changeset 0:b760f006cb6b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author bgruening
date Tue, 21 Jul 2020 05:24:46 -0400
parents
children 46fe89ea20ef
files macros.xml o3dalign.xml test-data/Kinase_inhibs.sdf test-data/XChemReactionMaker1.sdf test-data/cluster_butina_matrix_output1.tsv test-data/cluster_butina_output1.sdf test-data/constrained_conf_gen_output1.sdf test-data/dhfr_3d.sdf test-data/hits-17.sdf test-data/pbf_ev_output1.sdf test-data/poses.sdf test-data/pyrimethamine.mol test-data/ref_mol.sdf test-data/rxn_maker_output1.sdf test-data/screen_output1.sdf test-data/screen_output2.sdf test-data/sdf-aliphatic-primary-amines-175.sdf test-data/standardize_output1.sdf test-data/standardize_output2.sdf test-data/sulfonyl_chloride.sdf
diffstat 20 files changed, 271066 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,37 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.1.3</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">im-pipelines</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="input">
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format"/>
+    </xml>
+
+    <xml name="outputs" token_output_format="sdf" token_filetype="sdf">
+        <outputs>
+            <data name="outfile" format="@FILETYPE@" label="Output (@FILETYPE@) for ${tool.name}" from_work_dir="outp.@OUTPUT_FORMAT@"/>
+            <data name="logfile" format="txt" label="Logfile for ${tool.name}"/>
+        </outputs>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{rdkit,
+                    author = {Greg Landrum and others},
+                    title = {RDKit: Open-source cheminformatics},
+                    url = {http://www.rdkit.org}
+            }</citation>
+            <citation type="bibtex">
+                @article{im-pipelines,
+                    author = {Tim Dudgeon and others},
+                    title = {InformaticsMatters pipeline components for cheminformatics and computational chemistry.},
+                    url = {https://github.com/InformaticsMatters/pipelines}
+            }</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/o3dalign.xml	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,103 @@
+<tool id="ctb_im_o3dalign" name="Open 3D Align" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>with RDKit</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s $molquery ./molquery.sdf &&
+        o3dAlign
+            ./molquery.sdf  ##positional arg
+            -i '$infile'
+            -if sdf
+            --qmolidx '$qmolidx'
+            $crippen
+            -n '$number'
+            -t '$threshold'
+            -a '$attempts'
+            -r '$rmsd'
+            -e '$emin'
+            --meta
+            -of sdf
+            -o outp &>> $logfile &&
+        cat outp_metrics.txt &>> $logfile &&
+        gzip -d outp.sdf.gz
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+        <param name="molquery" type="data" format="sdf,mol" label="Mol query file" help="Mol file to align against"/>
+        <param name="qmolidx" type="integer" value="1" label="Query molecule index" help="Query molecule index in SD-file if not the first"/>
+        <param name="threshold" type="float" min="0" value="1" label="Threshold" help="Score cutoff relative to alignment of query to itself"/>
+        <param name="number" type="integer" value="0" label="Number of conformers" help="Number of conformers to generate, if 0 then input structures are assumed to already be)"/>
+        <param name="rmsd" type="float" min="0" value="1.0" label="RMSD Threshold" help="Prune RMSD threshold for excluding conformers"/>
+        <param name="attempts" type="integer" min="0" value="0" label="Number of attempts" help="If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up."/>
+        <param name="emin" type="integer" value="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/>
+        <param name="crippen" type="boolean" label="Crippen" truevalue="--crippen" falsevalue="" help="Use Crippen (logP) contributions"/>
+    </inputs>
+    
+    <expand macro="outputs" />
+    
+    <tests>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
+            <param name="threshold" value="30" />
+            <param name="number" value="2" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Perfect score: 0.0 134.34 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
+            <param name="threshold" value="30" />
+            <param name="number" value="2" />
+            <param name="crippen" value="--crippen" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Perfect score: 0.0 114.13359999999997 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Aligns molecules using RDKit's Open 3D Align.
+
+.. class:: infomark
+
+**Input**
+
+| - Input file in `SDF Format`_
+
+.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file of aligned compounds.
