changeset 34:72e0a9fd6abc draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/simsearch commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:36:37 -0400
parents 73b8c87779ae
children a9fd0995b5bf
files butina_clustering.py butina_clustering.xml mol2fps.xml nxn_clustering.py nxn_clustering.xml sdf2fps.xml simsearch.xml static/images/NxN_clustering.png static/images/NxN_clustering.svg test-data/CID_2244.can test-data/CID_2244.inchi test-data/CID_2244.sdf test-data/CID_2244.smi test-data/CID_2244_FP2.fps test-data/CID_2244_FP3.fps test-data/CID_2244_FP4.fps test-data/CID_2244_MACCS.fps test-data/CID_2244_maccs.fps test-data/NxN_Clustering_on_q.svg test-data/Taylor-Butina_Clustering_on_data_q.txt test-data/sdf2fps_result1.fps test-data/simsearch_on_tragets_and_q.tabular
diffstat 22 files changed, 140 insertions(+), 4004 deletions(-) [+]
line wrap: on
line diff
--- a/butina_clustering.py	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-#!/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 )
--- a/butina_clustering.xml	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<tool id="ctb_chemfp_butina_clustering" name="Taylor-Butina Clustering" version="0.2">
-    <description>of molecular fingerprints</description>
-    <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
-    </requirements>
-    <command detect_errors="exit_code">
-<![CDATA[
-        python '$__tool_directory__/butina_clustering.py'
-            -i '$infile'
-            -t $threshold
-            -o '$outfile'
-            -p \${GALAXY_SLOTS:-1}
-]]>
-    </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"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="infile" ftype="fps" value="targets.fps"/>
-            <param name='threshold' value='0.8' ></param>
-            <output name="outfile" ftype="tabular"  file='Taylor-Butina_Clustering_on_data_q.txt'/>
-        </test>
-    </tests>
-<help>
-<![CDATA[
-
-
-.. 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
-
-
-]]>
- </help>
-    <citations>
-        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
-    </citations>
-</tool>
--- a/mol2fps.xml	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,276 +0,0 @@
-<tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0">
-    <description>with different fingerprint types</description>
-    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
-    <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2016.03.3">rdkit</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-        #set $fptype = $fp_opts.fp_opts_selector
-
-        #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
-            ## Open Babel fingerprints
-            ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}'
-        #else:
-            ## RDKit fingerprints
-            rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}'
-            #if $fp_opts.fp_opts_selector == "--RDK":
-                --RDK
-                --fpSize $fp_opts.fpSize
-                --minPath $fp_opts.minPath
-                --maxPath $fp_opts.maxPath
-                --nBitsPerHash $fp_opts.nBitsPerHash
-                $fp_opts.useHs
-            #elif $fp_opts.fp_opts_selector == "--torsions":
-                --torsions
-                --fpSize $fp_opts.fpSize
-                --targetSize $fp_opts.targetSize
-            #elif $fp_opts.fp_opts_selector == "--morgan":
-                --morgan
-                --fpSize $fp_opts.fpSize
-                --radius $fp_opts.radius
-                $fp_opts.useFeatures
-                $fp_opts.useChirality
-                $fp_opts.useBondTypes
-            #elif $fp_opts.fp_opts_selector == "--pairs":
-                --paris
-                --fpSize $fp_opts.fpSize
-                --minLength $fp_opts.minLength
-                --maxLength $fp_opts.maxLength
-            #elif $fp_opts.fp_opts_selector == "--maccs166":
-                --maccs166
-            #elif $fp_opts.fp_opts_selector == "--substruct":
-                --substruct
-            #end if
-        #end if
-        --errors report 2>&1
-]]>
-    </command>
-    <inputs>
-        <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
-        <conditional name="fp_opts">
-            <param name="fp_opts_selector" type="select" label="Type of fingerprint">
-                <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
-                <option value='--FP3'>Open Babel FP3 fingerprints</option>
-                <option value='--FP4'>Open Babel FP4 fingerprints</option>
-                <option value='--MACCS'>Open Babel MACCS fingerprints</option>
-                <option value='--RDK'>RDKit topological fingerprint</option>
-                <option value='--torsions'>RDKit topological Torsion fingerprints</option>
-                <option value='--morgan'>RDKit Morgan fingerprints</option>
-                <option value='--pairs'>RDKit Atom Pair fingerprints</option>
-                <option value='--maccs166'>RDKit MACCS fingerprints</option>
-                <option value='--substruct'>RDKit substructure fingerprints</option>
-            </param>
-            <when value="--FP2" />
-            <when value="--FP3" />
-            <when value="--FP4" />
-            <when value="--MACCS" />
-            <when value="--RDK">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" 
-                    label="include information about the number of hydrogens on each atom" />
-            </when>
-            <when value="--torsions">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-            </when>
-            <when value="--morgan">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false"
-                    label="include information about the number of hydrogens on each atom" />
-                <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false"
-                    label="include information about the number of hydrogens on each atom" />
-                <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true"
-                    label="include information about the number of hydrogens on each atom" />
-            </when>
-            <when value="--pairs">
-                <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-                <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
-                    <validator type="in_range" min="1" />
-                </param>
