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author bgruening
date Tue, 26 Mar 2013 13:05:41 -0400
parents
children 8df9e27d8671
files chemfp_clustering/butina_clustering.py chemfp_clustering/butina_clustering.xml chemfp_clustering/nxn_clustering.py chemfp_clustering/nxn_clustering.xml chemfp_clustering/test-data/NxN_Clustering_on_q.svg chemfp_clustering/test-data/Taylor-Butina_Clustering_on_data_q.txt chemfp_ob2fps/ob2fps.xml chemfp_ob2fps/test-data/CID_2244.can chemfp_ob2fps/test-data/CID_2244.inchi chemfp_ob2fps/test-data/CID_2244.sdf chemfp_ob2fps/test-data/CID_2244.smi chemfp_ob2fps/test-data/CID_2244_FP2.fps chemfp_ob2fps/test-data/CID_2244_FP3.fps chemfp_ob2fps/test-data/CID_2244_FP4.fps chemfp_ob2fps/test-data/CID_2244_maccs.fps chemfp_sdf2fps/sdf2fps.xml repository_dependencies.xml tool_dependencies.xml
diffstat 18 files changed, 1512 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/butina_clustering.py	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+"""
+    Modified version of code examples from the chemfp project.
+    http://code.google.com/p/chem-fingerprints/
+    Thanks to Andrew Dalke of Andrew Dalke Scientific!
+"""
+
+import chemfp
+import sys
+import os
+
+chemfp_fingerprint_file = sys.argv[1]
+tanimoto_threshold = float(sys.argv[2])
+outfile = sys.argv[3]
+processors = int(sys.argv[4])
+
+
+def get_hit_indicies(hits):
+    return [id for (id, score) in hits]
+
+out = open(outfile, 'w')
+dataset = chemfp.load_fingerprints( chemfp_fingerprint_file )
+
+chemfp.set_num_threads( processors )
+search = dataset.threshold_tanimoto_search_arena(dataset, threshold = tanimoto_threshold)
+
+# Reorder so the centroid with the most hits comes first.
+# (That's why I do a reverse search.)
+# Ignore the arbitrariness of breaking ties by fingerprint index
+results = sorted( (  (len(hits), i, hits) for (i, hits) in enumerate(search.iter_indices_and_scores())  ),reverse=True)
+
+
+# Determine the true/false singletons and the clusters
+true_singletons = []
+false_singletons = []
+clusters = []
+
+seen = set()
+
+for (size, fp_idx, hits) in results:
+    if fp_idx in seen:
+        # Can't use a centroid which is already assigned
+        continue
+    seen.add(fp_idx)
+
+    if size == 1:
+        # The only fingerprint in the exclusion sphere is itself
+        true_singletons.append(fp_idx)
+        continue
+
+    members = get_hit_indicies(hits)
+    # Figure out which ones haven't yet been assigned
+    unassigned = [target_idx for target_idx in members if target_idx not in seen]
+
+    if not unassigned:
+        false_singletons.append(fp_idx)
+        continue
+
+    # this is a new cluster
+    clusters.append( (fp_idx, unassigned) )
+    seen.update(unassigned)
+
+len_cluster = len(clusters)
+#out.write( "#%s true singletons: %s\n" % ( len(true_singletons), " ".join(sorted(dataset.ids[idx] for idx in true_singletons)) ) )
+#out.write( "#%s false singletons: %s\n" % ( len(false_singletons), " ".join(sorted(dataset.ids[idx] for idx in false_singletons)) ) )
+
+out.write( "#%s true singletons\n" % len(true_singletons) )
+out.write( "#%s false singletons\n" % len(false_singletons) )
+out.write( "#clusters: %s\n" % len_cluster )
+
+
+# Sort so the cluster with the most compounds comes first,
+# then by alphabetically smallest id
+def cluster_sort_key(cluster):
+    centroid_idx, members = cluster
+    return -len(members), dataset.ids[centroid_idx]
+
+clusters.sort(key=cluster_sort_key)
+
+
+for centroid_idx, members in clusters:
+    centroid_name = dataset.ids[centroid_idx]
+    out.write("%s\t%s\t%s\n" % (centroid_name, len(members), " ".join(dataset.ids[idx] for idx in members)))
+    #ToDo: len(members) need to be some biggest top 90% or something ...
