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Changeset 0:354d3c6bb894 (2013-08-15)

Next changeset 1:43a9e7d9b24f (2015-11-01)

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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/butina_clustering.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/butina_clustering.py Thu Aug 15 03:27:06 2013 -0400

[

@@ -0,0 +1,135 @@
+#!/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
+import tempfile
+import argparse
+import subprocess
+from chemfp import search
+
+def unix_sort(results):
+    temp_unsorted = tempfile.NamedTemporaryFile(delete=False)
+    for (i,indices) in enumerate( results.iter_indices() ):
+        temp_unsorted.write('%s %s\n' % (len(indices), i))
+    temp_unsorted.close()
+    temp_sorted = tempfile.NamedTemporaryFile(delete=False)
+    temp_sorted.close()
+    p = subprocess.Popen(['sort', '-n', '-r', '-k', '1,1'], stdin=open(temp_unsorted.name), stdout=open(temp_sorted.name, 'w+'))
+    stdout, stderr = p.communicate()
+    return_code = p.returncode
+
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+    temp_sorted.close()
+    os.remove(temp_unsorted.name)
+
+    for line in open(temp_sorted.name):
+        size, fp_idx = line.strip().split()
+        yield (int(size), int(fp_idx))
+
+    os.remove(temp_sorted.name)
+
+def butina( args ):
+    """
+        Taylor-Butina clustering from the chemfp help.
+    """
+    out = args.output_path
+    targets = chemfp.open( args.input_path, format='fps' )
+    arena = chemfp.load_fingerprints( targets )
+
+    chemfp.set_num_threads( args.processors )
+    results = search.threshold_tanimoto_search_symmetric(arena, threshold = args.tanimoto_threshold)
+    results.reorder_all("move-closest-first")
+
+    sorted_ids = unix_sort(results)
+
+    # Determine the true/false singletons and the clusters
+    true_singletons = []
+    false_singletons = []
+    clusters = []
+
+    seen = set()
+    #for (size, fp_idx, members) in results:
+    for (size, fp_idx) in sorted_ids:
+        members = results[fp_idx].get_indices()
+        #print arena.ids[ fp_idx ], [arena.ids[ m ] for m in members]
+        if fp_idx in seen:
+            # Can't use a centroid which is already assigned
+            continue
+        seen.add(fp_idx)
+
+        if size == 0:
+            # The only fingerprint in the exclusion sphere is itself
+            true_singletons.append( fp_idx )
+            continue
+
+        # Figure out which ones haven't yet been assigned
+        unassigned = set(members) - 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(arena.ids[idx] for idx in true_singletons)) ) )
+    #out.write( "#%s false singletons: %s\n" % ( len(false_singletons), " ".join(sorted(arena.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), arena.ids[centroid_idx]
+
+    clusters.sort(key=cluster_sort_key)
+
+    for centroid_idx, members in clusters:
+        centroid_name = arena.ids[centroid_idx]
+        out.write("%s\t%s\t%s\n" % (centroid_name, len(members), " ".join(arena.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" % (arena.ids[idx], 0))
+
+    out.close()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="""Taylor-Butina clustering for fps files.
+For more details please see the original publication or the chemfp documentation:
+http://www.chemomine.co.uk/dbclus-paper.pdf
+https://chemfp.readthedocs.org
+""")
+
+    parser.add_argument("-i", "--input", dest="input_path",
+                    required=True,
+                    help="Path to the input file.")
+
+    parser.add_argument("-o", "--output", dest="output_path", type=argparse.FileType('w'),
+                    default=sys.stdout,
+                    help="Path to the output file.")
+
+    parser.add_argument("-t", "--threshold", dest="tanimoto_threshold", type=float,
+                    default=0.8,
+                    help="Tanimoto threshold [0.8]")
+
+    parser.add_argument('-p', '--processors', type=int,
+        default=4)
+
+    options = parser.parse_args()
+    butina( options )

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/butina_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/butina_clustering.xml Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,96 @@
+<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.1">
+    <description>of molecular fingerprints</description>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter='python'>
+        butina_clustering.py
+            -i $infile
+            -t $threshold
+            -o $outfile
+            -p 4
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.8'/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps"/>
+            <param name='threshold' value='0.8' ></param>
+            <output name="outfile" ftype="tabular"  file='Taylor-Butina_Clustering_on_data_q.txt'/>
+        </test>
+    </tests>
+<help>
+
+
+.. class:: infomark
+
+**What this tool does**
+
+Unsupervised non-hierarchical clustering method based on the Taylor-Butina algorithm, which guarantees that every cluster contains molecules which are within a distance cutoff of the central molecule. This tool is based on the chemfp_ project.
+
+.. _chemfp: http://chemfp.com/
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| Molecular fingerprints in FPS format.
+| Open Babel Fastsearch index is not supported.
+
+* Example::
+
+ -  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)
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+ 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
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+The chemfp_ project from Andrew Dalke!
+
+.. _chemfp: http://chemfp.com/
+
+ </help>
+
+</tool>

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/nxn_clustering.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/nxn_clustering.py Thu Aug 15 03:27:06 2013 -0400

