# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1374506947 -7200
# Node ID 9d1a5ff8c04f003f068ee876ccf1ff453b8b5037
# Parent  588e3ff42c28af7582a1472b0e1751d6780277d2
ChemicalToolBoX update.

diff -r 588e3ff42c28 -r 9d1a5ff8c04f align-it/align-it.xml
--- a/align-it/align-it.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/align-it/align-it.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -1,7 +1,7 @@
 <tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1">
     <description>and Optimization (Align-it)</description>
     <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="2.3.2">openbabel</requirement>
     </requirements>
     <command>
@@ -113,29 +113,32 @@
     </tests>
     <help>
 
-**What it does**
+.. class:: infomark
+
+**What this tool does**
 
-Align-it_ is a tool to align molecules according their pharmacophores.
+Align-it_ is a tool to align molecules according to their pharmacophores.
 A pharmacophore is an abstract concept based on the specific interactions 
-that have been observed in drug-receptor interactions: hydrogen bonding, 
+observed in drug-receptor interactions: hydrogen bonding, 
 charge transfer, electrostatic and hydrophobic interactions. 
 Molecular modeling and/or screening based on pharmacophore similarities 
-have proven to be an important and useful method in drug discovery.
+has been proven to be an important and useful method in drug discovery.
 
 The functionality of Align-it_ consists mainly of two parts. 
-The first functionality consists of the generation of pharmacophores from molecules 
-(use the tool *Pharmacophore generation* if you want to store these for later use).
-Second, pairs of **pharmacophores can be aligned** and the resulting 
-score is calculated from the volume overlap resulting from the alignments.
-
+The first functionality is the generation of pharmacophores from molecules 
+(use the tool **Pharmacophore generation** if you want to store these for further use).
+Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting 
+score is calculated from the volume overlap resulting of the alignments.
 
 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
 
 -----
 
-**Example**
+.. class:: infomark
 
-* input::
+**Input**
+
+* Example::
 
     - database
 
@@ -173,7 +176,42 @@
 
     - cutoff : 0.0
 
-* output::
+-----
+
+.. class:: infomark
+
+**Output**
+
+The format of the output file is shown in the table below:
+
++--------+-----------------------------------------------------------------------+
+| Column |                           Content                                     |
++========+=======================================================================+
+|    1   | Id of the reference structure                                         |
++--------+-----------------------------------------------------------------------+
+|    2   | Maximum volume of the reference structure                             |
++--------+-----------------------------------------------------------------------+
+|    3   | Id of the database structure                                          |
++--------+-----------------------------------------------------------------------+
+|    4   | Maximum volume of the database structure                              |
++--------+-----------------------------------------------------------------------+
+|    5   | Maximum volume overlap of the two structures                          |
++--------+-----------------------------------------------------------------------+
+|    6   | Overlap between pharmacophore and exclusion spheres in the reference  |
++--------+-----------------------------------------------------------------------+
+|    7   | Corrected volume overlap between database pharmacophore and reference |
++--------+-----------------------------------------------------------------------+
+|    8   | Number of pharmacophore points in the processed pharmacophore         |
++--------+-----------------------------------------------------------------------+
+|    9   | TANIMOTO score                                                        |
++--------+-----------------------------------------------------------------------+
+|   10   | TVERSKY_REF score                                                     |
++--------+-----------------------------------------------------------------------+
+|   11   | TVERSKY_DB score                                                      |
++--------+-----------------------------------------------------------------------+
+
+
+* Example::
     
     - aligned Pharmacophores 
 
@@ -185,25 +223,15 @@
         HACC    -2.7906    -1.9108    0.9092    1    1    -2.74368    -1.94015    1.90767
         $$$$    
 
+-----
 
-The format of this scores output file is as follows:
+.. class:: infomark
 
-======    =====================================================================
-Column    Content
-======    =====================================================================
-     1    Id of the reference structure
-     2    Maximum volume of the reference structure
-     3    Id of the database structure
-     4    Maximum volume of the database structure
-     5    Maximum volume overlap of the two structures
-     6    Overlap between pharmacophore and exclusion spheres in the reference
-     7    Corrected volume overlap between database pharmacophore and reference
-     8    Number of pharmacophore points in the processed pharmacophore
-     9    TANIMOTO score
-    10    TVERSKY_REF score
-    11    TVERSKY_DB score
-======    =====================================================================
+**Cite**
 