+
+for idx in true_singletons:
+    out.write("%s\t%s\n" % (dataset.ids[idx], 0))
+
+out.close()
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/butina_clustering.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,65 @@
+<tool id="chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1">
+    <description>of molecular libraries</description>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+    </requirements>
+    <command interpreter='python'>
+        butina_clustering.py $infile $threshold $outfile 4
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.8' ></param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps"/>
+            <param name='threshold' value='0.8' ></param>
+            <output name="outfile" ftype="txt"  file='Taylor-Butina_Clustering_on_data_q.txt'/>
+        </test>
+    </tests>
+<help>
+
+
+**What it does**
+Molecule library clustering using the Taylor-Butina algorithm.
+
+-----
+
+**Example**
+
+* input::
+
+	-  fingerprints in FPS format
+
+		#FPS1
+		#num_bits=881
+		#type=CACTVS-E_SCREEN/1.0 extended=2
+		#software=CACTVS/unknown
+		#source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
+		#date=2012-02-09T13:20:37
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
+		19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
+		19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+		........
+
+	- Tanimoto threshold : 0.8 (between 0 and 1)
+
+* output::
+
+	0 true singletons
+	=> 
+
+	0 false singletons
+	=> 
+
+	1 clusters
+	55091849 has 12 other members
+	=> 6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823
+
+ </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/nxn_clustering.py	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+"""
+    Modified version of code examples from the chemfp project.
+    http://code.google.com/p/chem-fingerprints/
+    Thanks to Andrew Dalke of Andrew Dalke Scientific!
+"""
+import matplotlib
+matplotlib.use('Agg')
+import sys
+import os
+import chemfp
+import scipy.cluster.hierarchy as hcluster
+import pylab
+import numpy
+
+
+def distance_matrix(arena,t):
+    n = len(arena)
+    # The Tanimoto search computes all of the scores when threshold=0.0.
+    # The SearchResult contains sparse data, so I set all values
+    # now to 1.0 so you can experiment with higher thresholds.
+    distances = numpy.ones((n, n), numpy.float64)
+
+    # Keep track of where the query subarena is in the query
+    query_row = 0
+
+    for query_arena in arena.iter_arenas():
+        results = arena.threshold_tanimoto_search_arena(query_arena, threshold=t)  
+    for q_i, hits in enumerate(results.iter_indices_and_scores()):
+            query_idx = query_row + q_i
+            for target_idx, score in hits:
+                distances[query_idx, target_idx] = 1.0 - score
+        query_row += len(query_arena)
+
+    return distances
+
+dataset = chemfp.load_fingerprints( sys.argv[1] )
+distances  = distance_matrix( dataset,float( sys.argv[2] ) )
+linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
+
+# Plot using matplotlib, which you must have installed
+hcluster.dendrogram(linkage, labels=dataset.ids)
+
+pylab.savefig( sys.argv[3], format='svg' )
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/nxn_clustering.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,61 @@
+<tool id="chemfp_nxn_clustering" name="NxN Clustering" version="0.1">
+    <description>of molecular libraries</description>
+    <requirements>
+        <requirement type="package" version="1.7.0">numpy</requirement>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+    </requirements>
+    <command interpreter='python'>
+        nxn_clustering.py $infile $threshold $outfile
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.75' ></param>
+    </inputs>
+    <outputs>
+        <data type="data" format="svg" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps" />
+            <param value='0.75' />
+            <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+Generating hierarchical clusters and visualizing clusters with dendrograms.
+
+-----
+
+**Example**
+
+* input::
+
+	-  fingerprints in FPS format
+
+		#FPS1
+		#num_bits=881
+		#type=CACTVS-E_SCREEN/1.0 extended=2
+		#software=CACTVS/unknown
+		#source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
+		#date=2012-02-09T13:20:37
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
+		19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000	55169009
+		07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
+		19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000	55079807
+		........