[

@@ -0,0 +1,80 @@
+#!/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 argparse
+import os
+import chemfp
+import scipy.cluster.hierarchy as hcluster
+import pylab
+import numpy
+
+def distance_matrix(arena, tanimoto_threshold = 0.0):
+    n = len(arena)
+    # Start off a similarity matrix with 1.0s along the diagonal
+    try:
+        similarities = numpy.identity(n, "d")
+    except:
+        raise Exception('Input dataset is to large!')
+    chemfp.set_num_threads( args.processors )
+
+    ## Compute the full similarity matrix.
+    # The implementation computes the upper-triangle then copies
+    # the upper-triangle into lower-triangle. It does not include
+    # terms for the diagonal.
+    results = chemfp.search.threshold_tanimoto_search_symmetric(arena, threshold=tanimoto_threshold)
+
+    # Copy the results into the NumPy array.
+    for row_index, row in enumerate(results.iter_indices_and_scores()):
+        for target_index, target_score in row:
+            similarities[row_index, target_index] = target_score
+
+    # Return the distance matrix using the similarity matrix
+    return 1.0 - similarities
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="""NxN clustering for fps files.
+For more details please see the chemfp documentation:
+https://chemfp.readthedocs.org
+""")
+
+    parser.add_argument("-i", "--input", dest="input_path",
+                    required=True,
+                    help="Path to the input file.")
+
+    parser.add_argument("-c", "--cluster", dest="cluster_image",
+                    help="Path to the output cluster image.")
+
+    parser.add_argument("-s", "--smatrix", dest="similarity_matrix",
+                    help="Path to the similarity matrix output file.")
+
+    parser.add_argument("-t", "--threshold", dest="tanimoto_threshold",
+                    type=float, default=0.0,
+                    help="Tanimoto threshold [0.0]")
+
+    parser.add_argument("--oformat", default='png', help="Output format (png, svg)")
+
+    parser.add_argument('-p', '--processors', type=int,
+        default=4)
+
+    args = parser.parse_args()
+
+    targets = chemfp.open( args.input_path, format='fps' )
+    arena = chemfp.load_fingerprints( targets )
+    distances  = distance_matrix( arena, args.tanimoto_threshold )
+
+    if args.similarity_matrix:
+        distances.tofile( args.similarity_matrix )
+
+    if args.cluster_image:
+        linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
+
+        hcluster.dendrogram(linkage, labels=arena.ids)
+
+        pylab.savefig( args.cluster_image, format=args.oformat )
+

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/nxn_clustering.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/nxn_clustering.xml Thu Aug 15 03:27:06 2013 -0400

[

@@ -0,0 +1,122 @@
+<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.2">
+    <description>of molecular fingerprints</description>
+    <requirements>
+        <requirement type="package" version="1.7.0">numpy</requirement>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+        <requirement type="package" version="1.2.1">matplotlib</requirement>
+        <requirement type="package" version="0.12.0">scipy</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter='python'>
+        nxn_clustering.py
+            -i $infile
+            -t $threshold
+            #if str($output_files) in ['both', 'image']:
+                --cluster $image
+            #end if
+            #if str($output_files) in ['both', 'matrix']:
+                --smatrix $smilarity_matrix
+            #end if
+            --oformat $oformat
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
+        <param name='threshold' type='float' value='0.0' />
+        <param name='oformat' type='select' format='text' label="Format of the resulting picture">
+            <option value='png'>PNG</option>
+            <option value='svg'>SVG</option>
+        </param>
+        <param name='output_files' type='select' format='text' label="Output options">
+            <option value='both'>NxN matrix and Image</option>
+            <option value='image'>Image</option>
+            <option value='matrix'>NxN Matrix</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="image" type="data" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
+            <filter>output_files == "both" or output_files == "image"</filter>
+            <change_format>
+                <when input="oformat" value="png" format="png"/>
+            </change_format>
+        </data>
+        <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
+            <filter>output_files == "both" or output_files == "matrix"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="fps" value="q.fps" />
+            <param name='treshold' value='0.75' />
+            <param name='output_files' value='image' />
+            <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Generating hierarchical clusters and visualizing clusters with dendrograms.
+For the clustering and the fingerprint handling the chemfp_ project is used.
+
+.. _chemfp: http://chemfp.com/
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+The plotting of the cluster image is sensible only with a small dataset.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported.
+
+* Example::
+
+ -  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)
+
+-----
+
+.. class:: informark
+
+**Output**
+
+* Example::
+
+ .. image:: $PATH_TO_IMAGES/NxN_clustering.png
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+The chemfp_ project from Andrew Dalke!
+
+.. _chemfp: http://chemfp.com/
+
+    </help>
+
+</tool>

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/butina_clustering_old.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/butina_clustering_old.py Thu Aug 15 03:27:06 2013 -0400

[

@@ -0,0 +1,97 @@
+#!/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
+import tempfile
+
+temp_file = tempfile.NamedTemporaryFile()
+temp_link = "%s.%s" % (temp_file.name, 'fps')
+temp_file.close()
+os.system('ln -s %s %s' % (os.path.realpath(sys.argv[1]), temp_link) )
+
+
+chemfp_fingerprint_file = temp_link
+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)
+#search = chemfp.search.threshold_tanimoto_search_symmetric (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)
+    print size, fp_idx, hits
+    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(sorted(dataset.ids[idx] for idx in members))))
+    #ToDo: len(members) need to be some biggest top 90% or something ...
+
+for idx in sorted(true_singletons):
+    out.write("%s\t%s\n" % (dataset.ids[idx], 0))
+
+out.close()
+os.remove( temp_link )