+
+]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Kinase_inhibs.sdf	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,2823 @@
+
+  SciTegic01171120562D
+
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+M  END
+> <mr_id>
+4358263
+
+> <SMI>
+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
+
+$$$$
+
+  SciTegic01171120562D
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+M  END
+> <mr_id>
+8573
+
+> <SMI>
+CO[C@@H]1[C@@H](C[C@H]2O[C@]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
+
+$$$$
+
+  SciTegic01171120562D
+
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+M  END
+> <mr_id>
+4027
+
+> <SMI>
+Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1
+
+$$$$
+
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+M  END
+> <mr_id>
+600
+
+> <SMI>
+CC[C@H](CO)Nc1nc(NCc2ccccc2)c3ncn(C(C)C)c3n1
+
+$$$$
+
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+M  END
+> <mr_id>
+8393
+
+> <SMI>
+Oc1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 27 30  0  0  0  0            999 V2000
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+    2.5973   -1.5031    0.0000 S   0  0
+    2.5956   -2.7031    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 C   0  0
+   -2.5987    1.5004    0.0000 C   0  0
+   -2.7390    2.9810    0.0000 N   0  0
+   -4.2067    3.2905    0.0000 C   0  0
+   -4.9546    1.9903    0.0000 C   0  0
+   -3.9492    0.8772    0.0000 N   0  0
+   -6.4469    1.8311    0.0000 C   0  0
+   -7.4153    2.9701    0.0000 C   0  0
+   -8.8906    2.6991    0.0000 C   0  0
+   -9.3937    1.2860    0.0000 N   0  0
+   -8.4213    0.1438    0.0000 C   0  0
+   -6.9460    0.4147    0.0000 C   0  0
+   -4.8193    4.6606    0.0000 C   0  0
+   -4.0353    5.9336    0.0000 C   0  0
+   -4.7489    7.2530    0.0000 C   0  0
+   -6.2483    7.2947    0.0000 C   0  0
+   -6.8192    8.3502    0.0000 F   0  0
+   -7.0341    6.0170    0.0000 C   0  0
+   -6.3205    4.6976    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
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+  8  9  1  0
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+ 24 26  2  0
+ 26 27  1  0
+ 21 27  2  0
+M  END
+> <mr_id>
+3250
+
+> <SMI>
+CS(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 29 33  0  0  0  0            999 V2000
+  -12.5295    0.6317    0.0000 N   0  0
+  -11.9608    1.6884    0.0000 C   0  0
+  -12.5918    2.7091    0.0000 O   0  0
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+   -9.6699    0.4580    0.0000 C   0  0
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+   -5.9730    1.9836    0.0000 C   0  0
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+   -3.7580    2.9756    0.0000 C   0  0
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+   -1.1867    3.6217    0.0000 C   0  0
+   -0.1511    4.7069    0.0000 C   0  0
+   -0.5731    6.1463    0.0000 C   0  0
+   -2.0307    6.5006    0.0000 C   0  0
+   -3.0662    5.4154    0.0000 N   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 O   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    1.7138    1.2033    0.0000 O   0  0
+    0.2917    0.7475    0.0000 C   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  1  0
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+  8  9  1  0
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+ 24 28  2  0
+ 28 29  1  0
+ 21 29  2  0
+M  END
+> <mr_id>
+4347423
+
+> <SMI>
+NC(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccccn3)c4ccc5OCOc5c4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 32 34  0  0  0  0            999 V2000
+    3.6331   -3.6060    0.0000 C   0  0
+    2.5951   -3.0039    0.0000 N   0  0
+    2.5973   -1.5031    0.0000 C   0  0
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+    0.0000    1.5000    0.0000 C   0  0
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+   -2.6108    5.9949    0.0000 C   0  0
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+   -9.0969    3.7133    0.0000 C   0  0
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+   -3.9021    3.7404    0.0000 C   0  0
+   -2.6005    2.9949    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 N   0  0
+  1  2  1  0
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+  5 32  2  0
+M  END
+> <mr_id>
+4255941
+
+> <SMI>
+CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 35 42  0  0  1  0            999 V2000
+   -1.9455    5.8387    0.0000 C   0  0
+   -2.5513    4.8029    0.0000 N   0  0
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+    1.4900    0.5400    0.0000 N   0  0
+    1.4500   -0.7600    0.0000 C   0  0
+    0.2400   -1.4400    0.0000 C   0  0
+  1  2  1  0
+  3  2  1  6
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+ 19 35  2  0
+M  END
+> <mr_id>
+66
+
+> <SMI>
+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35
+
+$$$$
+
+  SciTegic01171120562D
+
+ 32 35  0  0  1  0            999 V2000