+
+	- Tanimoto threshold : 0.8 (between 0 and 1)
+
+* output::
+
+	plot for the clustring
+
+.. image:: ./static/images/chemfpclustoutput.svg
+
+ 
+    </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/test-data/NxN_Clustering_on_q.svg	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,793 @@
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+       <use x="63.623046875" xlink:href="#DejaVuSans-2e"/>
+       <use x="95.41015625" xlink:href="#DejaVuSans-30"/>
+       <use x="159.033203125" xlink:href="#DejaVuSans-34"/>
+      </g>
+     </g>
+    </g>
+    <g id="ytick_6">
+     <g id="line2d_11">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="72.0" xlink:href="#me8a85f7bf6" y="152.927192279"/>
+      </g>
+     </g>
+     <g id="line2d_12">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="518.4" xlink:href="#m1a32005dea" y="152.927192279"/>
+      </g>
+     </g>
+     <g id="text_19">
+      <!-- 0.05 -->
+      <g transform="translate(43.120625 157.295004779)scale(0.12 -0.12)">
+       <use xlink:href="#DejaVuSans-30"/>
+       <use x="63.623046875" xlink:href="#DejaVuSans-2e"/>
+       <use x="95.41015625" xlink:href="#DejaVuSans-30"/>
+       <use x="159.033203125" xlink:href="#DejaVuSans-35"/>
+      </g>
+     </g>
+    </g>
+    <g id="ytick_7">
+     <g id="line2d_13">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="72.0" xlink:href="#me8a85f7bf6" y="105.752630735"/>
+      </g>
+     </g>
+     <g id="line2d_14">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="518.4" xlink:href="#m1a32005dea" y="105.752630735"/>
+      </g>
+     </g>
+     <g id="text_20">
+      <!-- 0.06 -->
+      <g transform="translate(42.828125 110.120443235)scale(0.12 -0.12)">
+       <use xlink:href="#DejaVuSans-30"/>
+       <use x="63.623046875" xlink:href="#DejaVuSans-2e"/>
+       <use x="95.41015625" xlink:href="#DejaVuSans-30"/>
+       <use x="159.033203125" xlink:href="#DejaVuSans-36"/>
+      </g>
+     </g>
+    </g>
+    <g id="ytick_8">
+     <g id="line2d_15">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="72.0" xlink:href="#me8a85f7bf6" y="58.5780691907"/>
+      </g>
+     </g>
+     <g id="line2d_16">
+      <g>
+       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="518.4" xlink:href="#m1a32005dea" y="58.5780691907"/>
+      </g>
+     </g>
+     <g id="text_21">
+      <!-- 0.07 -->
+      <g transform="translate(43.098125 62.9458816907)scale(0.12 -0.12)">
+       <use xlink:href="#DejaVuSans-30"/>
+       <use x="63.623046875" xlink:href="#DejaVuSans-2e"/>
+       <use x="95.41015625" xlink:href="#DejaVuSans-30"/>
+       <use x="159.033203125" xlink:href="#DejaVuSans-37"/>
+      </g>
+     </g>
+    </g>
+   </g>
+   <g id="patch_3">
+    <path d="
+M72 43.2
+L518.4 43.2" style="fill:none;stroke:#000000;"/>
+   </g>
+   <g id="patch_4">
+    <path d="
+M518.4 388.8
+L518.4 43.2" style="fill:none;stroke:#000000;"/>
+   </g>
+   <g id="patch_5">
+    <path d="
+M72 388.8
+L518.4 388.8" style="fill:none;stroke:#000000;"/>
+   </g>
+   <g id="patch_6">
+    <path d="
+M72 388.8
+L72 43.2" style="fill:none;stroke:#000000;"/>
+   </g>
+  </g>
+ </g>
+ <defs>
+  <clipPath id="p7ff5b81e1d">
+   <rect height="345.6" width="446.4" x="72.0" y="43.2"/>
+  </clipPath>
+ </defs>
+</svg>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/test-data/Taylor-Butina_Clustering_on_data_q.txt	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,4 @@
+#0 true singletons
+#0 false singletons
+#clusters: 1
+55091849	12	6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091752 55091467 55168823
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/ob2fps.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,143 @@
+<tool id="chemfp_ob2fps" name="Molecules to Fingerprints" version="0.1.2">
+    <description>with different fingerprint types</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="1.1p1">chemfp</requirement>
+    </requirements>
+    <command>
+        ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
+        <param name='fptype' type='select' format='text'>
+            <option value='--FP2'>FP2</option>
+            <option value='--FP3'>FP3</option>
+            <option value='--FP4'>FP4</option>
+            <option value='--MACCS'>MACCS</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps" />
+    </outputs>
+    <tests>
+        <!-- FP2 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <!-- FP3 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <!-- FP4 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <!-- MACCS -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Generate fingerprints using OpenBabel
+
+-----
+
+**Example**
+
+* input::
+	
+	      - SDF File
+
+		28434379
+		  -OEChem-02031205132D
+
+		 37 39  0     0  0  0  0  0  0999 V2000
+		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+		    7.3704    0.9433    0.0000 C   0  0  0  0 
+		    ......