+`Silicos-it`_ - align-it
+
+.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
 
 
     </help>
diff -r 588e3ff42c28 -r 9d1a5ff8c04f align-it/align-it_create_db.xml
--- a/align-it/align-it_create_db.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/align-it/align-it_create_db.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -28,30 +28,32 @@
     </tests>
     <help>
 
-**What it does**
+.. class:: infomark
+
+**What this tool does**
 
-Align-it_ is a tool to align molecules according their pharmacophores.
+Align-it_ is a tool to align molecules according to their pharmacophores.
 A pharmacophore is an abstract concept based on the specific interactions 
-that have been observed in drug-receptor interactions: hydrogen bonding, 
+observed in drug-receptor interactions: hydrogen bonding, 
 charge transfer, electrostatic and hydrophobic interactions. 
 Molecular modeling and/or screening based on pharmacophore similarities 
-have proven to be an important and useful method in drug discovery.
+has been proven to be an important and useful method in drug discovery.
 
 The functionality of Align-it_ consists mainly of two parts. 
-The first functionality consists of the **generation of pharmacophores from molecules** 
-(the function of this tool). Second, pairs of pharmacophores 
-can be aligned (use the tool *Pharmacophore Alignment*) and the resulting 
-score is calculated from the volume overlap resulting from the alignments.
-
+The first functionality is the generation of pharmacophores from molecules
+(the function of this tool). Secondly, pairs of pharmacophores 
+can be aligned (use the tool **Pharmacophore Alignment**). The resulting 
+score is calculated from the volume overlap resulting of the alignments.
 
 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
 
-
 -----
 
-**Example**
+.. class:: infomark
 
-* input::
+**Input**
+
+* Example::
 
     - database
 
@@ -89,7 +91,13 @@
 
     - cutoff : 0.0
 
-* output::
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
     
     - aligned Pharmacophores 
 
@@ -101,7 +109,15 @@
         HACC    -2.7906    -1.9108    0.9092    1    1    -2.74368    -1.94015    1.90767
         $$$$    
 
+-----
 
+.. class:: infomark
+
+**Cite**
+
+`Silicos-it`_ - align-it
+
+.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
 
     </help>
 </tool>
diff -r 588e3ff42c28 -r 9d1a5ff8c04f qed/silicos_qed.xml
--- 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>
diff -r 588e3ff42c28 -r 9d1a5ff8c04f repository_dependencies.xml
--- a/repository_dependencies.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/repository_dependencies.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -1,4 +1,4 @@
 <?xml version='1.0' encoding='utf-8'?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="a1474892287e" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <repository changeset_revision="e6493849afd3" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
 </repositories>
\ No newline at end of file
diff -r 588e3ff42c28 -r 9d1a5ff8c04f shape-it/shape-it.xml
--- a/shape-it/shape-it.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/shape-it/shape-it.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -1,7 +1,7 @@
 <tool id="ctb_shapeit" name="Shape alignment" version="0.1">
     <description>against a database of molecules (Shape-it)</description>
     <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="2.3.2">openbabel</requirement>
     </requirements>
     <command >
@@ -10,7 +10,9 @@
         --dbase $database
         --reference $reference
         --addIterations $addIterations
-        --best $best
+        #if int($best) > 0:
+            --best $best
+        #end if
         --cutoff $cutoff
         #if $scores == 'yes':
             --scores $output_scores
@@ -20,13 +22,13 @@
         --out $output  2>&#38;1
     </command>
     <inputs>
-        <param name="reference" type="data" format='sdf,mol,mol2,smi' label="Refrence molecule" />
-        <param name="database" type="data" format='sdf,mol,mol2' label="Database of Molecules (needs 3D coordinates)" />
-        <param name="cutoff" type="float" value="0.0">
+        <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" />
+        <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
+        <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported." help="The scoring function is defined by the scoring scheme.">
             <validator type="in_range" min="0.0" />
         </param>
-        <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' />
-        <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' />
+        <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' help="The default value is set to 0, which refers to only a local gradient ascent."/>
+        <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/>
         <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
         <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
         <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
@@ -53,31 +55,39 @@
     </tests>
     <help>
 
