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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:42:01 -0400
parents fc8d71a0fb9b
children
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0:fc8d71a0fb9b 1:b8809b15e1a4
1 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1"> 1 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
2 <description>extracts predefined scaffolds from molecules</description> 2 <description>extracts scaffolds from molecules</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0.2">strip_it</requirement> 5 <requirement type="package" version="1.0.2">strip_it</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
36 36
37 .. class:: infomark 37 .. class:: infomark
38 38
39 **What this tool does** 39 **What this tool does**
40 40
41 Strip-it is a program that extracts predefined scaffolds from organic small 41 Strip-it is a program that extracts scaffolds from organic small molecules,
42 molecules. 42 based on predefined scaffold types. The scaffold types used by Strip-it include
43
44 The program comes with a number of predefined molecular scaffolds for
45 extraction. These scaffolds include, amongst others
46 43
47 - `molecular frameworks`_ as originally described by Bemis and Murcko 44 - `molecular frameworks`_ as originally described by Bemis and Murcko
48 - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers 45 - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
49 - `scaffold topologies`_ as described by Sara Pollock and coworkers 46 - `scaffold topologies`_ as described by Sara Pollock and coworkers
50 47
57 .. class:: infomark 54 .. class:: infomark
58 55
59 56
60 **Input** 57 **Input**
61 58
62 | - `SD-Format`_ 59 | - `SDF format`_
63 | - `SMILES Format`_ 60 | - `SMILES format`_
64 | - `MOL2 Format`_ 61 | - `MOL2 format`_
65 62
66 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file 63 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
67 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification 64 .. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
68 .. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf 65 .. _MOL2 format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
69 66
70 67
71 ----- 68 -----
72 69
73 .. class:: infomark 70 .. class:: infomark
74 71
75 **Output** 72 **Output**
73
74 A tabular file with the name and SMILES of the molecule in the first two
75 columns; subsequent columns show scaffolds extracted by different methods.
76 76
77 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+ 77 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
78 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... | 78 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
79 +=============+================================+======================+========================+======================+=====+ 79 +=============+================================+======================+========================+======================+=====+
80 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... | 80 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
96 96
97 97
98 ]]> 98 ]]>
99 </help> 99 </help>
100 <citations> 100 <citations>
101 <citation type="bibtex">@misc{
102 title={Strip-it},
103 author={Silicos-it},
104 year={2014},
105
106 }</citation>
101 </citations> 107 </citations>
102 </tool> 108 </tool>