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/in.fps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/in.fps Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,8 @@
+#FPS1
+#num_bits=1021
+#type=OpenBabel-FP2/1
+#software=OpenBabel/2.3.90
+#source=/media/data/web/galaxy-central/database/job_working_directory/065/65986/task_0/dataset_69208.dat
+#date=2013-04-12T10:40:57
+00220160a00006e20000e6060f0300e4841084982840200c014e002c0410040014011115004010279800311100043605210244501832c000a2a801162080000144000c302065020881082000c2040738a2088150018a210090800b088049500019b00c08006440811300500021010120104c801102081842100003010a024200 a
+00220160a00006e20000e6060f0300e4841084982840200c014e002c0410040014011115004010279800311100043605210244501832c000a2a801162080000144000c302065020881082000c2040738a2088150018a210090800b088049500019b00c08006440811300500021010120104c801102081842100003010a024200 b

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/new.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/new.txt Thu Aug 15 03:27:06 2013 -0400

b'@@ -0,0 +1,10315 @@\n+#4831 true singletons\n+#7412 false singletons\n+#clusters: 5481\n+ZINC71602893\t661\tZINC04765100 ZINC05104846 ZINC04769792 ZINC04769794 ZINC04769797 ZINC04769800 ZINC05191386 ZINC04786883 ZINC04786885 ZINC04786888 ZINC04786890 ZINC04787909 ZINC01765469 ZINC05275407 ZINC05275425 ZINC05276235 ZINC05276256 ZINC02575335 ZINC05046463 ZINC01730614 ZINC05442645 ZINC02003567 ZINC05184936 ZINC05742758 ZINC05211501 ZINC05211510 ZINC05225291 ZINC02026704 ZINC05309659 ZINC05309665 ZINC05309998 ZINC05310000 ZINC01736727 ZINC02032622 ZINC02034633 ZINC05191648 ZINC02037188 ZINC01687049 ZINC02039429 ZINC02039430 ZINC12407621 ZINC06020484 ZINC15222822 ZINC15880088 ZINC06036257 ZINC16951501 ZINC02164095 ZINC17013835 ZINC17020625 ZINC02164129 ZINC02164131 ZINC17835665 ZINC18716182 ZINC08602617 ZINC08602618 ZINC18716185 ZINC02164168 ZINC02166571 ZINC12405013 ZINC02508039 ZINC02508043 ZINC02508044 ZINC02508087 ZINC02508096 ZINC02539331 ZINC13541814 ZINC13765172 ZINC13765175 ZINC13765178 ZINC14588590 ZINC14807062 ZINC14807075 ZINC03860614 ZINC03860615 ZINC16137972 ZINC16889870 ZINC16926751 ZINC04582342 ZINC04582343 ZINC04582344 ZINC05539679 ZINC34582485 ZINC05225259 ZINC05225340 ZINC05225465 ZINC05225470 ZINC05225476 ZINC05226159 ZINC05226163 ZINC05226167 ZINC05651120 ZINC04261946 ZINC04261947 ZINC22013264 ZINC22013268 ZINC22013273 ZINC22013279 ZINC31317854 ZINC31319331 ZINC31319335 ZINC31740234 ZINC31740239 ZINC15119988 ZINC32152665 ZINC32214132 ZINC43761699 ZINC43761700 ZINC43761701 ZINC43761702 ZINC01481755 ZINC34303159 ZINC34303160 ZINC34303161 ZINC34303162 ZINC45070295 ZINC02031628 ZINC02032404 ZINC34349782 ZINC02032619 ZINC34582222 ZINC71785898 ZINC71786843 ZINC01571260 ZINC01571261 ZINC43763722 ZINC45069745 ZINC45069748 ZINC45069752 ZINC34156324 ZINC01577370 ZINC01529247 ZINC01529451 ZINC01529452 ZINC70651338 ZINC70651339 ZINC70651340 ZINC01532765 ZINC01561953 ZINC01561960 ZINC01574321 ZINC01577208 ZINC71786720 ZINC01587683 ZINC01587688 ZINC02242645 ZINC00158103 ZINC00162386 ZINC01598495 ZINC01598496 ZINC01598497 ZINC01598498 ZINC01598518 ZINC01587614 ZINC00393753 ZINC00393754 ZINC00393755 