+		  1 15  1  0  0  0  0
+		  1 35  1  0  0  0  0
+		  2  5  1  0  0  0  0
+		  2 11  1  0  0  0  0
+		  2 12  1  0  0  0  0
+		  3 12  2  0  0  0  0
+		  3 13  1  0  0  0  0
+		  4 18  1  0  0  0  0
+		  ......
+
+			&gt;PUBCHEM_COMPOUND_CID&lt;
+			28434379
+
+			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			1
+
+			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			280
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			&gt;
+
+		- type : FP2
+
+* output::
+
+	#FPS1
+	#num_bits=1021
+	#type=OpenBabel-FP2/1
+	#software=OpenBabel/2.3.0
+	#source=/tmp/dataset_409.dat.sdf
+	#date=2012-02-03T11:13:39
+	c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
+	0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
+	10000000000080000000c0000060000c0000060810000010000000800102000000	28434379
+
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244.can	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,1 @@
+CC(=O)Oc1ccccc1C(=O)O	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244.inchi	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,1 @@
+InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244.sdf	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,155 @@
+2244
+  -OEChem-05151212332D
+
+ 21 21  0     0  0  0  0  0  0999 V2000
+    3.7320   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8660   -1.5600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.5981   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.8660   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0000   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.0611   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.8671   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    5.4641   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.8671   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3100    0.4769    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4631    0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    1.6900   -0.5969    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+    6.3301    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  5  1  0  0  0  0
+  1 12  1  0  0  0  0
+  2 11  1  0  0  0  0
+  2 21  1  0  0  0  0
+  3 11  2  0  0  0  0
+  4 12  2  0  0  0  0
+  5  6  1  0  0  0  0
+  5  7  2  0  0  0  0
+  6  8  2  0  0  0  0
+  6 11  1  0  0  0  0
+  7  9  1  0  0  0  0
+  7 14  1  0  0  0  0
+  8 10  1  0  0  0  0
+  8 15  1  0  0  0  0
+  9 10  2  0  0  0  0
+  9 16  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 18  1  0  0  0  0
+ 13 19  1  0  0  0  0
+ 13 20  1  0  0  0  0
+M  END
+> <PUBCHEM_COMPOUND_CID>
+2244
+
+> <PUBCHEM_COMPOUND_CANONICALIZED>
+1
+
+> <PUBCHEM_CACTVS_COMPLEXITY>
+212
+
+> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+4
+
+> <PUBCHEM_CACTVS_HBOND_DONOR>
+1
+
+> <PUBCHEM_CACTVS_ROTATABLE_BOND>
+3
+
+> <PUBCHEM_CACTVS_SUBSKEYS>
+AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==
+
+> <PUBCHEM_IUPAC_OPENEYE_NAME>
+2-acetoxybenzoic acid
+
+> <PUBCHEM_IUPAC_CAS_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
+2-acetyloxybenzoic acid
+
+> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
+2-acetoxybenzoic acid
+
+> <PUBCHEM_IUPAC_INCHI>
+InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
+
+> <PUBCHEM_IUPAC_INCHIKEY>
+BSYNRYMUTXBXSQ-UHFFFAOYSA-N
+
+> <PUBCHEM_XLOGP3>
+1.2
+
+> <PUBCHEM_EXACT_MASS>
+180.042259
+
+> <PUBCHEM_MOLECULAR_FORMULA>
+C9H8O4
+
+> <PUBCHEM_MOLECULAR_WEIGHT>
+180.15742
+
+> <PUBCHEM_OPENEYE_CAN_SMILES>
+CC(=O)OC1=CC=CC=C1C(=O)O
+
+> <PUBCHEM_OPENEYE_ISO_SMILES>
+CC(=O)OC1=CC=CC=C1C(=O)O
+
+> <PUBCHEM_CACTVS_TPSA>
+63.6
+
+> <PUBCHEM_MONOISOTOPIC_WEIGHT>
+180.042259
+
+> <PUBCHEM_TOTAL_CHARGE>
+0
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+13
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+1
+
+> <PUBCHEM_COORDINATE_TYPE>
+1
+5
+255
+
+> <PUBCHEM_BONDANNOTATIONS>
+5  6  8
+5  7  8
+6  8  8