-**What it does**
+
+.. class:: infomark
+
+**What this tool does**
 
 Shape-it_ is a tool that aligns a reference molecule against a set of database
 molecules using the shape of the molecules as the align criterion. 
-It is based on the use of Gaussian volumes as descriptor for molecular 
-shape as it was introduced by `Grant and Pickup`_.
+It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.
 
 The program expects one reference molecule with
 its three-dimensional coordinates and one database files containing one
 or more molecules in three dimensions. The results are either the alignment
 of all database molecules and their respective scores or the N best
-scoring molecules from the complete database.
-
+scoring molecules of the complete database.
 
+.. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
 .. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
-.. _`Grant and Pickup`: http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19961115)17:14%3C1653::AID-JCC7%3E3.0.CO;2-K/abstract
 
 -----
 
-**Example**
+.. class:: infomark
+
+**Input**
+
 
-* input::
+| - `formates recognized by OpenBabel`_
+
+.. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
+
+* Example::
 
 	- database
-		 27 28  0     0  0  0  0  0  0999 V2000
+		27 28  0     0  0  0  0  0  0999 V2000
 	   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 	    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 	   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
@@ -117,7 +127,7 @@
 	
 	- reference
 
-	 30 31  0     0  0  0  0  0  0999 V2000
+		30 31  0     0  0  0  0  0  0999 V2000
 	    1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 	    1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
 	   -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
@@ -162,7 +172,13 @@
 
 	- cutoff : 0.0
 
-* output::
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
 
 	 27 28  0  0  0  0  0  0  0  0999 V2000
 	   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
@@ -205,5 +221,16 @@
 	  6  8  2  0  0  0  0
 	  ......
 
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Silicos-it`_ - shape-it
+
+.. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
+
+
     </help>
 </tool>
diff -r 588e3ff42c28 -r 9d1a5ff8c04f strip-it/strip-it.xml
--- a/strip-it/strip-it.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/strip-it/strip-it.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -1,11 +1,12 @@
-<tool id="ctb_stripit" name="Strip-it" version="1.0.0">
+<tool id="ctb_stripit" name="Strip-it" version="1.0.1">
     <description> extracts predefined scaffolds from molecules</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>
-        <requirement type="package" version="1.0.0">silicos_it</requirement>
+        <requirement type="package" version="1.0.1">silicos_it</requirement>
     </requirements>
     <command>
-        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog 2>&#38;1
+        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog --noHeader 2>&#38;1
     </command>
     <inputs>
         <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
@@ -21,49 +22,71 @@
     </tests>
     <help>
 
-**What it does**
+
+.. class:: infomark
 
-Strip-it is a program that extracts predefined scaffolds from organic
-molecules
+**What this tool does**
+
+Strip-it is a program that extracts predefined scaffolds from organic small
+molecules.
 
 The program comes with a number of predefined molecular scaffolds for
 extraction. These scaffolds include, amongst others
 
-    - Molecular frameworks as originally described by Bemis and
-      Murcko;1
-    - Molecular frameworks and the reduced molecular frameworks as
-      described by Ansgar Schuffenhauer and coworkers;2
-    - Scaffold topologies as described by Sara Pollock and coworkers.3
+    - `molecular frameworks`_ as originally described by Bemis and
+      Murcko
+    - `molecular frameworks and the reduced molecular frameworks`_ as
+      described by Ansgar Schuffenhauer and coworkers
+    - `scaffold topologies`_ as described by Sara Pollock and coworkers
 
-
-http://silicos-it.com/software/strip-it/1.0.1/strip-it.html
+.. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
+.. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
+.. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
 
 -----
 
-Example
--------
+.. class:: infomark
+
+<<<<<<< HEAD
+http://www.silicos-it.com/software/strip-it/1.0.2/strip-it.html
+=======
+**Input**
 