ZINC00393756 ZINC01641048 ZINC16991119 ZINC00394761 ZINC00394806 ZINC00394807 ZINC00394808 ZINC02164097 ZINC01662386 ZINC00399241 ZINC02164128 ZINC01591808 ZINC01672871 ZINC01674839 ZINC01674842 ZINC00406932 ZINC00406933 ZINC02164132 ZINC00502094 ZINC00507608 ZINC01680238 ZINC02164158 ZINC18716183 ZINC01685148 ZINC18716184 ZINC01687047 ZINC01687048 ZINC00967533 ZINC01687050 ZINC02164167 ZINC00968099 ZINC00968100 ZINC00968101 ZINC00968128 ZINC01081099 ZINC01081323 ZINC01694726 ZINC01696964 ZINC01319163 ZINC01436122 ZINC01436123 ZINC01436124 ZINC01436125 ZINC01699906 ZINC01701838 ZINC01716732 ZINC01724736 ZINC01571243 ZINC01571245 ZINC02003566 ZINC02011663 ZINC02011664 ZINC01590023 ZINC02013559 ZINC02013560 ZINC02014257 ZINC02014258 ZINC02014867 ZINC02014868 ZINC02016526 ZINC02016527 ZINC02024203 ZINC02030897 ZINC01664354 ZINC01664389 ZINC02031663 ZINC02031664 ZINC02036681 ZINC02037295 ZINC02038302 ZINC02038947 ZINC02039356 ZINC01684585 ZINC01684714 ZINC02041115 ZINC02041265 ZINC02042933 ZINC02043763 ZINC02045088 ZINC02046918 ZINC02164102 ZINC02164138 ZINC01696943 ZINC02164171 ZINC01696963 ZINC02164174 ZINC02164175 ZINC02164177 ZINC02164178 ZINC02164180 ZINC02164183 ZINC02164185 ZINC02164186 ZINC02164188 ZINC02324820 ZINC01729357 ZINC01632734 ZINC02504418 ZINC01783052 ZINC02508035 ZINC02508046 ZINC02508063 ZINC02508071 ZINC02508078 ZINC01850974 ZINC02545280 ZINC02559331 ZINC02569878 ZINC02043148 ZINC02129241 ZINC02129243 ZINC03164162 ZINC03860308 ZINC02242637 ZINC03861506 ZINC02508249 ZINC04528636 ZINC04532208 ZINC04532209 ZINC04532210 ZINC02530724 ZINC04783008 ZINC02534413 ZINC02534432 ZINC02545294 ZINC02164169 ZINC02560409 ZINC05133736 ZINC02164172 ZINC02566228 ZINC02571329 ZINC05225162 ZINC05225172 ZINC05225175 ZINC05225381 ZINC05225388 ZINC05225399 ZINC05225403 ZINC05225491 ZINC05225496 ZINC05225500 ZINC05225504 ZINC03096510 ZINC058201'..b'ZINC37632182\t0\n+ZINC37631885\t0\n+ZINC37628972\t0\n+ZINC37628816\t0\n+ZINC34939445\t0\n+ZINC34939444\t0\n+ZINC34327972\t0\n+ZINC33362792\t0\n+ZINC33359474\t0\n+ZINC19387498\t0\n+ZINC19331291\t0\n+ZINC19331287\t0\n+ZINC16159295\t0\n+ZINC16159293\t0\n+ZINC16082659\t0\n+ZINC15771889\t0\n+ZINC14983445\t0\n+ZINC14628482\t0\n+ZINC12480368\t0\n+ZINC12153803\t0\n+ZINC06590260\t0\n+ZINC04721345\t0\n+ZINC04620596\t0\n+ZINC04352993\t0\n+ZINC04284434\t0\n+ZINC04284404\t0\n+ZINC03860745\t0\n+ZINC02585927\t0\n+ZINC02584614\t0\n+ZINC02575364\t0\n+ZINC02572120\t0\n+ZINC02563326\t0\n+ZINC02555213\t0\n+ZINC02170245\t0\n+ZINC02034508\t0\n+ZINC01997857\t0\n+ZINC01997856\t0\n+ZINC01682521\t0\n+ZINC01675291\t0\n+ZINC01657319\t0\n+ZINC01641030\t0\n+ZINC01608901\t0\n+ZINC01594670\t0\n+ZINC01586656\t0\n+ZINC01555332\t0\n+ZINC01439400\t0\n+ZINC00396158\t0\n+ZINC71621196\t0\n+ZINC66381592\t0\n+ZINC63148589\t0\n+ZINC59754680\t0\n+ZINC51074718\t0\n+ZINC51074717\t0\n+ZINC37632186\t0\n+ZINC37629044\t0\n+ZINC36533269\t0\n+ZINC34337607\t0\n+ZINC34337605\t0\n+ZINC34330539\t0\n+ZINC34330538\t0\n+ZINC31414746\t0\n+ZINC26896049\t0\n+ZINC26896046\t0\n+ZINC16138636\t0\n+ZINC16034387\t0\n+ZINC15777627\t0\n+ZINC15115331\t0\n+ZINC12416533\t0\n+ZINC05663502\t0\n+ZINC05576053\t0\n+ZINC05283247\t0\n+ZINC04051396\t0\n+ZINC03875370\t0