-            </when>
-            <when value="--maccs166" />
-            <when value="--substruct" />
-        </conditional>
-
-    </inputs>
-    <outputs>
-        <data name="outfile" format="fps" />
-    </outputs>
-    <tests>
-        <!-- FP2 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fp_opts.fp_opts_selector" value="--FP2" />
-            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fp_opts.fp_opts_selector" value="--FP2" />
-            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <!-- FP3 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fp_opts.fp_opts_selector" value="--FP3" />
-            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fp_opts.fp_opts_selector" value="--FP3" />
-            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <!-- FP4 -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fp_opts.fp_opts_selector" value="--FP4" />
-            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fp_opts.fp_opts_selector" value="--FP4" />
-            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <!-- MACCS -->
-        <test>
-            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
-            <param name="fp_opts.fp_opts_selector" value="--MACCS" />
-            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
-        </test>
-        <test>
-            <param name="infile" value="CID_2244.smi" ftype="smi" />
-            <param name="fp_opts.fp_opts_selector" value="--MACCS" />
-            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-
-.. class:: infomark
-
-**What this tool does**
-
-This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_.
-
-For more information check the websites listed below::
-
-	- http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
-	- http://openbabel.org/wiki/Tutorial:Fingerprints
-
------
-
-.. class:: infomark
-
-**Input**
-
-FPS fingerprint file format
-
-* Example::
-
-	      - 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
-		  ......
-
-			>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==
-
-			>
-
-		- type : FP2
-
------
-
-.. class:: infomark
-
-**Output**
-
-* Example::
-
-	#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>
-    <citations>
-        <citation type="doi">10.1186/1758-2946-3-33</citation>
-        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
-        <citation type="bibtex">
-            @electronic{rdkit,
-                title = {RDKit: Open-source cheminformatics},
-                url ={http://www.rdkit.org}
-            }
-        </citation>
-    </citations>
-</tool>
--- a/nxn_clustering.py	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-#!/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 )
-
--- a/nxn_clustering.xml	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +0,0 @@
-<tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4">
-    <description>of molecular fingerprints</description>
-    <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2">python</requirement>
-        <requirement type="package" version="2.0.2">matplotlib</requirement>
-        <requirement type="package" version="0.19.0">scipy</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
-    </requirements>
-    <command detect_errors="exit_code">
-<![CDATA[
-        python '$__tool_directory__/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" 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="targets.fps" />
-            <param name='treshold' value='0.75' />
-            <param name='oformat' value='svg' />
-            <param name='output_files' value='image' />
-            <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/>
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-
-.. 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:: $PATH_TO_IMAGES/NxN_clustering.png
-
-
-]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
-    </citations>
-</tool>
--- a/sdf2fps.xml	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2">
-    <description>extract fingerprints from sdf files metadata</description>
-    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
-    <requirements>
-        <requirement type="package" version="1.1p1">chemfp</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-        sdf2fps --pubchem '${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>
-        <test>
-            <param name="infile" ftype="sdf" value="CID_2244.sdf" />
-            <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-
-.. 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
-
-
-]]>
-    </help>
-    <citations>
-        <citation type="doi">10.1186/1758-2946-5-S1-P36</citation>
-    </citations>
-</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/simsearch.xml	Sat May 20 08:36:37 2017 -0400
@@ -0,0 +1,131 @@
+<tool id="ctb_simsearch" name="Similarity Search" version="0.1.1">
+    <description>of fingerprint data sets</description>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+        #if $method_opts.method_opts_selector == "chemfp":
+            ln -s "${method_opts.query_opts.targets}" ./targets.fps &&
+            #if $method_opts.query_opts.query_opts_selector == "normal":
+                ln -s "${method_opts.query_opts.query}" ./query.fps &&
+            #end if
+
+            simsearch
+                #if int($method_opts.knn) == 0:
+                    #set $k = 'all'
+                    ## count is only available if k nearest neighbor search is disabled
+                    $method_opts.counts
+                #else:
+                    #set $k = int($method_opts.knn)
+                #end if
+
+                -k $k
+                --threshold $method_opts.threshold
+                -o ./output.fps
+
+                ## build and search an in-memory data structure (faster for multiple queries)
+                --memory
+
+                #if $method_opts.query_opts.query_opts_selector == "normal":
+                    -q ./query.fps
+                #else:
+                    --NxN
+                #end if
+
+                ./targets.fps
+                &&
+                mv ./output.fps "${outfile}"
+        #else:
+            ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
+            ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
+            ## A workaround is to create a symlink with a proper file-extension.