-**input**
+| - `SD-Format`_
+| - `SMILES Format`_
+| - `MOL2 Format`_
 
-- `SDF Format`_
-- `SMILES Format`_
-- `MOL2 Format`_
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+.. _MOL2 Format: http://www.tripos.com/data/support/mol2.pdf
+>>>>>>> 67ce87e8ccf30f81f72248a7fde0896c5e9ae953
+
+-----
+
+.. class:: infomark
 
-.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
-.. _SMILES FORMAT: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
-.. _MOL2 FORMAT: http://www.tripos.com/data/support/mol2.pdf
-
-
-**output**
+**Output**
 
-TODO:
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+|     NAME    |            MOLECULE            | RINGS_WITH_LINKERS_1 |  RINGS_WITH_LINKERS_2  |       MURCKO_1       | ... |
++=============+================================+======================+========================+======================+=====+ 
+|  Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1  |   c1ccc(cc1)Nc1ccccc1  |  C1CCC(CC1)CC1CCCCC1 | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+| Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
+|     ...     |              ...               |         ...          |           ...          |          ...         | ... |
++-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
 
-    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========
-    NAME    MOLECULE                       RINGS_WITH_LINKERS_1    RINGS_WITH_LINKERS_2    MURCKO_1               MURCKO_2              OPREA_1       OPREA_2         OPREA_3
-    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========
-    3037    Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl    c1ccc(cc1)Cc1ccccc1     c1ccc(cc1)Cc1ccccc1     C1CCC(CC1)CC1CCCCC1    C1CCC(CC1)C1CCCCC1    C1CC1C1CC1    C1CC1C1CC1    C1CC1C1CC1
-    3037    Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl    c1ccc(cc1)Cc1ccccc1     c1ccc(cc1)Cc1ccccc1     C1CCC(CC1)CC1CCCCC1    C1CCC(CC1)C1CCCCC1    C1CC1C1CC1    C1CC1C1CC1    C1CC1C1CC1
-    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Silicos-it`_ - strip-it
+
+.. _Silicos-it: http://silicos-it.com/software/strip-it/1.0.2/strip-it.html
+
 
     </help>
 </tool>
diff -r 588e3ff42c28 -r 9d1a5ff8c04f tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jun 02 19:54:27 2013 +0200
+++ b/tool_dependencies.xml	Mon Jul 22 17:29:07 2013 +0200
@@ -1,18 +1,18 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="62fda117ad4a" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="openbabel" version="2.3.2">
         <repository changeset_revision="3a993ff17df5" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="rdkit" version="2012_12_1">
-        <repository changeset_revision="5b30ea84ba25" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="2560d8a02782" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
-    <package name="silicos_it" version="1.0.0">
+    <package name="silicos_it" version="1.0.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action>
+                <action type="download_by_url">https://github.com/bgruening/silicos-it_store/blob/master/strip-it/strip-it-1.0.2.tar.gz</action>
 
                 <!-- populate the environment variables from the dependend repos 
                     $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR
@@ -34,8 +34,8 @@
                 </action>
 
                 <!-- compiling align-it -->
-                <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=align-it-1.0.3.tar.gz</action>
-                <action type="shell_command">tar xfvz download.php?file=align-it-1.0.3.tar.gz &amp;&amp; 
+                <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/align-it/align-it-1.0.3.tar.gz</action>
+                <action type="shell_command">tar xfvz align-it-1.0.3.tar.gz &amp;&amp; 
                     cd align-it-1.0.3 &amp;&amp; 
                     cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                     make &amp;&amp; 
@@ -45,8 +45,8 @@
                 </action>
 
                 <!-- compiling shape-it -->
-                <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=shape-it-1.0.1.tar.gz</action>
-                <action type="shell_command">tar xfvz download.php?file=shape-it-1.0.1.tar.gz &amp;&amp; 
+                <action type="shell_command">wget https://github.com/bgruening/silicos-it_store/raw/master/shape-it/shape-it-1.0.1.tar.gz</action>
+                <action type="shell_command">tar xfvz shape-it-1.0.1.tar.gz &amp;&amp; 
                     cd shape-it-1.0.1 &amp;&amp; 
                     cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                     make &amp;&amp;