+7  9  8
+8  10  8
+9  10  8
+
+$$$$
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244.smi	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,1 @@
+O(c1c(cccc1)C(=O)O)C(=O)C	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244_FP2.fps	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=1021
+#type=OpenBabel-FP2/1
+#software=OpenBabel/2.3.1
+#source=CID_2244.sdf
+#date=2012-05-15T16:40:38
+00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244_FP3.fps	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=55
+#type=OpenBabel-FP3/1
+#software=OpenBabel/2.3.1
+#source=CID_2244.sdf
+#date=2012-05-15T16:59:15
+0400000c50b007	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244_FP4.fps	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=307
+#type=OpenBabel-FP4/1
+#software=OpenBabel/2.3.1
+#source=CID_2244.sdf
+#date=2012-05-15T16:59:22
+010000000000000000009800000000004001000000000000000000000000000000000240402801	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/test-data/CID_2244_maccs.fps	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,7 @@
+#FPS1
+#num_bits=166
+#type=OpenBabel-MACCS/2
+#software=OpenBabel/2.3.1
+#source=CID_2244.sdf
+#date=2012-05-15T17:00:39
+0000000000000000000000010000016480cca2d21e	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_sdf2fps/sdf2fps.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,93 @@
+<tool id="sdf2fps" name="SDF to Fingerprint" version="0.1.1">
+    <description>extract fingerprints from sdf files metadata</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="1.1p1">chemfp</requirement>
+    </requirements>
+    <command>
+        sdf2fps --pubchem "${infile}" > "${outfile}"
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Read a SDF file and extract the fingerprints, to stores them in a fps-file.
+TODO: currently it only works for PubChem
+
+-----
+
+**Example**
+	* input::
+	
+		SDF File
+
+		28434379
+		  -OEChem-02031205132D
+
+		 37 39  0     0  0  0  0  0  0999 V2000
+		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+		    7.3704    0.9433    0.0000 C   0  0  0  0 
+		    ......
+		  1 15  1  0  0  0  0
+		  1 35  1  0  0  0  0
+		  2  5  1  0  0  0  0
+		  2 11  1  0  0  0  0
+		  2 12  1  0  0  0  0
+		  3 12  2  0  0  0  0
+		  3 13  1  0  0  0  0
+		  4 18  1  0  0  0  0
+		  ......
+
+			&gt;PUBCHEM_COMPOUND_CID&lt;
+			28434379
+
+			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			1
+
+			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			280
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			&gt;
+
+* output::
+
+	#FPS1
+	#num_bits=881
+	#type=CACTVS-E_SCREEN/1.0 extended=2
+	#software=CACTVS/unknown
+	#source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
+	#date=2012-02-03T10:44:12
+	07ce04000000000000000000000000000080060000000c0600
+	00000000001a800f0000780008100000101487e9608c0bed32
+	48000580644626204101b4844805901b041c2e19511e45039b
+	8b2924101609401b13e4080000000000010020000004008000
+	0010000002000000000000	28434379
+
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,5 @@
+<?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="chemical_datatypes" owner="bgruening" changeset_revision="dbf93116a809" />
+    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="3bc566b84b93" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,20 @@
+<tool_dependency>
+    <package name="chemfp" version="1.1p1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        The core chemfp functionality does not depend on a third-party library but you will need a chemistry toolkit in order to generate new fingerprints 
+        from structure files. chemfp supports the free Open Babel and RDKit toolkits and the proprietary OEChem toolkit.
+        Currently the Galaxy-wrappers are using openbabel as underlying toolkit.
+        Compiling chemfp requires gcc and a python2.5+ version.</readme>
+    </package>
+</tool_dependency>