+            #import tempfile
+            #set $temp_file = tempfile.NamedTemporaryFile()
+            #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
+            $temp_file.close()
+            ln -s $method_opts.query $temp_link;
+            obabel -i fs "${os.path.join($method_opts.fastsearch.files_path,'molecule.fs')}" -S "${temp_link}" -at${method_opts.threshold} -O "${outfile}" -osmi -aa 2>&1;
+            rm $temp_link
+        #end if
+]]>
+    </command>
+    <inputs>
+
+        <conditional name="method_opts">
+            <param name="method_opts_selector" type="select" label="Subject database/sequences">
+              <option value="chemfp">Chemfp fingerprint file</option>
+              <option value="obabel">OpenBabel Fastsearch Index</option>
+            </param>
+            <when value="chemfp">
+                <conditional name="query_opts">
+                    <param name="query_opts_selector" type="select" label="Query Mode">
+                      <option value="normal">Query molecules are stores in a separate file</option>
+                      <option value="nxn">Target molecules are also queries (NxN)</option>
+                    </param>
+                    <when value="normal">
+                        <param name='query' type='data' format="fps" label='Query molecules'/>
+                        <param name='targets' type='data' format="fps" label='Target molecules'/>
+                    </when>
+                    <when value="nxn">
+                        <param name='targets' type='data' format="fps" label='Target moleculs'/>
+                    </when>
+                </conditional>
+                <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
+                   <validator type="in_range" min="0" />
+                </param>
+                <param name='threshold' type='float' value='0.7' label='threshold' />
+                <param name="counts" type="boolean" truevalue="-c" falsevalue="" checked="false" label="report counts (-c)" help="Is ignored if k nearest neighbor search is enabled" />
+            </when>
+            <when value="obabel">
+                <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
+                <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
+                <param name="threshold" type='float' label="threshold" value='0.7'/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="targets" ftype="fps" value="targets.fps"/>
+            <param name="query" ftype="fps" value="q.fps"/>
+            <param name="k" value='4'/>
+            <param name="th" value='0.7'/>
+            <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+
+.. class:: infomark
+
+**What this tool does**
+
+Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
+
+.. _chemfp: http://chemfp.com/
+.. _FastSearch: http://openbabel.org/wiki/FastSearch
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+| The chemfp_ project
+|
+| N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison - `Open Babel: An open chemical toolbox`_
+
+.. _`Open Babel: An open chemical toolbox`: http://www.jcheminf.com/content/3/1/33
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
+    </citations>
+</tool>
Binary file static/images/NxN_clustering.png has changed
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-     <g id="line2d_14">
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-       <use style="stroke:#000000;stroke-linecap:butt;stroke-width:0.5;" x="518.4" xlink:href="#m0d5b0a6425" y="83.0159827526"/>
-      </g>
-     </g>
-     <g id="text_86">
-      <!-- 1.2 -->
-      <g transform="translate(51.43625 87.4691077526)scale(0.12 -0.12)">
-       <use xlink:href="#BitstreamVeraSans-Roman-31"/>
-       <use x="63.623046875" xlink:href="#BitstreamVeraSans-Roman-2e"/>
-       <use x="95.41015625" xlink:href="#BitstreamVeraSans-Roman-32"/>
-      </g>
-     </g>
-    </g>
-   </g>
-   <g id="patch_3">