\n+ZINC03612758\t0\n+ZINC02539354\t0\n+ZINC02390369\t0\n+ZINC02041062\t0\n+ZINC02034873\t0\n+ZINC02030980\t0\n+ZINC01733027\t0\n+ZINC01693132\t0\n+ZINC01684527\t0\n+ZINC01680393\t0\n+ZINC01674462\t0\n+ZINC01609947\t0\n+ZINC01603496\t0\n+ZINC01482803\t0\n+ZINC71617645\t0\n+ZINC71257177\t0\n+ZINC66351573\t0\n+ZINC66351572\t0\n+ZINC64370185\t0\n+ZINC63148423\t0\n+ZINC63146279\t0\n+ZINC53993715\t0\n+ZINC53993714\t0\n+ZINC39242270\t0\n+ZINC39242269\t0\n+ZINC37633669\t0\n+ZINC37633667\t0\n+ZINC37633133\t0\n+ZINC34539501\t0\n+ZINC33753907\t0\n+ZINC32182223\t0\n+ZINC30678251\t0\n+ZINC20475278\t0\n+ZINC19324731\t0\n+ZINC19319501\t0\n+ZINC19166968\t0\n+ZINC14807113\t0\n+ZINC14448389\t0\n+ZINC04984177\t0\n+ZINC04895939\t0\n+ZINC04804787\t0\n+ZINC04775232\t0\n+ZINC04706620\t0\n+ZINC04521315\t0\n+ZINC04261780\t0\n+ZINC03875935\t0\n+ZINC03861020\t0\n+ZINC03140714\t0\n+ZINC02584263\t0\n+ZINC02527961\t0\n+ZINC02168531\t0\n+ZINC01845619\t0\n+ZINC01682053\t0\n+ZINC01680814\t0\n+ZINC01611664\t0\n+ZINC01598156\t0\n+ZINC01586364\t0\n+ZINC01575687\t0\n+ZINC66381590\t0\n+ZINC66377722\t0\n+ZINC57217534\t0\n+ZINC39274309\t0\n+ZINC31938007\t0\n+ZINC06403302\t0\n+ZINC04744395\t0\n+ZINC04742364\t0\n+ZINC04722803\t0\n+ZINC03860254\t0\n+ZINC03070145\t0\n+ZINC01730558\t0\n+ZINC01690285\t0\n+ZINC01621716\t0\n+ZINC71614813\t0\n+ZINC66377720\t0\n+ZINC64370193\t0\n+ZINC39369735\t0\n+ZINC39221831\t0\n+ZINC36720865\t0\n+ZINC32163098\t0\n+ZINC19321044\t0\n+ZINC06734738\t0\n+ZINC05178397\t0\n+ZINC05167654\t0\n+ZINC05157937\t0\n+ZINC04963934\t0\n+ZINC04268917\t0\n+ZINC04097424\t0\n+ZINC03875757\t0\n+ZINC03875372\t0\n+ZINC03860600\t0\n+ZINC02040420\t0\n+ZINC02037807\t0\n+ZINC02037390\t0\n+ZINC02037305\t0\n+ZINC02015871\t0\n+ZINC02004049\t0\n+ZINC01845620\t0\n+ZINC01712063\t0\n+ZINC01702289\t0\n+ZINC01693334\t0\n+ZINC01693329\t0\n+ZINC01648252\t0\n+ZINC01627348\t0\n+ZINC00400095\t0\n+ZINC71647667\t0\n+ZINC57988933\t0\n+ZINC55345805\t0\n+ZINC39278760\t0\n+ZINC25695466\t0\n+ZINC12350099\t0\n+ZINC05650406\t0\n+ZINC05177750\t0\n+ZINC04742917\t0\n+ZINC04722893\t0\n+ZINC03861678\t0\n+ZINC03861677\t0\n+ZINC03860808\t0\n+ZINC02039983\t0\n+ZINC02034592\t0\n+ZINC01845913\t0\n+ZINC01734876\t0\n+ZINC01658753\t0\n+ZINC01648381\t0\n+ZINC01613078\t0\n+ZINC01601383\t0\n+ZINC01577259\t0\n+ZINC38343415\t0\n+ZINC34593547\t0\n+ZINC34115094\t0\n+ZINC33505753\t0\n+ZINC32163202\t0\n+ZINC32163200\t0\n+ZINC13410577\t0\n+ZINC06691140\t0\n+ZINC05158078\t0\n+ZINC05112484\t0\n+ZINC05019026\t0\n+ZINC04899414\t0\n+ZINC04712486\t0\n+ZINC03958467\t0\n+ZINC02036753\t0\n+ZINC01699944\t0\n+ZINC01690289\t0\n+ZINC01585463\t0\n+ZINC24718443\t0\n+ZINC19169386\t0\n+ZINC19167376\t0\n+ZINC05700932\t0\n+ZINC03957736\t0\n+ZINC02388228\t0\n+ZINC02168687\t0\n+ZINC01754610\t0\n+ZINC01677558\t0\n+ZINC01591817\t0\n+ZINC01491944\t0\n+ZINC01439067\t0\n+ZINC00967522\t0\n+ZINC71602724\t0\n+ZINC57989955\t0\n+ZINC40454334\t0\n+ZINC31667387\t0\n+ZINC31297995\t0\n+ZINC15440412\t0\n+ZINC05225679\t0\n+ZINC04658606\t0\n+ZINC01632445\t0\n+ZINC00967532\t0\n+ZINC19324737\t0\n+ZINC19230186\t0\n+ZINC08221057\t0\n+ZINC05224188\t0\n+ZINC01688358\t0\n+ZINC71769114\t0\n+ZINC60272425\t0\n+ZINC01846023\t0\n+ZINC71769112\t0\n+ZINC08214586\t0\n'

