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UNTITLED() LOCAL UNTITLED() NAME obabel -- a converter for chemistry and molecular modeling data files SYNOPSIS obabel [-H help-options] obabel [OPTIONS] [-i input-type | -:SMILES-string] infile [-o output-type] -O outfile DESCRIPTION obabel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chem- istry and related areas. Open Babel is also a complete programmers toolkit for developing chem- istry software. For more information, see 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 might need to be enclosed in quotation marks to avoid shell interpretation. More than one can be used, and a molecule title can be included if enclosed in quotes. -aoptions Format-specific input options. See -H format-ID for options al- lowed 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 n 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 con- secutively 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 -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 -xoptions Format-specific output options. See -H format-ID for options al- lowed 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: abinit -- ABINIT Output Format [Read-only] acesin -- ACES input format [Write-only] acesout -- ACES output format [Read-only] acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only] adfband -- ADF Band output format [Read-only] adfdftb -- ADF DFTB output format [Read-only] adfout -- ADF output format [Read-only] alc -- Alchemy format aoforce -- Turbomole AOFORCE output format [Read-only] arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] ascii -- ASCII format [Write-only] axsf -- XCrySDen Structure Format [Read-only] bgf -- MSI BGF format box -- Dock 3.5 Box format bs -- Ball and Stick format c09out -- Crystal 09 output format [Read-only] c3d1 -- Chem3D Cartesian 1 format c3d2 -- Chem3D Cartesian 2 format cac -- CAChe MolStruct format [Write-only] 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] castep -- CASTEP format [Read-only] ccc -- CCC format [Read-only] cdjson -- ChemDoodle JSON cdx -- ChemDraw binary format [Read-only] cdxml -- ChemDraw CDXML format cht -- Chemtool format [Write-only] cif -- Crystallographic Information File cjson -- Chemical JSON ck -- ChemKin format cml -- Chemical Markup Language cmlr -- CML Reaction format cof -- Culgi object file format com -- Gaussian Input [Write-only] confabreport -- Confab report format [Write-only] CONFIG -- DL-POLY CONFIG CONTCAR -- VASP format CONTFF -- MDFF format copy -- Copy raw text [Write-only] crk2d -- Chemical Resource Kit diagram(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 cub -- Gaussian cube format cube -- Gaussian cube format dallog -- DALTON output format [Read-only] dalmol -- DALTON input format dat -- Generic Output file format [Read-only] dmol -- DMol3 coordinates format dx -- OpenDX cube format for APBS ent -- Protein Data Bank format exyz -- Extended XYZ cartesian coordinates format fa -- FASTA format fasta -- FASTA format 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] fhiaims -- FHIaims XYZ format fix -- SMILES FIX format [Write-only] fps -- FPS text fingerprint format (Dalke) [Write-only] fpt -- Fingerprint format [Write-only] fract -- Free Form Fractional format fs -- Fastsearch format fsa -- FASTA format g03 -- Gaussian Output [Read-only] g09 -- Gaussian Output [Read-only] g16 -- Gaussian Output [Read-only] g92 -- Gaussian Output [Read-only] g94 -- Gaussian Output [Read-only] g98 -- Gaussian Output [Read-only] gal -- Gaussian Output [Read-only] gam -- GAMESS Output [Read-only] gamess -- GAMESS Output [Read-only] gamin -- GAMESS Input gamout -- GAMESS Output [Read-only] gau -- Gaussian Input [Write-only] gjc -- Gaussian Input [Write-only] gjf -- Gaussian Input [Write-only] got -- GULP format [Read-only] gpr -- Ghemical format gr96 -- GROMOS96 format [Write-only] gro -- GRO format gukin -- GAMESS-UK Input gukout -- GAMESS-UK Output gzmat -- Gaussian Z-Matrix Input hin -- HyperChem HIN format HISTORY -- DL-POLY HISTORY [Read-only] inchi -- InChI format inchikey -- InChIKey [Write-only] inp -- GAMESS Input ins -- ShelX format [Read-only] jin -- Jaguar input format jout -- Jaguar output format [Read-only] k -- Compare molecules using InChI [Write-only] lmpdat -- The LAMMPS data format [Write-only] log -- Generic Output file format [Read-only] lpmd -- LPMD format mae -- Maestro format maegz -- Maestro format mcdl -- MCDL format mcif -- Macromolecular Crystallographic Info MDFF -- MDFF format mdl -- MDL MOL format ml2 -- Sybyl Mol2 format mmcif -- Macromolecular Crystallographic Info mmd -- MacroModel format mmod -- MacroModel format mna -- Multilevel Neighborhoods of Atoms (MNA) [Write-only] mol -- MDL MOL format mol2 -- Sybyl Mol2 format mold -- Molden format molden -- Molden format molf -- Molden 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] mp -- Molpro input format [Write-only] mpc -- MOPAC Cartesian format mpd -- MolPrint2D format [Write-only] mpo -- Molpro output format [Read-only] mpqc -- MPQC output format [Read-only] mpqcin -- MPQC simplified input format [Write-only] mrv -- Chemical Markup Language msi -- Accelrys/MSI Cerius II MSI format [Read-only] msms -- M.F. Sanner's MSMS input format [Write-only] nul -- Outputs nothing [Write-only] nw -- NWChem input format [Write-only] nwo -- NWChem output format [Read-only] orca -- ORCA output format [Read-only] orcainp -- ORCA input format [Write-only] out -- Generic Output file format [Read-only] outmol -- DMol3 coordinates format output -- Generic Output file format [Read-only] paint -- Painter format [Write-only] pc -- PubChem format [Read-only] pcjson -- PubChem JSON pcm -- PCModel Format pdb -- Protein Data Bank format pdbqt -- AutoDock PDBQT format png -- PNG 2D depiction pointcloud -- Point cloud on VDW surface [Write-only] pos -- POS cartesian coordinates format [Read-only] POSCAR -- VASP format POSFF -- MDFF format pov -- POV-Ray input format [Write-only] pqr -- PQR format pqs -- Parallel Quantum Solutions format prep -- Amber Prep format [Read-only] pwscf -- PWscf 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] rinchi -- RInChI [Write-only] rsmi -- Reaction SMILES format rxn -- MDL RXN format sd -- MDL MOL format sdf -- MDL MOL format siesta -- SIESTA format [Read-only] smi -- SMILES format smiles -- SMILES format smy -- SMILES format using Smiley parser [Read-only] stl -- STL 3D-printing format [Write-only] svg -- SVG 2D depiction [Write-only] sy2 -- Sybyl Mol2 format t41 -- ADF TAPE41 format [Read-only] tdd -- Thermo format text -- Read and write raw text therm -- Thermo format tmol -- TurboMole Coordinate format txt -- Title format txyz -- Tinker XYZ format unixyz -- UniChem XYZ format VASP -- VASP format vmol -- ViewMol format wln -- Wiswesser Line Notation [Read-only] xed -- XED format [Write-only] xml -- General XML format [Read-only] xsf -- XCrySDen Structure 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 format-type, e.g., -Hcml EXAMPLES Standard conversion: obabel ethanol.xyz -Oethanol.pdb Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT: obabel -ismi -omol2 Split a multi-molecule file into new1.smi, new2.smi, etc.: obabel infile.mol -Onew.smi -m SEE ALSO 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/> AUTHORS A cast of many, including the current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have con- tributed 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 MER- CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.1 Oct 10, 2019 obabel(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILE FORMATS | FORMAT OPTIONS | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
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