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+  1  2  1  0
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+ 27 32  1  0
+M  END
+> <mr_id>
+4362206
+
+> <SMI>
+Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 33 37  0  0  0  0            999 V2000
+    2.3383   -1.3500    0.0000 C   0  0
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+   -6.4894   -0.7597    0.0000 C   0  0
+   -7.7846   -1.5163    0.0000 C   0  0
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+   -5.8923   -8.7147    0.0000 C   0  0
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+   -5.1866   -1.5032    0.0000 C   0  0
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+  1  2  1  0
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+  8 33  2  0
+M  END
+> <mr_id>
+4270681
+
+> <SMI>
+CN1CCN(CC1)c2cc(Nc3cc(C)n[nH]3)nc(Sc4ccc(NC(=O)C5CC5)cc4)n2
+
+$$$$
+
+  SciTegic01171120562D
+
+ 28 31  0  0  0  0            999 V2000
+   -3.8915    7.2028    0.0000 F   0  0
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+   -3.9067    3.0027    0.0000 C   0  0
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+   -1.2964   -1.4973    0.0000 C   0  0
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+    1.2964   -2.9980    0.0000 C   0  0
+    2.5942   -3.7503    0.0000 C   0  0
+    3.6345   -3.1520    0.0000 Cl  0  0
+    2.5918   -5.2503    0.0000 C   0  0
+    1.2915   -5.9981    0.0000 C   0  0
+   -0.0063   -5.2460    0.0000 C   0  0
+   -0.0038   -3.7460    0.0000 C   0  0
+   -1.0421   -3.1443    0.0000 Cl  0  0
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+    3.6321   -1.3486    0.0000 O   0  0
+    2.5929    0.7486    0.0000 N   0  0
+    1.2964    1.4973    0.0000 C   0  0
+    0.0000    0.7486    0.0000 N   0  0
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+   -5.2030    3.7575    0.0000 C   0  0
+   -6.2444    3.1613    0.0000 F   0  0
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+  1  2  1  0
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+  2 28  2  0
+M  END
+> <mr_id>
+13932
+
+> <SMI>
+Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 30 33  0  0  0  0            999 V2000
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+    0.0000   -0.7486    0.0000 C   0  0
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+   -5.2047   -5.2560    0.0000 C   0  0
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+   -7.8030   -3.7564    0.0000 C   0  0
+   -6.5041   -3.0062    0.0000 C   0  0
+  1  2  1  0
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+  3  4  1  0
+  4  5  2  0
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+ 24 30  1  0
+M  END
+> <mr_id>
+13669
+
+> <SMI>
+COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC4CCN(C)CC4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 28 31  0  0  0  0            999 V2000
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+    1.7138   -1.2033    0.0000 N   0  0
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+    0.2917    0.7475    0.0000 C   0  0
+   -4.9291    9.7428    0.0000 C   0  0
+  1  2  1  0
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+  2 28  2  0
+M  END
+> <mr_id>
+4343227
+
+> <SMI>
+Cc1ccc(F)c(NC(=O)Nc2ccc(cc2)c3cccc4[nH]nc(N)c34)c1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 28 31  0  0  0  0            999 V2000
+    0.9024   -2.0874    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 C   0  0
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+   -1.0028   -1.5132    0.0000 C   0  0
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+  1  2  1  0
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+  2 28  1  0
+M  END
+> <mr_id>
+4309480
+
+> <SMI>
+CC1(C)CNc2cc(NC(=O)c3cccnc3NCc4ccncc4)ccc21
+
+$$$$
+
+  SciTegic01171120562D
+
+ 38 41  0  0  0  0            999 V2000
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+  1  2  1  0
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+  3 38  1  0
+M  END
+> <mr_id>
+4210240
+
+> <SMI>
+CCN1CCN(Cc2ccc(NC(=O)Nc3ccc(Oc4cc(NC)ncn4)cc3)cc2C(F)(F)F)CC1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 37 40  0  0  0  0            999 V2000
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+ 11 37  2  0
+M  END
+> <mr_id>
+4345887
+
+> <SMI>
+CCN(CCO)CCCOc1ccc2c(Nc3cc(CC(=O)Nc4cccc(F)c4)[nH]n3)ncnc2c1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 39 43  0  0  0  0            999 V2000
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+ 36 39  1  0
+M  END
+> <mr_id>
+7815
+
+> <SMI>
+Cc1ccc(cc1)n2nc(cc2NC(=O)Nc3ccc(OCCN4CCOCC4)c5ccccc35)C(C)(C)C
+
+$$$$
+
+  SciTegic01171120562D
+
+ 25 27  0  0  0  0            999 V2000
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+  8 25  1  0
+  5 25  1  0
+M  END
+> <mr_id>
+4209966
+
+> <SMI>
+CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCNCC3)s2)o1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 29 33  0  0  0  0            999 V2000
+  -10.5010    9.6183    0.0000 C   0  0
