# HG changeset patch
# User bgruening
# Date 1369344551 14400
# Node ID d051544e94dadd67aeca51a4fa9cb20c8b8a11b8
# Parent  fa78faf6ee4f90aabdcb23ef2248a141c86030f5
Uploaded

diff -r fa78faf6ee4f -r d051544e94da convert/ob_convert.xml
--- a/convert/ob_convert.xml	Tue May 14 17:01:10 2013 -0400
+++ b/convert/ob_convert.xml	Thu May 23 17:29:11 2013 -0400
@@ -48,6 +48,8 @@
         $oformat.cml_omit
         $oformat.cml_continuous
         $oformat.cml_properties
+        $oformat.cml_gen2d
+        $oformat.cml_gen3d
     #elif $format == 'inchi':
         ##ignore less import warnings
         -w
@@ -82,6 +84,8 @@
         $oformat.sdf_no_prop
         $oformat.sdf_wedge_bonds
         $oformat.sdf_alias_out
+        $oformat.sdf_gen2d
+        $oformat.sdf_gen3d
     #elif $format == 'fpt':
         $oformat.fpt_fptype
         #if int($oformat.fpt_fold) > 0:
@@ -93,6 +97,8 @@
         $oformat.fpt_unset
     #elif $format == 'mol2':
         $oformat.mol2_ignore_res
+        $oformat.mol2_gen2d
+        $oformat.mol2_gen3d
     #end if
 
     ## Uniqueness according to stripped InChI's or canonical SMILES
@@ -233,6 +239,8 @@
                 <param name="cml_omit" type="boolean" label="omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
                 <param name="cml_continuous" type="boolean" label="continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
                 <param name="cml_properties" type="boolean" label="write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
+                <param name="cml_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="cml_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="cmlr" />
             <when value="com" />
@@ -319,6 +327,8 @@
             <when value="mmod" />
             <when value="mol2">
                 <param name="mol2_ignore_res" type="boolean" label="Output ignores residue information for ligands (-xl)" truevalue="-xl" falsevalue="" checked="false" />
+                <param name="mol2_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="mol2_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="molreport" />
             <when value="mop" />
@@ -340,6 +350,8 @@
                 <param name="sdf_no_prop" type="boolean" label="write no properties (-xm)" truevalue="-xm" falsevalue="" checked="false" />
                 <param name="sdf_wedge_bonds" type="boolean" label="use wedge and hash bonds from input (2D structures only) (-xw)" truevalue="-xw" falsevalue="" checked="false" />
                 <param name="sdf_alias_out" type="boolean" label="output in Alias form, e.g. Ph (-xA)" truevalue="-xA" falsevalue="" checked="false" />
+                <param name="sdf_gen2d" type="boolean" label="Generate 2D coordinates (--gen2d)" truevalue="--gen2d" falsevalue="" checked="false" />
+                <param name="sdf_gen3d" type="boolean" label="Generate 3D coordinates (--gen3d)" truevalue="--gen3d" falsevalue="" checked="false" />
             </when>
             <when value="smi">
                 <param name="smi_exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="-xh" falsevalue="" checked="false" />
diff -r fa78faf6ee4f -r d051544e94da filter/ob_remIons.xml
--- a/filter/ob_remIons.xml	Tue May 14 17:01:10 2013 -0400
+++ b/filter/ob_remIons.xml	Thu May 23 17:29:11 2013 -0400
@@ -1,6 +1,6 @@
 <tool id="ctb_remIons" name="Remove counterions and fragments" version="1.0">
     <description></description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
diff -r fa78faf6ee4f -r d051544e94da repository_dependencies.xml
--- a/repository_dependencies.xml	Tue May 14 17:01:10 2013 -0400
+++ b/repository_dependencies.xml	Thu May 23 17:29:11 2013 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="1b63345907ec" />
+    <repository changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r fa78faf6ee4f -r d051544e94da tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 14 17:01:10 2013 -0400
+++ b/tool_dependencies.xml	Thu May 23 17:29:11 2013 -0400
@@ -1,6 +1,7 @@
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="dc6a907dd737" />
+        <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="cheminfolib" version="0.1">
         <install version="1.0">
@@ -11,7 +12,7 @@
                     <destination>$INSTALL_DIR</destination>
                 </action>
                 <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>