File: obgrep.html

package info (click to toggle)
openbabel 2.0.2-1
  • links: PTS
  • area: main
  • in suites: etch, etch-m68k
  • size: 15,652 kB
  • ctags: 15,998
  • sloc: cpp: 128,176; ansic: 86,170; sh: 8,920; perl: 1,847; python: 1,369; pascal: 793; makefile: 381; xml: 97
file content (166 lines) | stat: -rw-r--r-- 4,500 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
<!-- manual page source format generated by PolyglotMan v3.0.8+XFree86, -->
<!-- available at http://polyglotman.sourceforge.net/ -->

<html>
<head>
<title>man page(1) manual page</title>
</head>
<body bgcolor='#efefef' text='black' link='blue' vlink='#551A8B' alink='red'>
<a href='#toc'>Table of Contents</a><p>

<h2><a name='sect0' href='#toc0'>Name</a></h2>

<p>
<b>obgrep</b> -- an advanced molecular grep program using SMARTS

<p>
<h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2>

<p>
<b>obgrep</b> [<i>OPTIONS</i>] <i>`SMARTS-pattern'</i> <i>filename</i>

<p>
<h2><a name='sect2' href='#toc2'><b>Description</b></a></h2>

<p>
The obgrep tool can be used to search for molecules inside multi-molecule
database files (e.g., SMILES, SDF, etc.) or across multiple files.

<p>
<h2><a name='sect3' href='#toc3'><b>Options</b></a></h2>

<p>
If only a filename is given, obgrep will attempt to guess the file type
from the filename extension.

<p>
<dl>

<dt><b>-c</b> </dt></dt>
<dd>   Print the number of matches

<p></dd>

<dt><b>-f</b> </dt></dt>
<dd>   Full match, print matching-molecules only when the number of heavy
atoms is also equal to the number of atoms in the SMARTS pattern

<p></dd>

<dt><b>-i</b> <i>format</i></dt></dt>
<dd>
Specifies input and output format, see <a href='babel.1.html'>babel(1)</a>
 for available formats

<p></dd>

<dt><b>-n</b> </dt></dt>
<dd>   Only print the name of the molecules

<p></dd>

<dt><b>-t</b> <i>#</i> </dt></dt>
<dd>Print a molecule only if the pattern occurs # times inside the molecule

<p></dd>

<dt><b>-v</b> </dt></dt>
<dd>   Invert the matching, print non-matching molecules

<p></dd>
</dl>

<h2><a name='sect4' href='#toc4'><b>Examples</b></a></h2>

<p>
Note that in all examples, the SMARTS pattern is enclosed in single
quotes `...' to ensure it is not changed by the shell.

<p><p>
Print all the molecules with a methylamine group:
obgrep `CN' database.smi

<p><p>
Print all the molecules without a methylamine group:
obgrep -v `CN' database.smi

<p><p>
Print the number of molecules without a methylamine group:
obgrep -v -c `CN' database.smi

<p><p>
Print methylamine (if it exists in the file):
obgrep -f `CN' database.smi

<p><p>
Print methylamine and/or methanol (if they exist):
obgrep -f `C[N,O]' database.smi<br>

Print all molecules with aromatic carbon in all SMILES files in the
directory (i.e., *.smi)<br>

obgrep `c' *.smi

<p>
<h2><a name='sect5' href='#toc5'><b>See</b> <b>Also</b></a></h2>

<p>
<a href='babel.1.html'>babel(1)</a>
, <a href='obchiral.1.html'>obchiral(1)</a>
, <a href='obfit.1.html'>obfit(1)</a>
, <a href='obprop.1.html'>obprop(1)</a>
, <a href='obrotate.1.html'>obrotate(1)</a>
.

<p><p>
The web pages for Open Babel can be found at: &lt;<b>http://openbabel.sourceforge.net/</b>&gt;

<p><p>
A guide for constructing SMARTS patterns can be found at:
&lt;<b>http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html</b>&gt;

<p>
<h2><a name='sect6' href='#toc6'><b>Authors</b></a></h2>

<p>
The obgrep program was contributed by Fabien Fontaine

<p><p>
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 &lt;<b>http://openbabel.sourceforge.net/THANKS.shtml</b>&gt;

<p>
<h2><a name='sect7' href='#toc7'><b>Copyright</b></a></h2>

<p>
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Some portions
Copyright (C) 2001-2005 by Geoffrey R. Hutchison and other contributors.

<p><p>
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.

<p><p>
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.
<p>

<hr><p>
<a name='toc'><b>Table of Contents</b></a><p>
<ul>
<li><a name='toc0' href='#sect0'>Name</a></li>
<li><a name='toc1' href='#sect1'>Synopsis</a></li>
<li><a name='toc2' href='#sect2'>Description</a></li>
<li><a name='toc3' href='#sect3'>Options</a></li>
<li><a name='toc4' href='#sect4'>Examples</a></li>
<li><a name='toc5' href='#sect5'>See Also</a></li>
<li><a name='toc6' href='#sect6'>Authors</a></li>
<li><a name='toc7' href='#sect7'>Copyright</a></li>
</ul>
</body>
</html>