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+    1.2964    2.6973    0.0000 F   0  0
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+    2.5929   -0.7486    0.0000 C   0  0
+    1.2964   -1.4973    0.0000 C   0  0
+    0.0000   -0.7486    0.0000 C   0  0
+   -1.2964   -1.4973    0.0000 N   0  0
+   -2.6111   -0.7486    0.0000 C   0  0
+   -3.6486   -1.3517    0.0000 O   0  0
+  1  2  1  0
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+  3  4  1  0
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+ 17 28  1  0
+ 28 29  2  0
+M  END
+> <mr_id>
+4362207
+
+> <SMI>
+CN1CCN(CC1)c2ccc3nc([nH]c3c2)c4c(N)c5c(F)cccc5[nH]c4=O
+
+$$$$
+
+  SciTegic01171120562D
+
+ 37 41  0  0  0  0            999 V2000
+    2.0907   -2.3426    0.0000 C   0  0
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+  1  2  1  0
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+ 16 37  2  0
+M  END
+> <mr_id>
+4349584
+
+> <SMI>
+Cn1c(Nc2ccc(cc2)C(F)(F)F)nc3cc(Oc4ccnc(c4)c5ncc([nH]5)C(F)(F)F)ccc13
+
+$$$$
+
+  SciTegic01171120562D
+
+ 34 37  0  0  0  0            999 V2000
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+M  END
+> <mr_id>
+902
+
+> <SMI>
+Fc1ccc(Nc2ncnc3cc(OCCCN4CCOCC4)c(NC(=O)C=C)cc23)cc1Cl
+
+$$$$
+
+  SciTegic01171120562D
+
+ 23 25  0  0  1  0            999 V2000
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+  2  1  1  6
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+M  END
+> <mr_id>
+4362208
+
+> <SMI>
+C[C@@H]1CCN(C[C@@H]1N(C)c2ncnc3[nH]ccc23)C(=O)CC#N
+
+$$$$
+
+  SciTegic01171120562D
+
+ 33 36  0  0  0  0            999 V2000
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+   -6.5731  -10.6832    0.0000 C   0  0
+    0.0935   -6.1100    0.0000 S   0  0
+  1  2  1  0
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+M  END
+> <mr_id>
+4272835
+
+> <SMI>
+Cc1cccc(Cl)c1NC(=O)c2cnc(Nc3cc(nc(C)n3)N4CCN(CCO)CC4)s2
+
+$$$$
+
+  SciTegic01171120562D
+
+ 33 35  0  0  0  0            999 V2000
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+  1  2  1  0
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+M  END
+> <mr_id>
+2423880
+
+> <SMI>
+CCOc1cc2ncc(C#N)c(Nc3ccc(F)c(Cl)c3)c2cc1NC(=O)/C=C/CN(C)C
+
+$$$$
+
+  SciTegic01171120562D
+
+ 29 31  0  0  0  0            999 V2000
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+  6 24  2  0
+ 24 25  1  0
+ 25 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  1  0
+M  END
+> <mr_id>
+2050
+
+> <SMI>
+COCCOc1cc2ncnc(Nc3cccc(C#C)c3)c2cc1OCCOC
+
+$$$$
+
+  SciTegic01171120562D
+
+ 28 31  0  0  1  0            999 V2000
+   -1.2770    7.1982    0.0000 C   0  0
+   -1.2813    5.9982    0.0000 N   0  0
+   -2.5829    5.2528    0.0000 C   0  0
+   -2.5882    3.7528    0.0000 C   0  0
+   -1.2919    2.9980    0.0000 C   0  0  1  0  0  0
+    0.0099    3.7437    0.0000 C   0  0  2  0  0  0
+    1.0470    3.1401    0.0000 O   0  0
+    0.0151    5.2437    0.0000 C   0  0
+   -1.2964    1.4973    0.0000 C   0  0
+   -2.6111    0.7486    0.0000 C   0  0
+   -3.6486    1.3517    0.0000 O   0  0
+   -2.6111   -0.7486    0.0000 C   0  0
+   -1.2964   -1.4973    0.0000 C   0  0
+   -1.2928   -2.6973    0.0000 O   0  0
+    0.0000   -0.7486    0.0000 C   0  0
+    1.2964   -1.4973    0.0000 C   0  0
+    1.2964   -2.6973    0.0000 O   0  0
+    2.5929   -0.7486    0.0000 C   0  0
+    2.5929    0.7486    0.0000 C   0  0
+    1.2964    1.4973    0.0000 O   0  0
+    0.0000    0.7486    0.0000 C   0  0
+    3.8926    1.4990    0.0000 C   0  0
+    5.1905    0.7469    0.0000 C   0  0
+    6.4908    1.4949    0.0000 C   0  0
+    6.4931    2.9949    0.0000 C   0  0
+    5.1953    3.7469    0.0000 C   0  0
+    3.8951    2.9990    0.0000 C   0  0
+    2.8568    3.6007    0.0000 Cl  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  7  1  1
+  6  8  1  0
+  2  8  1  0
+  5  9  1  1
+  9 10  1  0
+ 10 11  1  0
+ 10 12  2  0
+ 12 13  1  0
+ 13 14  1  0
+ 13 15  2  0
+ 15 16  1  0
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+ 15 21  1  0
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+ 23 24  2  0
+ 24 25  1  0
+ 25 26  2  0
+ 26 27  1  0
+ 22 27  2  0
+ 27 28  1  0
+M  END
+> <mr_id>
+3645
+
+> <SMI>
+CN1CC[C@@H]([C@H](O)C1)c2c(O)cc(O)c3c(=O)cc(oc23)c4ccccc4Cl
+
+$$$$
+
+  SciTegic01171120562D
+
+ 31 34  0  0  0  0            999 V2000
+   -3.9072    2.7019    0.0000 C   0  0
+   -3.9091    1.5019    0.0000 O   0  0
+   -2.6111    0.7486    0.0000 C   0  0
+   -1.2964    1.4973    0.0000 C   0  0
+    0.0000    0.7486    0.0000 C   0  0
+    1.2964    1.4973    0.0000 N   0  0
+    2.5929    0.7486    0.0000 C   0  0
+    2.5929   -0.7486    0.0000 N   0  0
+    1.2964   -1.4973    0.0000 C   0  0
+    1.2995   -2.9981    0.0000 N   0  0
+    2.6003   -3.7467    0.0000 C   0  0
+    2.6056   -5.2467    0.0000 C   0  0
+    3.9072   -5.9922    0.0000 C   0  0
+    5.2037   -5.2377    0.0000 C   0  0
