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1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
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2 <description>quantitative estimation (QED)</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="1.0.1">silicos_it</requirement>
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6 <requirement type="package" version="2012_12_1">rdkit</requirement>
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7 <requirement type="package" version="1.7.1">numpy</requirement>
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8 </requirements>
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9 <command interpreter="python">
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10 qed.py -i "${infile}"
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11 --method "${method}"
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12 --iformat ${infile.ext}
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13 -o "${outfile}" $header 2>&1
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14 </command>
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15 <inputs>
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16 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
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17 <param name="method" type="select" label="Method">
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18 <option value="max">Max weight (QEDw,max)</option>
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19 <option value="mean">Mean weight (QEDw,mo)</option>
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20 <option value="unweighted">unweighted (QEDw,u)</option>
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21 </param>
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22 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="outfile" />
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26 </outputs>
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27 <tests>
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28 <!--
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29 Test a tabular input with the first line being a comment without a # character to start
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30 -->
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31 <test>
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32 <param name="infile" value="qed_test.smi"/>
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33 <param name="method" value="max"/>
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34 <output name="outfile" file="qed_test_max.tab"/>
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35 </test>
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36 <test>
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37 <param name="infile" value="qed_test.smi"/>
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38 <param name="method" value="mean"/>
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39 <output name="outfile" file="qed_test_mean.tab"/>
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40 </test>
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41 <test>
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42 <param name="infile" value="qed_test.smi"/>
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43 <param name="method" value="unweighted"/>
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44 <output name="outfile" file="qed_test_unweighted.tab"/>
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45 </test>
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46 </tests>
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47 <help>
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48
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49 .. class:: infomark
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50
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51 **What this tool does**
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52
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53 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` ).
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54
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55 -----
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56
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57 .. class:: warningmark
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58
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59 **HINT**
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60
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61 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item.
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62
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63 - QED\ :sub:`w,max` using the set of weights that give maximal information content
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64
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65 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
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66
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67 - QED\ :sub:`w,u` with all weights as unity, hence unweighted.
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68
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69 -----
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70
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71 .. class:: infomark
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72
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73 **Input**
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74
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75
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76 | - `SD-Format`_
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77 | - `SMILES Format`_
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78
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79 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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80 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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81
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82 -----
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83
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84 .. class:: infomark
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85
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86 **Output**
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87
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88 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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89 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
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90 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
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91 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |
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92 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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93 | 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 |
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94 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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95 | 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 |
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96 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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97 | 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 |
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98 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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99 | 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 |
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100 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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101 | 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 |
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102 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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103 | 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 |
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104 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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105 | 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 |
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106 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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107 | 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 |
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108 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
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109
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110 -----
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111
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112 .. class:: infomark
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113
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114 **Cite**
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115
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116 Bickerton et al. - `Quantifying the chemical beauty of drugs`_
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117
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118 .. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html
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119
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120 </help>
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121 </tool>
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