silicos_it: qed/silicos_qed.xml annotate

annotate qed/silicos_qed.xml @ 20:9d1a5ff8c04f

ChemicalToolBoX update.

author	Bjoern Gruening <bjoern.gruening@gmail.com>
date	Mon, 22 Jul 2013 17:29:07 +0200
parents	fd84ab7af088
children

rev	line source
18 fd84ab7af088 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 9 diff changeset	1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
0 80efb29755f3 Uploaded bgruening parents: diff changeset	2 <description>quantitative estimation (QED)</description>
80efb29755f3 Uploaded bgruening parents: diff changeset	3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
80efb29755f3 Uploaded bgruening parents: diff changeset	4 <requirements>
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	5 <requirement type="package" version="1.0.1">silicos_it</requirement>
8 147814e45209 Uploaded bgruening parents: 5 diff changeset	6 <requirement type="package" version="2012_12_1">rdkit</requirement>
147814e45209 Uploaded bgruening parents: 5 diff changeset	7 <requirement type="package" version="1.7.1">numpy</requirement>
0 80efb29755f3 Uploaded bgruening parents: diff changeset	8 </requirements>
9 6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	9 <command interpreter="python">
6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	10 qed.py -i "${infile}"
6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	11 --method "${method}"
6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	12 --iformat ${infile.ext}
6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	13 -o "${outfile}" $header 2>&1
6e6b05e75a3f several updates to the silics-it repository Björn Grüning <bjoern.gruening@gmail.com> parents: 8 diff changeset	14 </command>
0 80efb29755f3 Uploaded bgruening parents: diff changeset	15 <inputs>
80efb29755f3 Uploaded bgruening parents: diff changeset	16 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	17 <param name="method" type="select" label="Method">
80efb29755f3 Uploaded bgruening parents: diff changeset	18 <option value="max">Max weight (QEDw,max)</option>
80efb29755f3 Uploaded bgruening parents: diff changeset	19 <option value="mean">Mean weight (QEDw,mo)</option>
80efb29755f3 Uploaded bgruening parents: diff changeset	20 <option value="unweighted">unweighted (QEDw,u)</option>
80efb29755f3 Uploaded bgruening parents: diff changeset	21 </param>
5 987524196f3e Uploaded bgruening parents: 1 diff changeset	22 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
0 80efb29755f3 Uploaded bgruening parents: diff changeset	23 </inputs>
80efb29755f3 Uploaded bgruening parents: diff changeset	24 <outputs>
80efb29755f3 Uploaded bgruening parents: diff changeset	25 <data format="tabular" name="outfile" />
80efb29755f3 Uploaded bgruening parents: diff changeset	26 </outputs>
80efb29755f3 Uploaded bgruening parents: diff changeset	27 <tests>
80efb29755f3 Uploaded bgruening parents: diff changeset	28 <!--
80efb29755f3 Uploaded bgruening parents: diff changeset	29 Test a tabular input with the first line being a comment without a # character to start
80efb29755f3 Uploaded bgruening parents: diff changeset	30 -->
80efb29755f3 Uploaded bgruening parents: diff changeset	31 <test>
80efb29755f3 Uploaded bgruening parents: diff changeset	32 <param name="infile" value="qed_test.smi"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	33 <param name="method" value="max"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	34 <output name="outfile" file="qed_test_max.tab"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	35 </test>
80efb29755f3 Uploaded bgruening parents: diff changeset	36 <test>
80efb29755f3 Uploaded bgruening parents: diff changeset	37 <param name="infile" value="qed_test.smi"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	38 <param name="method" value="mean"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	39 <output name="outfile" file="qed_test_mean.tab"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	40 </test>
80efb29755f3 Uploaded bgruening parents: diff changeset	41 <test>
80efb29755f3 Uploaded bgruening parents: diff changeset	42 <param name="infile" value="qed_test.smi"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	43 <param name="method" value="unweighted"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	44 <output name="outfile" file="qed_test_unweighted.tab"/>
80efb29755f3 Uploaded bgruening parents: diff changeset	45 </test>
80efb29755f3 Uploaded bgruening parents: diff changeset	46 </tests>
80efb29755f3 Uploaded bgruening parents: diff changeset	47 <help>
80efb29755f3 Uploaded bgruening parents: diff changeset	48
80efb29755f3 Uploaded bgruening parents: diff changeset	49 .. class:: infomark
80efb29755f3 Uploaded bgruening parents: diff changeset	50
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	51 What this tool does
0 80efb29755f3 Uploaded bgruening parents: diff changeset	52
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	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` ).
0 80efb29755f3 Uploaded bgruening parents: diff changeset	54
80efb29755f3 Uploaded bgruening parents: diff changeset	55 -----
80efb29755f3 Uploaded bgruening parents: diff changeset	56
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	57 .. class:: warningmark