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/old.res
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/old.res Thu Aug 15 03:27:06 2013 -0400

b'@@ -0,0 +1,5790 @@\n+#1432 true singletons\n+#1581 false singletons\n+#clusters: 4355\n+ZINC71621761\t1604\tZINC00002687 ZINC00025200 ZINC00025201 ZINC00033574 ZINC00033576 ZINC00050696 ZINC00051186 ZINC00093403 ZINC00093407 ZINC00103395 ZINC00128696 ZINC00135212 ZINC00140739 ZINC00140746 ZINC00153929 ZINC00154430 ZINC00154431 ZINC00154439 ZINC00154441 ZINC00157589 ZINC00158261 ZINC00158393 ZINC00158439 ZINC00159317 ZINC00160268 ZINC00160270 ZINC00201438 ZINC00201439 ZINC00201442 ZINC00332029 ZINC00332032 ZINC00332774 ZINC00336705 ZINC00388102 ZINC00388107 ZINC00388243 ZINC00388912 ZINC00389642 ZINC00389643 ZINC00393998 ZINC00394259 ZINC00394260 ZINC00394261 ZINC00394917 ZINC00407037 ZINC00409877 ZINC00409878 ZINC00500705 ZINC00586785 ZINC00896223 ZINC01055289 ZINC01057001 ZINC01075984 ZINC01075986 ZINC01075987 ZINC01075990 ZINC01233190 ZINC01235041 ZINC01235043 ZINC01235045 ZINC01235046 ZINC01235047 ZINC01235048 ZINC01296023 ZINC01296024 ZINC01296026 ZINC01296039 ZINC01296064 ZINC01296065 ZINC01296077 ZINC01296165 ZINC01296167 ZINC01296263 ZINC01299913 ZINC01299914 ZINC01299915 ZINC01420527 ZINC01433213 ZINC01481910 ZINC01482094 ZINC01482137 ZINC01486612 ZINC01486613 ZINC01504039 ZINC01529080 ZINC01529277 ZINC01530366 ZINC01536989 ZINC01555363 ZINC01556128 ZINC01559667 ZINC01559720 ZINC01562012 ZINC01562014 ZINC01562159 ZINC01570850 ZINC01574316 ZINC01576547 ZINC01576864 ZINC01577159 ZINC01581015 ZINC01581722 ZINC01581723 ZINC01584638 ZINC01585343 ZINC01585344 ZINC01585345 ZINC01585350 ZINC01585353 ZINC01585537 ZINC01587671 ZINC01593180 ZINC01601226 ZINC01609647 ZINC01609650 ZINC01609652 ZINC01609656 ZINC01609756 ZINC01609966 ZINC01611324 ZINC01614479 ZINC01620991 ZINC01621724 ZINC01621741 ZINC01622139 ZINC01622140 ZINC01622141 ZINC01627037 ZINC01627101 ZINC01627245 ZINC01634320 ZINC01640007 ZINC01640941 ZINC01641394 ZINC01646213 ZINC01646411 ZINC01646412 ZINC01646417 ZINC01646418 ZINC01646652 ZINC01648180 ZINC01648181 ZINC01655612 ZINC01657466 ZINC01666118 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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/old.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/old.txt Thu Aug 15 03:27:06 2013 -0400

b'@@ -0,0 +1,13577 @@\n+#6111 true singletons\n+#2168 false singletons\n+#clusters: 7463\n+ZINC71602893\t661\tZINC00158103 ZINC00162386 ZINC00388163 ZINC00393753 ZINC00393754 ZINC00393755 ZINC00393756 ZINC00394761 ZINC00394806 ZINC00394807 ZINC00394808 ZINC00399241 ZINC00404394 ZINC00404395 ZINC00404396 ZINC00406932 ZINC00406933 ZINC00502094 ZINC00507608 ZINC00967511 ZINC00967515 ZINC00967533 ZINC00968099 ZINC00968100 ZINC00968101 ZINC00968128 ZINC00968131 ZINC01057145 ZINC01057147 ZINC01081099 ZINC01081323 ZINC01271111 ZINC01295991 ZINC01297856 ZINC01319163 ZINC01319182 ZINC01420477 ZINC01436122 ZINC01436123 ZINC01436124 ZINC01436125 ZINC01481755 ZINC01482164 ZINC01529247 ZINC01529451 ZINC01529452 ZINC01532735 ZINC01532765 ZINC01555566 ZINC01561953 ZINC01561960 ZINC01562407 ZINC01571243 ZINC01571245 ZINC01571260 ZINC01571261 ZINC01571613 ZINC01574321 ZINC01577208 ZINC01577368 ZINC01577369 ZINC01577370 ZINC01577376 ZINC01586761 ZINC01587612 ZINC01587613 ZINC01587614 ZINC01587683 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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/oldm.res
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/oldm.res Thu Aug 15 03:27:06 2013 -0400

b'@@ -0,0 +1,3952 @@\n+#787 true singletons\n+#1827 false singletons\n+#clusters: 3162\n+ZINC71621761\t2105\tZINC00001592 ZINC00002687 ZINC00025200 ZINC00025201 ZINC00033574 ZINC00033576 ZINC00050696 ZINC00051186 ZINC00074846 ZINC00093403 ZINC00093407 ZINC00103395 ZINC00128696 ZINC00135212 ZINC00140739 ZINC00140746 ZINC00153929 ZINC00154430 ZINC00154431 ZINC00154439 ZINC00154441 ZINC00157259 ZINC00157541 ZINC00157589 ZINC00158261 ZINC00158393 ZINC00158421 ZINC00158439 ZINC00159317 ZINC00160268 ZINC00160270 ZINC00161414 ZINC00173567 ZINC00201438 ZINC00201439 ZINC00201442 ZINC00332029 ZINC00332032 ZINC00332774 ZINC00336705 ZINC00336723 ZINC00388102 ZINC00388107 ZINC00388243 ZINC00388246 ZINC00388248 ZINC00388340 ZINC00388341 ZINC00388342 ZINC00388343 ZINC00388344 ZINC00388346 ZINC00388699 ZINC00388910 ZINC00388912 ZINC00389642 ZINC00389643 ZINC00392996 ZINC00393134 ZINC00393639 ZINC00393998 ZINC00394259 ZINC00394260 ZINC00394261 ZINC00394917 ZINC00399457 ZINC00399458 ZINC00399459 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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/out.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/out.txt Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,5 @@
+#1 true singletons
+#0 false singletons
+#clusters: 1
+b 1 a
+c 0

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/u_new.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/u_new.txt Thu Aug 15 03:27:06 2013 -0400

