diff qed/silicos_qed.xml @ 20:9d1a5ff8c04f

ChemicalToolBoX update.

--- a/qed/silicos_qed.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/qed/silicos_qed.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -2,7 +2,7 @@
   <description>quantitative estimation (QED)</description>
   <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
   <requirements>
-    <requirement type="package" version="1.0.0">silicos_it</requirement>
+    <requirement type="package" version="1.0.1">silicos_it</requirement>
     <requirement type="package" version="2012_12_1">rdkit</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
@@ -48,59 +48,74 @@
 
 .. class:: infomark
 
-**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data
+**What this tool does**
 
+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` ).
 
 -----
 
-**Syntax**
+.. class:: warningmark
+
+**HINT**
+
+- All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item.
+
+- QED\ :sub:`w,max` using the set of weights that give maximal information content
 
-The QED function comes in three flavors, each differing in the relative weight that is imposed on the underlying molecular descriptors (see [1]).
-These three flavors correspond to the three different QED measures that were described in the original publication:
+- QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
+
+- QED\ :sub:`w,u` with all weights as unity, hence unweighted.
+
+-----
+
+.. class:: infomark
+
+**Input**
 
 
-- All invalid, blank and comment lines are skipped when performing computations.  The number of skipped lines is displayed in the resulting history item.
-
-- **QEDw,max** using the set of weights that give maximal information content.:
+| - `SD-Format`_
+| - `SMILES Format`_
 
-- **QEDw,mo** using the mean weights of the optimal 1,000 weight combinations that give the highest information content.
-
-- **QEDw,u** with all weights as unity, hence unweighted.
-
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
 
 -----
 
-**Example**
-
-- Input file::
+.. class:: infomark
 
-    - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file)
-    - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)
-
-- Result::
+**Output**
 
-    ====== ===== === === ====== ==== ==== ====== ===== ==============
-        MW ALOGP HBA HBD    PSA ROTB AROM ALERTS   QED NAME
-    ------ ----- --- --- ------ ---- ---- ------ ----- --------------
-    286.34 1.092   6   3 101.88    4    2      1 0.737 Abacavir
-    181.21 0.481   4   2  83.47    5    0      2 0.487 Acamprosate
-    336.43 2.365   5   3  87.66   11    1      1 0.540 Acebutolol
-    151.16 1.351   2   2  49.33    2    1      1 0.633 Acetaminophen
-    222.25 0.225   5   2 115.04    3    1      1 0.727 Acetazolamide
-    324.40 3.291   4   2  92.34    6    1      1 0.772 Acetohexamide
-    411.57 3.492   6   1  47.02    7    2      1 0.688 Acetophenazine
-    329.37 3.327   4   1  39.72    4    2      0 0.917 Paroxetine
-    270.21 3.146   3   1  55.13    4    2      0 0.915 Leflunomide
-    ====== ===== === === ====== ==== ==== ====== ===== ==============
-
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+|   MW   | ALOGP | HBA | HBD |   PSA  | ROTB | AROM | ALERTS |  QED  |      NAME      | Ro5 |
++========+=======+=====+=====+========+======+======+========+=======+================+=====+ 
+| 286.34 | 1.092 |  6  |  3  | 101.88 |   4  |   2  |    1   | 0.737 | Abacavir       |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 181.21 | 0.481 |  4  |  2  |  83.47 |   5  |   0  |    2   | 0.487 | Acamprosate    |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 336.43 | 2.365 |  5  |  3  |  87.66 |  11  |   1  |    1   | 0.540 | Acebutolol     |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 151.16 | 1.351 |  2  |  2  |  49.33 |   2  |   1  |    1   | 0.633 | Acetaminophen  |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 222.25 | 0.225 |  5  |  2  | 115.04 |   3  |   1  |    1   | 0.727 | Acetazolamide  |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 324.40 | 3.291 |  4  |  2  |  92.34 |   6  |   1  |    1   | 0.772 | Acetohexamide  |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 411.57 | 3.492 |  6  |  1  |  47.02 |   7  |   2  |    1   | 0.688 | Acetophenazine |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 329.37 | 3.327 |  4  |  1  |  39.72 |   4  |   2  |    0   | 0.917 | Paroxetine     |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
+| 270.21 | 3.146 |  3  |  1  |  55.13 |   4  |   2  |    0   | 0.915 | Leflunomide    |  0  |
++--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
 
 -----
 
+.. class:: infomark
 
 **Cite**
 
-[1] Bickerton, G.R.; Paolini, G.V.; Besnard, J.; Muresan, S.; Hopkins, A.L. (2012) ‘Quantifying the chemical beauty of drugs’, Nature Chemistry, 4, 90-98
+Bickerton et al. - `Quantifying the chemical beauty of drugs`_
 
-http://dx.doi.org/10.1038/nchem.1243
+.. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html
+
   </help>
 </tool>