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babel
Langue: en
Version: 110451 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
BSD mandoc
NAME
babel - a converter for chemistry and molecular modeling data filesSYNOPSIS
[-H help-options ][OPTIONS ] [-i input-type ] infile [-o output-type ] 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.Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages <http://openbabel.sourceforge.net/>.
OPTIONS
If only input and ouput files are given, Open Babel will guess the file type from the filename extension.- -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 file ...
- 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 consecutively
- numbered output files
- Batch conversion - convert each of multiple input files into a
- specified output format
- -l file ...
- For multiple entry input, stop import with molecule # as the last entry
- -o format-ID
- Specifies output format, see below for the available formats
- -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<format-type>
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), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1), obrotamer(1). The web pages for Open Babel can be found at: <http://openbabel.sourceforge.net/>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 <http://openbabel.sourceforge.net/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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre