Difference between revisions of "Obgrep"

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==Name==
 
==Name==
  
'''obgrep''' -- an advanced molecular grep program using SMARTS
+
'''obgrep''' -- an advanced molecular grep program using [[SMARTS]]
  
 
==Synopsis==
 
==Synopsis==
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==Description==
 
==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.
+
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==
 
==Options==
  
If only a filename is given, obgrep will attempt to guess the file type from the filename extension.
+
If only a filename is given, obgrep will attempt to guess the file type from the [[List of extensions|filename extension]].
  
 
; '''-c'''
 
; '''-c'''
 
: Print the number of matches
 
: Print the number of matches
 
; '''-f'''
 
; '''-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
+
: 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''
 
; '''-i''' ''format''
: Specifies input and output format, see [[babel]] for available formats
+
: Specifies input and output [[format]], see [[babel]] for available formats
 
; '''-n'''
 
; '''-n'''
 
: Only print the name of the molecules
 
: Only print the name of the molecules
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==Examples==
 
==Examples==
  
Note that in all examples, the SMARTS pattern is enclosed in single quotes ...' to ensure it is not changed by the shell.
+
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:
 
Print all the molecules with a methylamine group:
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  obgrep -f 'C[N,O]' database.smi
 
  obgrep -f 'C[N,O]' database.smi
  
Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., *.smi)
+
Print all molecules with aromatic carbon in all [[SMILES]] files in the directory (i.e., *.smi)
  
 
  obgrep 'c' *.smi
 
  obgrep 'c' *.smi
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The web pages for Open Babel can be found at: <'''http://openbabel.sourceforge.net/'''>
 
The web pages for Open Babel can be found at: <'''http://openbabel.sourceforge.net/'''>
  
A guide for constructing SMARTS patterns can be found at: <'''http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html'''>
+
A guide for constructing [[SMARTS]] patterns can be found at: <'''http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html'''>
  
 
==Authors==
 
==Authors==

Revision as of 15:39, 31 January 2006

Name

obgrep -- an advanced molecular grep 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 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, obchiral, obfit, obprop, obrotate.

The web pages for Open Babel can be found at: <http://openbabel.sourceforge.net/>

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 others who have contributed fixes and additions. For more contributors to Open Babel, see the Contributor list

Copyright

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright (C) 2001-2005 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, version 2, as published by the Free Software Foundation.

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.