It mpd -- Sybyl descriptor format [Write-only] .It mpqc -- MPQC output format [Read-only] .It mpqcin -- MPQC simplified input format [Write-only] .It nw -- NWChem input format [Write-only] .It nwo -- NWChem output format [Read-only] .It pc -- PubChem format [Read-only] .It pcm -- PCModel format .It pdb -- Protein Data Bank format .It pov -- POV-Ray input format [Write-only] .It pqs -- Parallel Quantum Solutions format .It prep -- Amber Prep format [Read-only] .It qcin -- Q-Chem input format [Write-only] .It qcout -- Q-Chem output format [Read-only] .It report -- Open Babel report format [Write-only] .It res -- ShelX format [Read-only] .It rxn -- MDL RXN format .It sd -- MDL MOL format .It sdf -- MDL MOL format .It smi -- SMILES format .It sy2 -- Sybyl Mol2 format .It tdd -- Thermo format .It test -- Test format [Write-only] .It therm -- Thermo format .It tmol -- TurboMole Coordinate format .It txyz -- Tinker MM2 format [Write-only] .It unixyz -- UniChem XYZ format .It vmol -- ViewMol format .It xed -- XED format [Write-only] .It xml -- General XML format [Read-only] .It xyz -- XYZ cartesian coordinates format .It yob -- YASARA.org YOB format .It zin -- ZINDO input format [Write-only] .El .Sh "FORMAT OPTIONS" Individual file formats may have additional formatting options. .Pp Input format options are preceded by 'a', e.g. \-as .Pp Output format options are preceded by 'x', e.g. \-xn .Pp For further specific information and options, use \-H .br e.g., \-Hcml .Sh EXAMPLES Standard conversion: .Dl "obabel ethanol.xyz \-Oethanol.pdb" Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT: .Dl "obabel \-ismi \-omol2" Split a multi-molecule file into new1.smi, new2.smi, etc.: .Dl "obabel infile.mol -Onew.smi \-m" .Sh SEE ALSO .Xr obenergy 1 , .Xr obfit 1 , .Xr obgrep 1 , .Xr obminimize 1 , .Xr obprop 1 , .Xr obrotate 1 , .Xr obrotamer 1 . The web pages for Open Babel can be found at: \%<\fBhttp://openbabel.org/\fR> .Sh AUTHORS .An -nosplit A cast of many, including the currrent maintainers .An Geoff Hutchison , .An Chris Morley , .An Michael Banck , and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see \%<\fBhttp://openbabel.org/wiki/THANKS\fR> .Sh COPYRIGHT Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. .br Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison .Pp 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. .Pp 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.