Mercurial > repos > bgruening > rdkit

comparison rdkit_descriptors.xml @ 0:6bb56f3a8de0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 15 Aug 2013 03:35:10 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:6bb56f3a8de0
1 <tool id="ctb_rdkit_describtors" name="Descriptors" version="0.1">
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="2012_12_1">rdkit</requirement>
6 </requirements>
7 <command interpreter="python">rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&#38;1</command>
8 <inputs>
9 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
10 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
11 </inputs>
12 <outputs>
13 <data format="tabular" name="outfile" />
14 </outputs>
15 <tests>
16 </tests>
17 <help>
18
19 .. class:: infomark
20
21 **What this tool does**
22
23 | RDKit is an open source toolkit for cheminformatics and machine learning.
24 | This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions.
25 |
26 | The table below shows a brief overview of the descriptors.
27 |
28
29 +-----------------------------------+------------+
30 | Descriptor/Descriptor Family | Language |
31 +===================================+============+
32 | Gasteiger/Marsili Partial Charges | C++ |
33 +-----------------------------------+------------+
34 | BalabanJ | Python |
35 +-----------------------------------+------------+
36 | BertzCT | Python |
37 +-----------------------------------+------------+
38 | Ipc | Python |
39 +-----------------------------------+------------+
40 | HallKierAlpha | Python |
41 +-----------------------------------+------------+
42 | Kappa1 - Kappa3 | Python |
43 +-----------------------------------+------------+
44 | Chi0, Chi1 | Python |
45 +-----------------------------------+------------+
46 | Chi0n - Chi4n | Python |
47 +-----------------------------------+------------+
48 | Chi0v - Chi4v | Python |
49 +-----------------------------------+------------+
50 | MolLogP | C++ |
51 +-----------------------------------+------------+
52 | MolMR | C++ |
53 +-----------------------------------+------------+
54 | MolWt | C++ |
55 +-----------------------------------+------------+
56 | HeavyAtomCount | Python |
57 +-----------------------------------+------------+
58 | HeavyAtomMolWt | Python |
59 +-----------------------------------+------------+
60 | NHOHCount | C++ |
61 +-----------------------------------+------------+
62 | NOCount | C++ |
63 +-----------------------------------+------------+
64 | NumHAcceptors | C++ |
65 +-----------------------------------+------------+
66 | NumHDonors | C++ |
67 +-----------------------------------+------------+
68 | NumHeteroatoms | C++ |
69 +-----------------------------------+------------+
70 | NumRotatableBonds | C++ |
71 +-----------------------------------+------------+
72 | NumValenceElectrons | Python |
73 +-----------------------------------+------------+
74 | RingCount | C++ |
75 +-----------------------------------+------------+
76 | TPSA | C++ |
77 +-----------------------------------+------------+
78 | LabuteASA | C++ |
79 +-----------------------------------+------------+
80 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
81 +-----------------------------------+------------+
82 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
83 +-----------------------------------+------------+
84 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
85 +-----------------------------------+------------+
86 | EState_VSA1 - EState_VSA11 | Python |
87 +-----------------------------------+------------+
88 | VSA_EState1 - VSA_EState10 | Python |
89 +-----------------------------------+------------+
90 | Topliss fragments | Python |
91 +-----------------------------------+------------+
92
93 |
94 | A full list of the descriptors can be obtained here_.
95
96 .. _here: https://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
97
98 -----
99
100 .. class:: warningmark
101
102 **HINT**
103
104 Use the **cut columns from a table** tool to select just the desired descriptors.
105
106 -----
107
108 .. class:: infomark
109
110 **Input**
111
112 | - `SD-Format`_
113 | - `SMILES Format`_
114 | - TDT_
115 | - SLN
116 | - `Corina MOL2`_
117
118 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
119 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
120 .. _TDT: https://earray.chem.agilent.com/earray/helppages/index.htm#tdt_format_files.htm
121 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
122
123 -----
124
125 .. class:: infomark
126
127 **Output**
128
129 Tabularfile, where each descriptor (value) is shown in a seperate column.
130
131 -----
132
133 .. class:: informark
134
135 **Cite**
136
137 Greg Landrum - RDKit_: Open-source cheminformatics
138
139 .. _RDKit: http://www.rdkit.org
140
141
142 </help>
143 </tool>