Mercurial > repos > bgruening > ctb_rdkit_describtors
comparison rdkit_descriptors.xml @ 0:d7ea4e8cb1f3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
author | bgruening |
---|---|
date | Sat, 20 May 2017 12:41:19 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:d7ea4e8cb1f3 |
---|---|
1 <tool id="ctb_rdkit_describtors" name="Descriptors" version="0.3"> | |
2 <description>calculated with RDKit</description> | |
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> | |
4 <requirements> | |
5 <requirement type="package" version="2016.03.3">rdkit</requirement> | |
6 </requirements> | |
7 <command> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/rdkit_descriptors.py' | |
10 -i '${infile}' | |
11 --iformat '${infile.ext}' | |
12 -o '${outfile}' | |
13 $header | |
14 ]]> | |
15 </command> | |
16 <inputs> | |
17 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data" | |
18 help="In SD- or SMILES-format"/> | |
19 <param name="header" type="boolean" label="Include the descriptor name as header" | |
20 truevalue="--header" falsevalue="" checked="false" /> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="tabular" name="outfile" /> | |
24 </outputs> | |
25 <tests> | |
26 <test> | |
27 <param name="infile" ftype='sdf' value="CID_3037.sdf" /> | |
28 <param name="header" value="True" /> | |
29 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" /> | |
30 </test> | |
31 </tests> | |
32 <help> | |
33 <![CDATA[ | |
34 | |
35 .. class:: infomark | |
36 | |
37 **What this tool does** | |
38 | |
39 | RDKit is an open source toolkit for cheminformatics and machine learning. | |
40 | This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions. | |
41 | | |
42 | The table below shows a brief overview of the descriptors. | |
43 | | |
44 | |
45 +-----------------------------------+------------+ | |
46 | Descriptor/Descriptor Family | Language | | |
47 +===================================+============+ | |
48 | Gasteiger/Marsili Partial Charges | C++ | | |
49 +-----------------------------------+------------+ | |
50 | BalabanJ | Python | | |
51 +-----------------------------------+------------+ | |
52 | BertzCT | Python | | |
53 +-----------------------------------+------------+ | |
54 | Ipc | Python | | |
55 +-----------------------------------+------------+ | |
56 | HallKierAlpha | Python | | |
57 +-----------------------------------+------------+ | |
58 | Kappa1 - Kappa3 | Python | | |
59 +-----------------------------------+------------+ | |
60 | Chi0, Chi1 | Python | | |
61 +-----------------------------------+------------+ | |
62 | Chi0n - Chi4n | Python | | |
63 +-----------------------------------+------------+ | |
64 | Chi0v - Chi4v | Python | | |
65 +-----------------------------------+------------+ | |
66 | MolLogP | C++ | | |
67 +-----------------------------------+------------+ | |
68 | MolMR | C++ | | |
69 +-----------------------------------+------------+ | |
70 | MolWt | C++ | | |
71 +-----------------------------------+------------+ | |
72 | HeavyAtomCount | Python | | |
73 +-----------------------------------+------------+ | |
74 | HeavyAtomMolWt | Python | | |
75 +-----------------------------------+------------+ | |
76 | NHOHCount | C++ | | |
77 +-----------------------------------+------------+ | |
78 | NOCount | C++ | | |
79 +-----------------------------------+------------+ | |
80 | NumHAcceptors | C++ | | |
81 +-----------------------------------+------------+ | |
82 | NumHDonors | C++ | | |
83 +-----------------------------------+------------+ | |
84 | NumHeteroatoms | C++ | | |
85 +-----------------------------------+------------+ | |
86 | NumRotatableBonds | C++ | | |
87 +-----------------------------------+------------+ | |
88 | NumValenceElectrons | Python | | |
89 +-----------------------------------+------------+ | |
90 | RingCount | C++ | | |
91 +-----------------------------------+------------+ | |
92 | TPSA | C++ | | |
93 +-----------------------------------+------------+ | |
94 | LabuteASA | C++ | | |
95 +-----------------------------------+------------+ | |
96 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ | | |
97 +-----------------------------------+------------+ | |
98 | SMR_VSA1 - SMR_VSA10 | Python/C++ | | |
99 +-----------------------------------+------------+ | |
100 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ | | |
101 +-----------------------------------+------------+ | |
102 | EState_VSA1 - EState_VSA11 | Python | | |
103 +-----------------------------------+------------+ | |
104 | VSA_EState1 - VSA_EState10 | Python | | |
105 +-----------------------------------+------------+ | |
106 | Topliss fragments | Python | | |
107 +-----------------------------------+------------+ | |
108 | |
109 | | |
110 | A full list of the descriptors can be obtained here_. | |
111 | |
112 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors | |
113 | |
114 ----- | |
115 | |
116 .. class:: warningmark | |
117 | |
118 **HINT** | |
119 | |
120 Use the **cut columns from a table** tool to select just the desired descriptors. | |
121 | |
122 ----- | |
123 | |
124 .. class:: infomark | |
125 | |
126 **Input** | |
127 | |
128 | - `SD-Format`_ | |
129 | - `SMILES Format`_ | |
130 | - `Corina MOL2`_ | |
131 | |
132 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file | |
133 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
134 .. _Corina MOL2: http://www.molecular-networks.com/products/corina | |
135 | |
136 ----- | |
137 | |
138 .. class:: infomark | |
139 | |
140 **Output** | |
141 | |
142 Tabularfile, where each descriptor (value) is shown in a seperate column. | |
143 | |
144 | |
145 ]]> | |
146 </help> | |
147 <citations> | |
148 <citation type="bibtex"> | |
149 @article{rdkit, | |
150 author = {Greg Landrum}, | |
151 title = {RDKit: Open-source cheminformatics}, | |
152 url ={http://www.rdkit.org} | |
153 }</citation> | |
154 </citations> | |
155 </tool> |