+    6.2450   -5.8341    0.0000 F   0  0
+    5.1985   -3.7377    0.0000 C   0  0
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+    3.8969   -2.9922    0.0000 C   0  0
+    0.0000   -0.7486    0.0000 C   0  0
+   -1.2964   -1.4973    0.0000 C   0  0
+   -2.6111   -0.7486    0.0000 C   0  0
+   -3.9091   -1.5019    0.0000 O   0  0
+   -3.9067   -3.0027    0.0000 C   0  0
+   -5.2049   -3.7560    0.0000 C   0  0
+   -5.2025   -5.2568    0.0000 C   0  0
+   -6.5006   -6.0101    0.0000 N   0  0
+   -6.5005   -7.5101    0.0000 C   0  0
+   -7.7994   -8.2603    0.0000 C   0  0
+   -9.0986   -7.5105    0.0000 O   0  0
+   -9.0988   -6.0105    0.0000 C   0  0
+   -7.7999   -5.2603    0.0000 C   0  0
+  1  2  1  0
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+  3  4  1  0
+  4  5  2  0
+  5  6  1  0
+  6  7  2  0
+  7  8  1  0
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+ 28 29  1  0
+ 29 30  1  0
+ 30 31  1  0
+ 26 31  1  0
+M  END
+> <mr_id>
+7006
+
+> <SMI>
+COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN4CCOCC4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 27 29  0  0  0  0            999 V2000
+    2.5956   -2.7031    0.0000 C   0  0
+    2.5973   -1.5031    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
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+   -2.6003    1.4977    0.0000 C   0  0
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+   -5.2003    1.4932    0.0000 C   0  0
+   -5.2004    2.9933    0.0000 C   0  0
+   -6.4995    3.7432    0.0000 C   0  0
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+   -9.0998    3.7409    0.0000 C   0  0
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+  -10.3933    1.4885    0.0000 C   0  0
+  -11.6898    0.7340    0.0000 N   0  0
+  -12.9914    1.4795    0.0000 C   0  0
+  -14.0285    0.8758    0.0000 N   0  0
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+  -11.7044    4.9340    0.0000 N   0  0
+   -7.7985    1.4932    0.0000 C   0  0
+   -6.4994    0.7432    0.0000 C   0  0
+   -6.5025   -0.7576    0.0000 O   0  0
+   -7.5426   -1.3561    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 C   0  0
+  1  2  1  0
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+  3  4  1  0
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+  6 26  2  0
+ 26 27  1  0
+  3 27  2  0
+M  END
+> <mr_id>
+4362210
+
+> <SMI>
+COc1ccc(COc2ccc(Cc3cnc(N)nc3N)cc2OC)cc1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 31 34  0  0  0  0            999 V2000
+   -4.6549    0.8867    0.0000 C   0  0
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+    1.5634    1.4998    0.0000 S   0  0
+    2.6021    0.8990    0.0000 O   0  0
+    0.5238    0.9004    0.0000 O   0  0
+    1.5626    0.2998    0.0000 N   0  0
+   -2.3301    3.7470    0.0000 N   0  0
+  1  2  1  0
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+  3  4  1  0
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+  6  7  2  0
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+ 27 30  1  0
+ 18 31  1  0
+ 14 31  2  0
+M  END
+> <mr_id>
+4303161
+
+> <SMI>
+CN(c1ccc2c(C)n(C)nc2c1)c3ccnc(Nc4ccc(C)c(c4)S(=O)(=O)N)n3
+
+$$$$
+
+  SciTegic01171120562D
+
+ 37 41  0  0  0  0            999 V2000
+    2.3383   -1.3500    0.0000 C   0  0
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+  -11.6789    0.7109    0.0000 C   0  0
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+  -10.3776   -3.0341    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 C   0  0
+  1  2  1  0
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+  2 37  1  0
+M  END
+> <mr_id>
+2087
+
+> <SMI>
+CN1CCN(Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)CC1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 27 29  0  0  0  0            999 V2000
+    4.0391   -6.2662    0.0000 N   0  0
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+    0.0000   -1.5000    0.0000 C   0  0
+   -2.5988    1.5004    0.0000 S   0  0
+   -2.5996    2.7004    0.0000 O   0  0
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+   -3.6383    2.0999    0.0000 N   0  0
+    1.3786   -3.8595    0.0000 N   0  0
+    1.8372   -5.2877    0.0000 N   0  0
+    0.9498   -6.4949    0.0000 C   0  0
+    1.4321   -7.5937    0.0000 O   0  0
+   -0.5420   -6.3307    0.0000 C   0  0
+   -1.4322   -7.5380    0.0000 C   0  0
+   -0.9518   -8.6377    0.0000 F   0  0
+   -2.9229   -7.3709    0.0000 C   0  0
+   -3.5234   -5.9963    0.0000 C   0  0
+   -2.6333   -4.7890    0.0000 C   0  0
+   -1.1427   -4.9561    0.0000 C   0  0
+   -0.4306   -3.9902    0.0000 F   0  0
+  1  2  1  0
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+ 20 26  2  0
+ 26 27  1  0
+M  END
+> <mr_id>
+4197090
+
+> <SMI>
+Nc1nc(Nc2ccc(cc2)S(=O)(=O)N)nn1C(=O)c3c(F)cccc3F
+
+$$$$
+
+  SciTegic01171120562D
+
+ 40 44  0  0  0  0            999 V2000
+  -12.6605   -0.2645    0.0000 C   0  0
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+> <SMI>
