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comparison filter/multi_obgrep.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
34 <test> 34 <test>
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help> 37 <help>
38 38
39 .. class:: infomark
39 40
40 **What it does** 41 **What this tool does**
41 42
42 Providing a query file with SMARTS pattern in each line. These tool will run obgreg_ in parallel and merges the results. 43 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
43 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. 44 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
44 45
45 46 .. _Obgrep: http://openbabel.org/wiki/Obgrep
46 .. _obgrep: http://openbabel.org/wiki/Obgrep
47 .. _here: http://openbabel.org/wiki/SMARTS 47 .. _here: http://openbabel.org/wiki/SMARTS
48 48
49 ----- 49 -----
50 50
51 **Example** 51 .. class:: infomark
52 52
53 **Input**
53 54
55 | - `SD-Format`_
56 | - `SMILES Format`_
57
58 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
59 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
60
61 -----
62
63 .. class:: infomark
64
65 **Output**
66
67 Same as input format.
68
69 -----
70
71 .. class:: infomark
72
73 **Cite**
74
75 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
76
77 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
78
79 `Open Babel`_
80
81 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
54 82
55 </help> 83 </help>
56 </tool> 84 </tool>