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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/old/u_old.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/old/u_old.txt Thu Aug 15 03:27:06 2013 -0400

diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/test-data/NxN_Clustering_on_q.svg
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diff -r 000000000000 -r 354d3c6bb894 chemfp_clustering/test-data/Taylor-Butina_Clustering_on_data_q.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_clustering/test-data/Taylor-Butina_Clustering_on_data_q.txt Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,4 @@
+#0 true singletons
+#0 false singletons
+#clusters: 1
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diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/mol2fps.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/mol2fps.xml Thu Aug 15 03:27:06 2013 -0400

[

b'@@ -0,0 +1,276 @@\n+<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0">\n+ <description>with different fingerprint types</description>\n+ <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>\n+ <requirements>\n+ <requirement type="package" version="1.1p1">chemfp</requirement>\n+ <requirement type="package" version="2012_12_1">rdkit</requirement>\n+ <requirement type="package" version="2.3.2">openbabel</requirement>\n+ </requirements>\n+ <command>\n+ #set $fptype = $fp_opts.fp_opts_selector\n+\n+ #if $fptype in [\'--FP2\', \'--FP3\', \'--FP4\', \'--MACCS\']:\n+ ## Open Babel fingerprints\n+ ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}"\n+ #else:\n+ ## RDKit fingerprints\n+ rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"\n+ #if $fp_opts.fp_opts_selector == "--RDK":\n+ --RDK\n+ --fpSize $fp_opts.fpSize\n+ --minPath $fp_opts.minPath\n+ --maxPath $fp_opts.maxPath\n+ --nBitsPerHash $fp_opts.nBitsPerHash\n+ $fp_opts.useHs\n+ #elif $fp_opts.fp_opts_selector == "--torsions":\n+ --torsions\n+ --fpSize $fp_opts.fpSize\n+ --targetSize $fp_opts.targetSize\n+ #elif $fp_opts.fp_opts_selector == "--morgan":\n+ --morgan\n+ --fpSize $fp_opts.fpSize\n+ --radius $fp_opts.radius\n+ $fp_opts.useFeatures\n+ $fp_opts.useChirality\n+ $fp_opts.useBondTypes\n+ #elif $fp_opts.fp_opts_selector == "--pairs":\n+ --paris\n+ --fpSize $fp_opts.fpSize\n+ --minLength $fp_opts.minLength\n+ --maxLength $fp_opts.maxLength\n+ #elif $fp_opts.fp_opts_selector == "--maccs166":\n+ --maccs166\n+ #elif $fp_opts.fp_opts_selector == "--substruct":\n+ --substruct\n+ #end if\n+ #end if\n+ --errors report 2>&1\n+ </command>\n+ <inputs>\n+ <param name="infile" type=\'data\' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>\n+ <conditional name="fp_opts">\n+ <param name="fp_opts_selector" type="select" label="Type of fingerprint">\n+ <option value=\'--FP2\' selected="True">Open Babel FP2 fingerprints</option>\n+ <option value=\'--FP3\'>Open Babel FP3 fingerprints</option>\n+ <option value=\'--FP4\'>Open Babel FP4 fingerprints</option>\n+ <option value=\'--MACCS\'>Open Babel MACCS fingerprints</option>\n+ <option value=\'--RDK\'>RDKit topological fingerprint</option>\n+ <option value=\'--torsions\'>RDKit topological Torsion fingerprints</option>\n+ <option value=\'--morgan\'>RDKit Morgan fingerprints</option>\n+ <option value=\'--pairs\'>RDKit Atom Pair fingerprints</option>\n+ <option value=\'--maccs166\'>RDKit MACCS fingerprints</option>\n+ <option value=\'--substruct\'>RDKit substructure fingerprints</option>\n+ </param>\n+ <when value="--FP2" />\n+ <when value="--FP3" />\n+ <when value="--FP4" />\n+ <when value="--MACCS" />\n+ <when value="--RDK">\n+ <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">\n+ <validator type="in_range" min="1" />\n+ </param>\n+ <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">\n+ <validator type="in_range" min="1" />\n+ </param>\n+ <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the s'..b'm name="infile" value="CID_2244.smi" ftype="smi" />\n+ <param name="fp_opts.fp_opts_selector" value="--FP3" />\n+ <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />\n+ </test>\n+ \n+ <test>\n+ <param name="infile" value="CID_2244.sdf" ftype="sdf" />\n+ <param name="fp_opts.fp_opts_selector" value="--FP4" />\n+ <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />\n+ </test>\n+ <test>\n+ <param name="infile" value="CID_2244.smi" ftype="smi" />\n+ <param name="fp_opts.fp_opts_selector" value="--FP4" />\n+ <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />\n+ </test>\n+ \n+ <test>\n+ <param name="infile" value="CID_2244.sdf" ftype="sdf" />\n+ <param name="fp_opts.fp_opts_selector" value="--MACCS" />\n+ <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />\n+ </test>\n+ <test>\n+ <param name="infile" value="CID_2244.smi" ftype="smi" />\n+ <param name="fp_opts.fp_opts_selector" value="--MACCS" />\n+ <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />\n+ </test>\n+ </tests>\n+ <help>\n+\n+.. class:: infomark\n+\n+**What this tool does**\n+\n+This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_.\n+\n+For more information check the websites listed below::\n+\n+\t- http://code.google.com/p/rdkit/wiki/FingerprintsInTheRDKit\n+\t- http://openbabel.org/wiki/Tutorial:Fingerprints\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+FPS fingerprint file format\n+\n+* Example::\n+\t\n+\t - SDF File\n+\n+\t\t28434379\n+\t\t -OEChem-02031205132D\n+\n+\t\t 37 39 0 0 0 0 0 0 0999 V2000\n+\t\t 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+\t\t 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+\t\t 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+\t\t 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+\t\t 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+\t\t 7.3704 0.9433 0.0000 C 0 0 0 0 \n+\t\t ......\n+\t\t 1 15 1 0 0 0 0\n+\t\t 1 35 1 0 0 0 0\n+\t\t 2 5 1 0 0 0 0\n+\t\t 2 11 1 0 0 0 0\n+\t\t 2 12 1 0 0 0 0\n+\t\t 3 12 2 0 0 0 0\n+\t\t 3 13 1 0 0 0 0\n+\t\t 4 18 1 0 0 0 0\n+\t\t ......\n+\n+\t\t\t>PUBCHEM_COMPOUND_CID<\n+\t\t\t28434379\n+\n+\t\t\t> <PUBCHEM_COMPOUND_CANONICALIZED>\n+\t\t\t1\n+\n+\t\t\t> <PUBCHEM_CACTVS_COMPLEXITY>\n+\t\t\t280\n+\n+\t\t\t> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>\n+\t\t\t2\n+\n+\t\t\t> <PUBCHEM_CACTVS_HBOND_DONOR>\n+\t\t\t2\n+\n+\t\t\t> <PUBCHEM_CACTVS_ROTATABLE_BOND>\n+\t\t\t2\n+\n+\t\t\t> <PUBCHEM_CACTVS_SUBSKEYS>\n+\t\t\tAAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==\n+\n+\t\t\t>\n+\n+\t\t- type : FP2\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+* Example::\n+\n+\t#FPS1\n+\t#num_bits=1021\n+\t#type=OpenBabel-FP2/1\n+\t#software=OpenBabel/2.3.0\n+\t#source=/tmp/dataset_409.dat.sdf\n+\t#date=2012-02-03T11:13:39\n+\tc0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c\n+\t0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300\n+\t10000000000080000000c0000060000c0000060810000010000000800102000000\t28434379\n+\n+-----\n+\n+.. class:: infomark\n+\n+**Cite**\n+\n+| `Open Babel`_ \n+| RDKit_ project \n+| chemfp_ project.\n+| \n+| N M O\'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison. `Open Babel: An open chemical toolbox.`_\n+\n+.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33\n+.. _OpenEye: http://www.eyesopen.com/\n+.. _chemfp: http://chemfp.com/\n+.. _RDKit: http://www.rdkit.org/\n+.. _`Open Babel`: http://openbabel.org/\n+\n+\n+ </help>\n+</tool>\n'