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+$$$$
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+M  END
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+> <SMI>
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+
+$$$$
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+M  END
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+> <SMI>
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+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/XChemReactionMaker1.sdf	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,5393 @@
+
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+    3.9658    1.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4848    0.9418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.9580    0.2266    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.9049    1.3899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.3858    1.1515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.9198   -0.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.4008   -0.4887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9729   -1.4136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4920   -1.1752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0 
+  2  3  1  0  0  0  0 
+  3  4  1  0  0  0  0 
+  4  5  2  0  0  0  0 
+  5  6  1  0  0  0  0 
+  6  7  2  0  0  0  0 
+  7  8  1  0  0  0  0 
+  7  9  1  0  0  0  0 
+  9 10  2  0  0  0  0 
+  2 11  1  0  0  0  0 
+ 11 12  2  0  0  0  0 
+ 12 13  1  0  0  0  0 
+ 13 14  2  0  0  0  0 
+ 14 15  1  0  0  0  0 
+ 14 16  1  0  0  0  0 
+ 16 17  2  0  0  0  0 
+ 10  4  1  0  0  0  0 
+ 17 11  1  0  0  0  0 
+M  END
+> <reactant_uuid>
+9750a3fa-97eb-444a-bc34-8ea1560759f4
+
+> <source_uuid>
+33509b1f-56f4-4a43-bc9f-5aea174b9dad
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster_butina_matrix_output1.tsv	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,101 @@
+ID1	ID2	Cluster1	Cluster2	Similarity	M1	M2
+030.0001	030.0001	30	30	1.0		
+030.0001	003.0002	30	3	0.5227148330596606		
+003.0002	030.0001	3	30	0.5227148330596606		
+003.0002	003.0002	3	3	1.0		
+029.0003	029.0003	29	29	1.0		
+028.0004	028.0004	28	28	1.0		
+004.0005	004.0005	4	4	1.0		
+004.0005	004.0006	4	4	0.8354898336414048		
+004.0006	004.0005	4	4	0.8354898336414048		
+004.0006	004.0006	4	4	1.0		
+004.0005	027.0007	4	27	0.5833333333333334		
+027.0007	004.0005	27	4	0.5833333333333334		
+027.0007	027.0007	27	27	1.0		
+026.0008	026.0008	26	26	1.0		
+030.0001	003.0009	30	3	0.5038975501113586		
+003.0009	030.0001	3	30	0.5038975501113586		
+003.0002	003.0009	3	3	0.9488636363636364		
+003.0009	003.0002	3	3	0.9488636363636364		
+003.0009	003.0009	3	3	1.0		
+003.0002	025.0010	3	25	0.5425935973955507		
+025.0010	003.0002	25	3	0.5425935973955507		
+003.0009	025.0010	3	25	0.5200880572372042		
+025.0010	003.0009	25	3	0.5200880572372042		
+025.0010	025.0010	25	25	1.0		
+024.0011	024.0011	24	24	1.0		
+023.0012	023.0012	23	23	1.0		
+001.0013	001.0013	1	1	1.0		
+022.0014	022.0014	22	22	1.0		
+021.0015	021.0015	21	21	1.0		
+020.0016	020.0016	20	20	1.0		
+001.0013	001.0017	1	1	0.5799676898222941		
+001.0017	001.0013	1	1	0.5799676898222941		
+001.0017	001.0017	1	1	1.0		
+019.0018	019.0018	19	19	1.0		
+018.0019	018.0019	18	18	1.0		
+017.0020	017.0020	17	17	1.0		
+016.0021	016.0021	16	16	1.0		
+001.0013	001.0022	1	1	0.6111111111111112		
+001.0022	001.0013	1	1	0.6111111111111112		
+001.0017	001.0022	1	1	0.6430278884462152		
+001.0022	001.0017	1	1	0.6430278884462152		
+001.0022	001.0022	1	1	1.0		
+015.0023	015.0023	15	15	1.0		
+014.0024	014.0024	14	14	1.0		
+001.0022	002.0025	1	2	0.6679841897233202		
+002.0025	001.0022	2	1	0.6679841897233202		
+002.0025	002.0025	2	2	1.0		
+001.0013	001.0026	1	1	0.7357001972386588		
+001.0026	001.0013	1	1	0.7357001972386588		
+001.0017	001.0026	1	1	0.5691263782866837		
+001.0026	001.0017	1	1	0.5691263782866837		
+001.0022	001.0026	1	1	0.5707070707070707		
+001.0026	001.0022	1	1	0.5707070707070707		
+001.0026	001.0026	1	1	1.0		
+003.0002	013.0027	3	13	0.5373297002724796		
+013.0027	003.0002	13	3	0.5373297002724796		
+003.0009	013.0027	3	13	0.5247634947134112		
+013.0027	003.0009	13	3	0.5247634947134112		
+013.0027	013.0027	13	13	1.0		
+001.0013	001.0028	1	1	0.7685631629701061		
+001.0028	001.0013	1	1	0.7685631629701061		
+001.0017	001.0028	1	1	0.6140939597315436		
+001.0028	001.0017	1	1	0.6140939597315436		
+001.0022	001.0028	1	1	0.7275155832591274		
+001.0028	001.0022	1	1	0.7275155832591274		
+001.0026	001.0028	1	1	0.7472194135490394		
+001.0028	001.0026	1	1	0.7472194135490394		
+001.0028	001.0028	1	1	1.0		
+012.0029	012.0029	12	12	1.0		
+011.0030	011.0030	11	11	1.0		
+010.0031	010.0031	10	10	1.0		
+009.0032	009.0032	9	9	1.0		
+001.0013	008.0033	1	8	0.5191740412979351		
+008.0033	001.0013	8	1	0.5191740412979351		
+001.0022	008.0033	1	8	0.5416370106761565		
+008.0033	001.0022	8	1	0.5416370106761565		
+001.0026	008.0033	1	8	0.5100463678516228		