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	58
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	59 HINT
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	60
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	61 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item.
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	62
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	63 - QED\ :sub:`w,max` using the set of weights that give maximal information content
0 80efb29755f3 Uploaded bgruening parents: diff changeset	64
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	65 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	66
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	67 - QED\ :sub:`w,u` with all weights as unity, hence unweighted.
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	68
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	69 -----
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	70
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	71 .. class:: infomark
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	72
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	73 Input
0 80efb29755f3 Uploaded bgruening parents: diff changeset	74
80efb29755f3 Uploaded bgruening parents: diff changeset	75
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	76 \| - `SD-Format`_
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	77 \| - `SMILES Format`_
0 80efb29755f3 Uploaded bgruening parents: diff changeset	78
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	79 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	80 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
0 80efb29755f3 Uploaded bgruening parents: diff changeset	81
80efb29755f3 Uploaded bgruening parents: diff changeset	82 -----
80efb29755f3 Uploaded bgruening parents: diff changeset	83
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	84 .. class:: infomark
0 80efb29755f3 Uploaded bgruening parents: diff changeset	85
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	86 Output
0 80efb29755f3 Uploaded bgruening parents: diff changeset	87
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	88 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	89 \| MW \| ALOGP \| HBA \| HBD \| PSA \| ROTB \| AROM \| ALERTS \| QED \| NAME \| Ro5 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	90 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	91 \| 286.34 \| 1.092 \| 6 \| 3 \| 101.88 \| 4 \| 2 \| 1 \| 0.737 \| Abacavir \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	92 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	93 \| 181.21 \| 0.481 \| 4 \| 2 \| 83.47 \| 5 \| 0 \| 2 \| 0.487 \| Acamprosate \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	94 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	95 \| 336.43 \| 2.365 \| 5 \| 3 \| 87.66 \| 11 \| 1 \| 1 \| 0.540 \| Acebutolol \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	96 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	97 \| 151.16 \| 1.351 \| 2 \| 2 \| 49.33 \| 2 \| 1 \| 1 \| 0.633 \| Acetaminophen \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	98 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	99 \| 222.25 \| 0.225 \| 5 \| 2 \| 115.04 \| 3 \| 1 \| 1 \| 0.727 \| Acetazolamide \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	100 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	101 \| 324.40 \| 3.291 \| 4 \| 2 \| 92.34 \| 6 \| 1 \| 1 \| 0.772 \| Acetohexamide \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	102 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	103 \| 411.57 \| 3.492 \| 6 \| 1 \| 47.02 \| 7 \| 2 \| 1 \| 0.688 \| Acetophenazine \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	104 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	105 \| 329.37 \| 3.327 \| 4 \| 1 \| 39.72 \| 4 \| 2 \| 0 \| 0.917 \| Paroxetine \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	106 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	107 \| 270.21 \| 3.146 \| 3 \| 1 \| 55.13 \| 4 \| 2 \| 0 \| 0.915 \| Leflunomide \| 0 \|
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	108 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
0 80efb29755f3 Uploaded bgruening parents: diff changeset	109
80efb29755f3 Uploaded bgruening parents: diff changeset	110 -----
80efb29755f3 Uploaded bgruening parents: diff changeset	111
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	112 .. class:: infomark
0 80efb29755f3 Uploaded bgruening parents: diff changeset	113
80efb29755f3 Uploaded bgruening parents: diff changeset	114 Cite
80efb29755f3 Uploaded bgruening parents: diff changeset	115
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	116 Bickerton et al. - `Quantifying the chemical beauty of drugs`_
0 80efb29755f3 Uploaded bgruening parents: diff changeset	117
20 9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	118 .. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html
9d1a5ff8c04f ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 18 diff changeset	119
0 80efb29755f3 Uploaded bgruening parents: diff changeset	120 </help>
80efb29755f3 Uploaded bgruening parents: diff changeset	121 </tool>

Mercurial > repos > bgruening > silicos_it

annotate qed/silicos_qed.xml @ 20:9d1a5ff8c04f