diff filter/ob_filter.xml @ 2:125da3a296ca draft default tip

Uploaded

--- a/filter/ob_filter.xml	Wed Aug 21 03:06:02 2013 -0400
+++ b/filter/ob_filter.xml	Wed Jul 15 12:13:08 2015 -0400
@@ -6,6 +6,7 @@
     <requirement type="package" version="0.1">cheminfolib</requirement>
   </requirements>
   <command interpreter="python">
+<![CDATA[
     ob_filter.py
       -i "${infile}"
       -o "${outfile}"
@@ -40,6 +41,7 @@
           #end for
         #end if
       }'
+]]>
   </command>
   <inputs>
     <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/>
@@ -136,13 +138,14 @@
     -->
   </tests>
   <help>
+<![CDATA[
 
 
 .. class:: infomark
 
 **What this tool does**
 
-Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. 
+Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.
 
 -----
 
@@ -151,9 +154,9 @@
 **Hint**
 
 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
-| 
+|
 | For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
-| 
+|
 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).
 
 -----
@@ -163,38 +166,38 @@
 **Definition of the pre-defined filtering rules**
 
   **# Lipinski's Rule of Five:**
-    =&lt; 5 Hydrogen-bond donor groups
+    =< 5 Hydrogen-bond donor groups
 
-    =&lt; 10 Hydrogen-bond acceptor groups
+    =< 10 Hydrogen-bond acceptor groups
 
-    =&lt; 500 Molecular weight
+    =< 500 Molecular weight
 
-    =&lt; 5 octanol/water partition coefficient (log P)
+    =< 5 octanol/water partition coefficient (log P)
 
   **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
-    =&lt; 7 rotatable bonds
+    =< 7 rotatable bonds
 
-    =&lt; 350 Molecular weight
+    =< 350 Molecular weight
 
-    =&lt; 3.5 octanol/water partition coefficient (log P)
+    =< 3.5 octanol/water partition coefficient (log P)
 
   **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
-    =&lt; 10 Hydrogen-bond acceptor groups
+    =< 10 Hydrogen-bond acceptor groups
 
-    =&lt; 8 rotatable bonds
+    =< 8 rotatable bonds
 
-    150 =&lt; Molecular weight =&lt; 500
+    150 =< Molecular weight =< 500
 
-    =&lt; 150 Polar Surface Area
+    =< 150 Polar Surface Area
 
-    =&lt; 5 octanol/water partition coefficient (log P)
+    =< 5 octanol/water partition coefficient (log P)
 
   **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
-    =&lt; 5 rotatable bonds
+    =< 5 rotatable bonds
 
-    =&lt; 250 Molecular weight
+    =< 250 Molecular weight
 
-    =&lt; 2.5 octanol/water partition coefficient (log P)
+    =< 2.5 octanol/water partition coefficient (log P)
 
 -----
 
@@ -212,10 +215,10 @@
 
 .. class:: infomark
 
-**Output** 
+**Output**
 
 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
-| 
+|
 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.
 
 -----
@@ -236,5 +239,6 @@
 
 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
+]]>
   </help>
 </tool>