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244.can
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244.can Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,1 @@
+CC(=O)Oc1ccccc1C(=O)O 2244

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244.inchi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244.inchi Thu Aug 15 03:27:06 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)

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244.sdf Thu Aug 15 03:27:06 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
+
+$$$$
+

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244.smi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244.smi Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,1 @@
+O(c1c(cccc1)C(=O)O)C(=O)C 2244

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244_FP2.fps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244_FP2.fps Thu Aug 15 03:27:06 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

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244_FP3.fps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244_FP3.fps Thu Aug 15 03:27:06 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

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244_FP4.fps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244_FP4.fps Thu Aug 15 03:27:06 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

diff -r 000000000000 -r 354d3c6bb894 chemfp_mol2fps/test-data/CID_2244_maccs.fps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_mol2fps/test-data/CID_2244_maccs.fps Thu Aug 15 03:27:06 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

diff -r 000000000000 -r 354d3c6bb894 chemfp_sdf2fps/sdf2fps.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_sdf2fps/sdf2fps.xml Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,115 @@
+<tool id="ctb_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>
+        <requirement type="package" version="2.3.2">openbabel</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>
+
+.. class:: infomark
+
+**What this tool does**
+
+Read an input SD file, extract the fingerprints and store them in a FPS-file.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+`SD-Format`_
+
+.. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file
+
+* Example::
+
+ 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
+   ......
+
+ >PUBCHEM_COMPOUND_CID<
+ 28434379
+
+ > <PUBCHEM_COMPOUND_CANONICALIZED>
+ 1
+
+ > <PUBCHEM_CACTVS_COMPLEXITY>
+ 280
+
+ > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
+ 2
+
+ > <PUBCHEM_CACTVS_HBOND_DONOR>
+ 2
+
+ > <PUBCHEM_CACTVS_ROTATABLE_BOND>
+ 2
+
+ > <PUBCHEM_CACTVS_SUBSKEYS>
+ AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+ >
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+ #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
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+chemfp_ project
+
+.. _chemfp: http://chemfp.com/
+
+
+    </help>
+</tool>

diff -r 000000000000 -r 354d3c6bb894 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format) and the python numpy package.">
+ <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>

diff -r 000000000000 -r 354d3c6bb894 static/images/NxN_clustering.png

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diff -r 000000000000 -r 354d3c6bb894 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Aug 15 03:27:06 2013 -0400

@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="rdkit" version="2012_12_1">
+        <repository changeset_revision="7c60f011c70c" name="package_rdkit_2012_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.7.1">
+        <repository changeset_revision="74c21f9bdc39" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.2.1">
+        <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="chemfp" version="1.1p1">
+        <repository changeset_revision="f2676c09c535" name="package_chemfp_1_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.12.0">
+        <repository changeset_revision="aa5180c893f5" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="openbabel" version="2.3.2">
+        <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>