# HG changeset patch
# User bgruening
# Date 1369500880 14400
# Node ID cc63a42fd22e734a249d8285c9c9d2da629a0ff5
# Parent  d051544e94dadd67aeca51a4fa9cb20c8b8a11b8
Uploaded

diff -r d051544e94da -r cc63a42fd22e convert/ob_convert.xml
--- a/convert/ob_convert.xml	Thu May 23 17:29:11 2013 -0400
+++ b/convert/ob_convert.xml	Sat May 25 12:54:40 2013 -0400
@@ -28,9 +28,9 @@
         -o "$format" -e
         -O ${os.path.join($outfile.extra_files_path,'molecule.fs')}
         #if int($oformat.fs_fold) > 0:
-            $oformat.fs_fold
+            -xN$oformat.fs_fold
         #end if
-        -xN$#str(${oformat.fs_fptype}).strip()
+        ${oformat.fs_fptype}
     #else:
         "${infile}"
         -o "$format"
diff -r d051544e94da -r cc63a42fd22e filter/ob_filter.xml
--- a/filter/ob_filter.xml	Thu May 23 17:29:11 2013 -0400
+++ b/filter/ob_filter.xml	Sat May 25 12:54:40 2013 -0400
@@ -3,6 +3,7 @@
   <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
   <requirements>
     <requirement type="package" version="2.3.2">openbabel</requirement>
+    <requirement type="package" version="0.1">cheminfolib</requirement>
   </requirements>
   <command interpreter="python">
     ob_filter.py
diff -r d051544e94da -r cc63a42fd22e filter/ob_remDuplicates.xml
--- a/filter/ob_remDuplicates.xml	Thu May 23 17:29:11 2013 -0400
+++ b/filter/ob_remDuplicates.xml	Sat May 25 12:54:40 2013 -0400
@@ -7,7 +7,7 @@
   <command>
     obabel
       -i"${infile.ext}"
-       "${infile}
+       "${infile}"
       -ocopy
       --unique "${descriptor}"
       -O "${outfile}"
diff -r d051544e94da -r cc63a42fd22e modify/ob_genProp.xml
--- a/modify/ob_genProp.xml	Thu May 23 17:29:11 2013 -0400
+++ b/modify/ob_genProp.xml	Sat May 25 12:54:40 2013 -0400
@@ -3,6 +3,7 @@
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>
+        <requirement type="package" version="0.1">cheminfolib</requirement>
     </requirements>
     <command interpreter="python">
     ob_genProp.py
diff -r d051544e94da -r cc63a42fd22e repository_dependencies.xml
--- a/repository_dependencies.xml	Thu May 23 17:29:11 2013 -0400
+++ b/repository_dependencies.xml	Sat May 25 12:54:40 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 changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r d051544e94da -r cc63a42fd22e search/ob_spectrophore_search.py
--- a/search/ob_spectrophore_search.py	Thu May 23 17:29:11 2013 -0400
+++ b/search/ob_spectrophore_search.py	Sat May 25 12:54:40 2013 -0400
@@ -10,6 +10,7 @@
 openbabel.obErrorLog.StopLogging()
 import pybel
 import math
+import numpy as np
 
 #TODO get rid of eval()
 
diff -r d051544e94da -r cc63a42fd22e search/ob_spectrophore_search.xml
--- a/search/ob_spectrophore_search.xml	Thu May 23 17:29:11 2013 -0400
+++ b/search/ob_spectrophore_search.xml	Sat May 25 12:54:40 2013 -0400
@@ -2,6 +2,7 @@
   <description>similarity search based on 1D chemical features</description>
   <requirements>
     <requirement type="package" version="2.3.2">openbabel</requirement>
+    <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
   <command interpreter="python">
     ob_spectrophore_search.py
diff -r d051544e94da -r cc63a42fd22e tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 23 17:29:11 2013 -0400
+++ b/tool_dependencies.xml	Sat May 25 12:54:40 2013 -0400
@@ -3,6 +3,9 @@
     <package name="openbabel" version="2.3.2">
         <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="7283651b62fe" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="cheminfolib" version="0.1">
         <install version="1.0">
             <actions>