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comparison filter/ob_grep.xml @ 16:3d3e7c1d0f49

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:27:52 +0200
parents ec87a42dccec
children
comparison
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15:ec87a42dccec 16:3d3e7c1d0f49
46 <param name="number_of_matches" value="" /> 46 <param name="number_of_matches" value="" />
47 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> 47 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
48 </test> 48 </test>
49 </tests> 49 </tests>
50 <help> 50 <help>
51 .. class:: warningmark
52 51
53 **What it does** 52 .. class:: infomark
54 53
55 The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files. 54 **What this tool does**
55
56 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
56 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. 57 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
57 58
58 59
59 .. _obgrep: http://openbabel.org/wiki/Obgrep 60 .. _Obgrep: http://openbabel.org/wiki/Obgrep
60 .. _here: http://openbabel.org/wiki/SMARTS 61 .. _here: http://openbabel.org/wiki/SMARTS
61 62
62 ----- 63 -----
63 64
64 **Output format** 65 .. class:: infomark
65 66
67 **Input**
66 68
67 **References** 69 | - `SD-Format`_
70 | - `SMILES Format`_
68 71
69 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_ 72 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
70 The Open Babel Package http://openbabel.sourceforge.net/ 73 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
71 74
72 .. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33 75 -----
76
77 .. class:: infomark
78
79 **Output**
80
81 Same as input format.
82
83 -----
84
85 .. class:: infomark
86
87 **Cite**
88
89 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
90
91 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
92
93 `Open Babel`_
94
95 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
73 96
74 </help> 97 </help>
75 </tool> 98 </tool>