+008.0033	001.0026	8	1	0.5100463678516228		
+001.0028	008.0033	1	8	0.5552147239263804		
+008.0033	001.0028	8	1	0.5552147239263804		
+008.0033	008.0033	8	8	1.0		
+003.0002	007.0034	3	7	0.5650474595198214		
+007.0034	003.0002	7	3	0.5650474595198214		
+003.0009	007.0034	3	7	0.550997150997151		
+007.0034	003.0009	7	3	0.550997150997151		
+007.0034	007.0034	7	7	1.0		
+001.0013	006.0035	1	6	0.5981772990886496		
+006.0035	001.0013	6	1	0.5981772990886496		
+001.0017	006.0035	1	6	0.530705079605762		
+006.0035	001.0017	6	1	0.530705079605762		
+001.0022	006.0035	1	6	0.5522501906941266		
+006.0035	001.0022	6	1	0.5522501906941266		
+001.0026	006.0035	1	6	0.570198105081826		
+006.0035	001.0026	6	1	0.570198105081826		
+001.0028	006.0035	1	6	0.5981465880370682		
+006.0035	001.0028	6	1	0.5981465880370682		
+006.0035	006.0035	6	6	1.0		
+003.0002	005.0036	3	5	0.5029364655632674		
+005.0036	003.0002	5	3	0.5029364655632674		
+005.0036	005.0036	5	5	1.0		
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster_butina_output1.sdf	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,2931 @@
+
+     RDKit          2D
+
+ 26 30  0  0  0  0  0  0  0  0999 V2000
+   -8.6396    0.9568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6023    1.5602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6071    3.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3104    3.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0090    3.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0040    1.5682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3008    0.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006   -0.6045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915   -1.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5059   -2.8197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2156   -3.5847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2329   -5.0846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5404   -5.8196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8308   -5.0547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8135   -3.5548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.3190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732   -1.3190    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732    1.5389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915    1.5389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  2  0
+  3  4  1  0
+  4  5  2  0
+  5  6  1  0
+  6  7  2  0
+  2  7  1  0
+  6  8  1  0
+  8  9  2  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  1  0
+ 15 16  1  0
+ 11 16  1  0
+ 10 17  2  0
+ 17 18  1  0
+ 18 19  1  0
+ 19 20  2  0
+ 20 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  2  0
+ 19 24  1  0
+ 24 25  1  0
+ 17 25  1  0
+ 25 26  2  0
+  8 26  1  0
+M  END
+>  <mr_id>  (1) 
+4358263
+
+>  <SMI>  (1) 
+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
+
+>  <Cluster>  (1) 
+29
+
+$$$$
+
+     RDKit          2D
+
+ 43 51  0  0  1  0  0  0  0  0999 V2000
+   -4.7204    3.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.1471    2.2890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6500    2.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8100    3.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2400    3.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.5000    2.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0600    2.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8300    0.9300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.2400   -1.4400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -1.9442    5.8382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0519    4.8135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.6588    3.7783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7941    6.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2940    6.1306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.0331    7.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2722    8.7286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7723    8.7160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0332    7.4108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  3  2  1  6
+  3  4  1  0
+  4  5  1  0
+  6  5  1  6
+  6  7  1  0
+  7  8  1  0
+  3  8  1  0
+  8  9  1  1
+  8 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+ 13 14  2  0
+ 14 15  1  0
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+ 17 18  1  0
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+ 20 21  1  0
+ 21 22  2  0
+ 21 23  1  0
+ 18 23  2  0
+ 23 24  1  0
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+ 25 26  2  0
+ 26 27  1  0
+ 27 28  2  0
+ 28 29  1  0
+ 29 30  2  0
+ 25 30  1  0
+ 30 31  1  0
+  6 31  1  0
+ 31 32  1  0
+ 24 32  2  0
+ 32 33  1  0
+ 10 33  1  0
+ 17 33  2  0
+  4 34  1  6
+ 34 35  1  0
+ 34 36  1  0
+ 36 37  2  0
+ 36 38  1  0
+ 38 39  2  0
+ 39 40  1  0
+ 40 41  2  0
+ 41 42  1  0
