Mercurial > repos > bgruening > rdkit
comparison rdkit_descriptors.xml @ 0:6bb56f3a8de0 draft default tip
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author | bgruening |
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date | Thu, 15 Aug 2013 03:35:10 -0400 |
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-1:000000000000 | 0:6bb56f3a8de0 |
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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>&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> |