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comparison silicos_qed.xml @ 1:ab73abead7fa draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:41:23 -0400
parents 5ccd3a432785
children fc45bf8b6e01
comparison
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0:5ccd3a432785 1:ab73abead7fa
1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1"> 1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.2">
2 <description>quantitative estimation (QED)</description> 2 <description>quantitative estimation (QED)</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2015.09.2">rdkit</requirement> 5 <requirement type="package" version="2019.03.1">rdkit</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
8 <![CDATA[ 8 <![CDATA[
9 python '$__tool_directory__/qed.py' 9 python '$__tool_directory__/qed.py'
10 -i '${infile}' 10 -i '${infile}'
13 -o '${outfile}' 13 -o '${outfile}'
14 $header 14 $header
15 ]]> 15 ]]>
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> 18 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SDF or SMILES format" help="Dataset missing? See TIP below"/>
19 <param name="method" type="select" label="Method"> 19 <param name="method" type="select" label="Method" help="Method for weighting features">
20 <option value="max">Max weight (QEDw,max)</option> 20 <option value="max">Max weight (QEDw,max)</option>
21 <option value="mean">Mean weight (QEDw,mo)</option> 21 <option value="mean">Mean weight (QEDw,mo)</option>
22 <option value="unweighted">unweighted (QEDw,u)</option> 22 <option value="unweighted">Unweighted (QEDw,u)</option>
23 </param> 23 </param>
24 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> 24 <param name="header" type="boolean" label="Include the descriptor names as header" truevalue="--header" falsevalue="" checked="false" />
25 </inputs> 25 </inputs>
26 <outputs> 26 <outputs>
27 <data format="tabular" name="outfile" /> 27 <data format="tabular" name="outfile" />
28 </outputs> 28 </outputs>
29 <tests> 29 <tests>
54 54
55 .. class:: infomark 55 .. class:: infomark
56 56
57 **What this tool does** 57 **What this tool does**
58 58
59 Estimates the drug-likeness of molecules and reports a score. Comes with three applicable varieties (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\ , QED\ :sub:`w,u` ). 59 Estimates the drug-likeness of molecules, based on eight commonly used molecular
60 properties, and reports a score between 0 (all properties unfavourable) to 1 (all
61 properties favourable). Two possible methods to weight the features are available
62 (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\), as well as an option to leave features
63 unweighted (QED\ :sub:`w,u`).
64
65 The eight properties used are: molecular weight (MW), octanol–water partition
66 coefficient (ALOGP), number of hydrogen bond donors (HBDs), number of hydrogen
67 bond acceptors (HBAs), molecular polar surface area (PSA), number of rotatable
68 bonds (ROTBs), number of aromatic rings (AROMs) and number of structural alerts
69 (ALERTS).
60 70
61 ----- 71 -----
62 72
63 .. class:: warningmark 73 .. class:: warningmark
64 74
65 **HINT** 75 **Hint**
66 76
67 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item. 77 All invalid, blank and comment lines are skipped when performing computations. The
78 number of skipped lines is displayed in the resulting history item. The method refers
79 to a set of weights that can be applied to the features. These are derived in the
80 `original paper`_ describing QED.
81
68 82
69 - QED\ :sub:`w,max` using the set of weights that give maximal information content 83 - QED\ :sub:`w,max` using the set of weights that give maximal information content
70 84
71 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content 85 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
72 86
73 - QED\ :sub:`w,u` with all weights as unity, hence unweighted. 87 - QED\ :sub:`w,u` with all weights as unity i.e. unweighted.
88
89 .. _original paper: https://www.nature.com/articles/nchem.1243
74 90
75 ----- 91 -----
76 92
77 .. class:: infomark 93 .. class:: infomark
78 94
79 **Input** 95 **Input**
80 96
81 97
82 | - `SD-Format`_ 98 | - `SDF format`_
83 | - `SMILES Format`_ 99 | - `SMILES format`_
84 100
85 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file 101 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
86 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification 102 .. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
87 103
88 ----- 104 -----
89 105
90 .. class:: infomark 106 .. class:: infomark
91 107
92 **Output** 108 **Output**
109
110 A table listing the values of the eight features, the QED score, the name of the
111 molecule, and the number of Lipinski rules which the molecule obeys.
93 112
94 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+ 113 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
95 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 | 114 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
96 +========+=======+=====+=====+========+======+======+========+=======+================+=====+ 115 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
97 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 | 116 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |