Mercurial > repos > bgruening > silicos_it

comparison strip-it/strip-it.xml @ 0:bb92d30b4f52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 15 Aug 2013 03:34:00 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:bb92d30b4f52
1 <tool id="ctb_stripit" name="Strip-it" version="1.0.1">
2 <description> extracts predefined scaffolds from molecules</description>
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism>
4 <requirements>
5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 <requirement type="package" version="1.0.1">silicos_it</requirement>
7 </requirements>
8 <command>
9 strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&#38;1
10 </command>
11 <inputs>
12 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
13 </inputs>
14 <outputs>
15 <data name="outfile" format="tabular" />
16 </outputs>
17 <tests>
18 <test>
19 <param name="infile" type='sdf' value="CID_3037.sdf"/>
20 <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
21 </test>
22 </tests>
23 <help>
24
25
26 .. class:: infomark
27
28 **What this tool does**
29
30 Strip-it is a program that extracts predefined scaffolds from organic small
31 molecules.
32
33 The program comes with a number of predefined molecular scaffolds for
34 extraction. These scaffolds include, amongst others
35
36 - `molecular frameworks`_ as originally described by Bemis and
37 Murcko
38 - `molecular frameworks and the reduced molecular frameworks`_ as
39 described by Ansgar Schuffenhauer and coworkers
40 - `scaffold topologies`_ as described by Sara Pollock and coworkers
41
42 .. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
43 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
44 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
45
46 -----
47
48 .. class:: infomark
49
50
51 **Input**
52
53 | - `SD-Format`_
54 | - `SMILES Format`_
55 | - `MOL2 Format`_
56
57 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
58 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
59 .. _MOL2 Format: http://www.tripos.com/data/support/mol2.pdf
60
61
62 -----
63
64 .. class:: infomark
65
66 **Output**
67
68 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
69 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
70 +=============+================================+======================+========================+======================+=====+
71 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
72 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
73 | Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
74 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
75 | ... | ... | ... | ... | ... | ... |
76 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
77
78 -----
79
80 .. class:: infomark
81
82 **Cite**
83
84 `Silicos-it`_ - strip-it
85
86 .. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html
87
88
89 </help>
90 </tool>