-    <path d="
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-   </g>
-   <g id="patch_4">
-    <path d="
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-    <path d="
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-   </g>
-   <g id="patch_6">
-    <path d="
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- <defs>
-  <clipPath id="p7ff5b81e1d">
-   <rect height="345.6" width="446.4" x="72.0" y="43.2"/>
-  </clipPath>
- </defs>
-</svg>
--- a/test-data/CID_2244.can	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-CC(=O)Oc1ccccc1C(=O)O	2244
--- a/test-data/CID_2244.inchi	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
--- a/test-data/CID_2244.sdf	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,154 +0,0 @@
-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
-
-$$$$
--- a/test-data/CID_2244.smi	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-O(c1c(cccc1)C(=O)O)C(=O)C	2244
--- a/test-data/CID_2244_FP2.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#FPS1
-#num_bits=1021
-#type=OpenBabel-FP2/1
-#software=OpenBabel/2.4.1
-#source=/tmp/tmptaAke4/files/000/dataset_3.dat
-#date=2017-05-19T13:52:59
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--- a/test-data/CID_2244_FP3.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#FPS1
-#num_bits=1021
-#type=OpenBabel-FP2/1
-#software=OpenBabel/2.4.1
-#source=/tmp/tmptaAke4/files/000/dataset_7.dat
-#date=2017-05-19T13:53:45
-00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004	2244
--- a/test-data/CID_2244_FP4.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#FPS1
-#num_bits=1021
-#type=OpenBabel-FP2/1
-#software=OpenBabel/2.4.1
-#source=/tmp/tmptaAke4/files/000/dataset_11.dat
-#date=2017-05-19T13:54:39
-00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004	2244
--- a/test-data/CID_2244_MACCS.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#FPS1
-#num_bits=1021
-#type=OpenBabel-FP2/1
-#software=OpenBabel/2.4.1
-#source=/tmp/tmptaAke4/files/000/dataset_15.dat
-#date=2017-05-19T13:55:30
-00000010004000c00000020000030000010000000008000000000080000000000400400000000010200a020800000000000042000000000000800002000002000c200800010001010000000002808002208000400000000040080000000100000008000000000002004002000010000000020100080100200808000000000004	2244
--- a/test-data/CID_2244_maccs.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#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
--- a/test-data/NxN_Clustering_on_q.svg	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,707 +0,0 @@
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--- a/test-data/Taylor-Butina_Clustering_on_data_q.txt	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#0 true singletons
-#0 false singletons
-#clusters: 1
-55091752	12	6499094 6485578 55079807 3153534 55102353 55091466 55091416 6485577 55169009 55091467 55168823 55091849
--- a/test-data/sdf2fps_result1.fps	Sat May 20 08:31:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#FPS1
-#num_bits=881
-#type=CACTVS-E_SCREEN/1.0 extended=2
-#software=CACTVS/unknown
-#source=/tmp/tmpN2w37z/files/000/dataset_1.dat
-#date=2017-05-19T14:27:41
-030e1c000000000000000000000000000000000000000c00000000000000008000000058000010000030200119004c70010060001140044b100040100024040010118060101330e46c21ac5841de06a50788109de11113047100000000001000000000000000080000000000000000	2244
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simsearch_on_tragets_and_q.tabular	Sat May 20 08:36:37 2017 -0400
@@ -0,0 +1,9 @@
+#Simsearch/1
+#num_bits=881
+#type=Tanimoto k=all threshold=0.7
+#software=chemfp/1.1p1
+#queries=./query.fps
+#targets=./targets.fps
+#query_sources=CID_28434379.sdf
+#target_sources=Desktop/3579363516810334491.sdf
+13	28434379	6499094	0.9615	6485578	0.9679	55079807	0.9313	3153534	0.9557	55102353	0.9682	55091466	0.9682	55091416	0.9682	6485577	0.9497	55169009	0.9560	55091752	0.9684	55091467	0.9623	55168823	0.9563	55091849	0.9563