obgrep(1) [debian man page]
obgrep(1) User's Reference Manual obgrep(1) NAME
obgrep -- an advanced molecular search program using SMARTS SYNOPSIS
obgrep [OPTIONS] 'SMARTS-pattern' filename DESCRIPTION
The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. OPTIONS
If only a filename is given, obgrep will attempt to guess the file type from the filename extension. -c Print the number of matches -f Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern -i format Specifies input and output format, see babel(1) for available formats -n Only print the name of the molecules -t # Print a molecule only if the pattern occurs # times inside the molecule -v Invert the matching, print non-matching molecules EXAMPLES
Note that in all examples, the SMARTS pattern is enclosed in single quotes '...' to ensure it is not changed by the shell. Print all the molecules with a methylamine group: obgrep 'CN' database.smi Print all the molecules without a methylamine group: obgrep -v 'CN' database.smi Print the number of molecules without a methylamine group: obgrep -v -c 'CN' database.smi Print methylamine (if it exists in the file): obgrep -f 'CN' database.smi Print methylamine and/or methanol (if they exist): obgrep -f 'C[N,O]' database.smi Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., *.smi) obgrep 'c' *.smi SEE ALSO
babel(1), obfit(1), obrotate(1). The web pages for Open Babel can be found at: <http://openbabel.org/> A guide for constructing SMARTS patterns can be found at: <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html> AUTHORS
The obgrep program was contributed by Fabien Fontaine Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable oth- ers who have contributed 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 and other contributors. 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 MERCHANTABIL- ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 2.2 July 4, 2008 Open Babel 2.2
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babel(1) User's Reference Manual babel(1) NAME
babel, obabel -- a converter for chemistry and molecular modeling data files SYNOPSIS
babel, [-H help-options] babel, [OPTIONS] [-i input-type] infile [-o output-type] outfile obabel [-H help-options] obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile [-o output-type] -O 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. obabel and babel, are slightly different. The first is closer to the normal Unix convention for commandline programs and more flexible when the user needs to specify parameter values on options. With babel this only works when the option is the last on the line; with obabel no such restriction applies. It further has a shortcut for entering SMILES strings, which can be used in place of an input file. Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages <http://openbabel.org/>. OPTIONS
If only input and ouput 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 should be enclosed in quotation marks. More than one can be used, and a molecule title can be included if enclosed in quotes. -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 # 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 # 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. This option applies to obabel only. -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.org/> AUTHORS
A cast of many, including the currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed 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 MERCHANTABIL- ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 2.2 July 4, 2008 Open Babel 2.2