+ 42 43  2  0
+ 38 43  1  0
+M  END
+>  <mr_id>  (2) 
+8573
+
+>  <SMI>  (2) 
+CO[C@@H]1[C@@H](C[C@H]2O[C@]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
+
+>  <Cluster>  (2) 
+2
+
+$$$$
+
+     RDKit          2D
+
+ 25 28  0  0  0  0  0  0  0  0999 V2000
+   -6.2193    5.8633    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
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+  2 25  1  0
+M  END
+>  <mr_id>  (3) 
+4027
+
+>  <SMI>  (3) 
+Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1
+
+>  <Cluster>  (3) 
+28
+
+$$$$
+
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+
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+M  END
+>  <mr_id>  (4) 
+600
+
+>  <SMI>  (4) 
+CC[C@H](CO)Nc1nc(NCc2ccccc2)c3ncn(C(C)C)c3n1
+
+>  <Cluster>  (4) 
+27
+
+$$$$
+
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+
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+M  END
+>  <mr_id>  (5) 
+8393
+
+>  <SMI>  (5) 
+Oc1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+>  <Cluster>  (5) 
+3
+
+$$$$
+
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+
+ 27 30  0  0  0  0  0  0  0  0999 V2000
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+M  END
+>  <mr_id>  (6) 
+3250
+
+>  <SMI>  (6) 
+CS(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+>  <Cluster>  (6) 
+3
+
+$$$$
+
+     RDKit          2D
+
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+M  END
+>  <mr_id>  (7) 
+4347423
+
+>  <SMI>  (7) 
+NC(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccccn3)c4ccc5OCOc5c4
+
+>  <Cluster>  (7) 
+26
+
+$$$$
+
+     RDKit          2D
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+M  END
+>  <mr_id>  (8) 
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+>  <SMI>  (8) 
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+>  <Cluster>  (8) 
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+$$$$
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+M  END
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+
+>  <Cluster>  (9) 
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+$$$$
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+M  END
+>  <mr_id>  (10) 
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+M  END
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+$$$$
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+M  END
+>  <mr_id>  (12) 
+13932
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+Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1
+
+>  <Cluster>  (12) 
+22
+
+$$$$
+
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+M  END
+>  <mr_id>  (13) 
+13669
+
+>  <SMI>  (13) 
+COc1cc2c(Nc3ccc(Br)cc3F)ncnc2cc1OCC4CCN(C)CC4
+
+>  <Cluster>  (13) 
+0
+
+$$$$
+
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+M  END
+>  <mr_id>  (14) 
+4343227
+
+>  <SMI>  (14) 
+Cc1ccc(F)c(NC(=O)Nc2ccc(cc2)c3cccc4[nH]nc(N)c34)c1
+
+>  <Cluster>  (14) 
+21
+
+$$$$
+
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+M  END
+>  <mr_id>  (15) 
+4309480
+
+>  <SMI>  (15) 
+CC1(C)CNc2cc(NC(=O)c3cccnc3NCc4ccncc4)ccc21
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+>  <Cluster>  (15) 
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+$$$$
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+M  END
+>  <mr_id>  (16) 
+4210240
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+>  <SMI>  (16) 
+CCN1CCN(Cc2ccc(NC(=O)Nc3ccc(Oc4cc(NC)ncn4)cc3)cc2C(F)(F)F)CC1
+
+>  <Cluster>  (16) 
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+$$$$
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+M  END
+>  <mr_id>  (17) 
+4345887
+
+>  <SMI>  (17) 
+CCN(CCO)CCCOc1ccc2c(Nc3cc(CC(=O)Nc4cccc(F)c4)[nH]n3)ncnc2c1
+
+>  <Cluster>  (17) 
+0
+
+$$$$
+
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+M  END
+>  <mr_id>  (18) 
+7815
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+>  <SMI>  (18) 
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+
+>  <Cluster>  (18) 
+18
+
+$$$$
+
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+M  END
+>  <mr_id>  (19) 
+4209966
+
+>  <SMI>  (19) 
+CC(C)(C)c1cnc(CSc2cnc(NC(=O)C3CCNCC3)s2)o1
+
+>  <Cluster>  (19) 
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+
+$$$$
+
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+M  END
+>  <mr_id>  (20) 
+4362207
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+$$$$
+
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+M  END
+>  <mr_id>  (21) 
+4349584
+
+>  <SMI>  (21) 
+Cn1c(Nc2ccc(cc2)C(F)(F)F)nc3cc(Oc4ccnc(c4)c5ncc([nH]5)C(F)(F)F)ccc13
+
+>  <Cluster>  (21) 
+15
+
+$$$$
+
+     RDKit          2D
+
+ 34 37  0  0  0  0  0  0  0  0999 V2000
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+M  END
+>  <mr_id>  (22) 
+902
+
+>  <SMI>  (22) 
+Fc1ccc(Nc2ncnc3cc(OCCCN4CCOCC4)c(NC(=O)C=C)cc23)cc1Cl
+
+>  <Cluster>  (22) 
+0
+
+$$$$
+
+     RDKit          2D
+
+ 23 25  0  0  1  0  0  0  0  0999 V2000
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