Mercurial > repos > bgruening > ctb_rdkit_descriptors

annotate rdkit_descriptors.xml @ 0:749cc765636b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:40:22 -0400
parents
children 13c6f797f1c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
1 <tool id="ctb_rdkit_descriptors" name="Descriptors" version="0.4">
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
2 <description>calculated with RDKit</description>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
4 <requirements>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
5 <requirement type="package" version="2019.03.1">rdkit</requirement>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
6
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
7 </requirements>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
8 <command>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
9 <![CDATA[
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
10 python '$__tool_directory__/rdkit_descriptors.py'
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
11 -i '${infile}'
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
12 --iformat '${infile.ext}'
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
13 -o '${outfile}'
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
14 $header
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
15 ]]>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
16 </command>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
17 <inputs>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
18 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data"
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
19 help="In SDF or SMILES format"/>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
20 <param name="header" type="boolean" label="Include the descriptor name as header"
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
21 truevalue="--header" falsevalue="" checked="false" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
22 </inputs>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
23 <outputs>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
24 <data format="tabular" name="outfile" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
25 </outputs>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
26 <tests>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
27 <test>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
28 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
29 <param name="header" value="True" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
30 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" />
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
31 </test>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
32 </tests>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
33 <help>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
34 <![CDATA[
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
35
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
36 .. class:: infomark
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
37
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
38 **What this tool does**
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
39
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
40 | RDKit is an open source toolkit for cheminformatics and machine learning.
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
41 | This tool calculates various molecular descriptors for the input data. The table below shows a brief overview of the descriptors.
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
42 |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
43
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
44 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
45 | Descriptor/Descriptor Family | Language |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
46 +===================================+============+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
47 | Gasteiger/Marsili Partial Charges | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
48 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
49 | BalabanJ | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
50 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
51 | BertzCT | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
52 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
53 | Ipc | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
54 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
55 | HallKierAlpha | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
56 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
57 | Kappa1 - Kappa3 | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
58 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
59 | Chi0, Chi1 | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
60 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
61 | Chi0n - Chi4n | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
62 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
63 | Chi0v - Chi4v | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
64 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
65 | MolLogP | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
66 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
67 | MolMR | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
68 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
69 | MolWt | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
70 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
71 | HeavyAtomCount | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
72 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
73 | HeavyAtomMolWt | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
74 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
75 | NHOHCount | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
76 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
77 | NOCount | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
78 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
79 | NumHAcceptors | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
80 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
81 | NumHDonors | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
82 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
83 | NumHeteroatoms | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
84 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
85 | NumRotatableBonds | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
86 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
87 | NumValenceElectrons | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
88 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
89 | RingCount | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
90 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
91 | TPSA | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
92 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
93 | LabuteASA | C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
94 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
95 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
96 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
97 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
98 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
99 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
100 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
101 | EState_VSA1 - EState_VSA11 | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
102 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
103 | VSA_EState1 - VSA_EState10 | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
104 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
105 | Topliss fragments | Python |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
106 +-----------------------------------+------------+
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
107
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
108 |
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
109 | A full list of the descriptors can be obtained here_.
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
110
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
111 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
112
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
113 -----
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
114
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
115 .. class:: warningmark
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
116
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
117 **Hint**
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
118
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
119 Use the **cut columns from a table** tool to select just the desired descriptors.
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
120
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
121 -----
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
122
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
123 .. class:: infomark
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
124
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
125 **Input**
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
126
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
127 | - `SDF Format`_
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
128 | - `SMILES Format`_
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
129 | - `Corina MOL2`_
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
130
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
131 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
132 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
133 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
134
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
135 -----
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
136
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
137 .. class:: infomark
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
138
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
139 **Output**
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
140
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
141 Tabular file, where each descriptor (value) is shown in a separate column.
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
142
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
143
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
144 ]]>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
145 </help>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
146 <citations>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
147 <citation type="bibtex">
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
148 @article{rdkit,
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
149 author = {Greg Landrum and others},
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
150 title = {RDKit: Open-source cheminformatics},
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
151 url ={http://www.rdkit.org}
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
152 }</citation>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
153 </citations>
749cc765636b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents:
diff changeset
154 </tool>