| Next changeset 1:05cc95060024 (2020-07-27) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9" |
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added:
macros.xml screen.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 |
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| diff -r 000000000000 -r 2c11d1f9e00b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 21 05:22:46 2020 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r 2c11d1f9e00b screen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/screen.xml Tue Jul 21 05:22:46 2020 -0400 |
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| @@ -0,0 +1,145 @@ +<tool id="ctb_im_screen" name="Screen" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>a compound against a library using RDKit</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + screen + #if $comparator.comparator_opts == 'str': + --qsmiles '${comparator.input}' + #else: + --qmolfile ${comparator.input} + #end if + + -i '$infile' + -if sdf + #if $comparator.comparator_opts == 'mol' + --isMol + #end if + #if $fragment_opts + -f '$fragment_opts' + #end if + --simmin '$sim_min' + --simmax '$sim_max' + -d '$descriptor_opts' + -m '$metric_opts' + #if $hac_min != '' + --hacmin '$hac_min' + #end if + #if $hac_max != '' + --hacmax '$hac_max' + #end if + #if $mw_min != '' + --mwmin '$mw_min' + #end if + #if $mw_max != '' + --mwmax '$mw_max' + #end if + --meta + -o outp &>> $logfile && ## the script does not exit 0 + cat outp_metrics.txt &>> $logfile && + gzip -d outp.sdf.gz + ]]></command> + <inputs> + <conditional name="comparator"> + <param name='comparator_opts' type='select' label="Input type" help="Enter SMILES string or Mol file."> + <option value='file'>Mol/SDF file</option> + <option value='str'>SMILES string</option> + </param> + <when value='str'> + <param name="input" type="text" label="SMILES input" help="Enter SMILES for a compound."> + <validator type='length' min='5'/> + </param> + </when> + <when value='file'> + <param name="input" type="data" format="sdf,mol" label="Input" help="Input file in mol/sdf format"/> + </when> + </conditional> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format, for comparison"/> + <param name="sim_min" type="float" label="Similarity lower cutoff" value="0.7" min="0" max="1" help="(1.0 means identical)"/> + <param name="sim_max" type="float" label="Similarity upper cutoff" value="1.0" min="0" max="1" help="(1.0 means identical)"/> + <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is rdkit"> + <option value="rdkit" selected="true">rdkit</option> + <option value="maccs">maccs</option> + <option value="morgan2">morgan2</option> + <option value="morgan3">morgan3</option> + </param> + <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient"> + <option value="tanimoto" selected="true">tanimoto</option> + <option value="asymmetric">asymmetric</option> + <option value="braunblanquet">braunblanquet</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="kulczynski">kulczynski</option> + <option value="mcconnaughey">mcconnaughey</option> + <option value="rogotgoldberg">rogotgoldberg</option> + <option value="russel">russel</option> + <option value="sokal">sokal</option> + </param> + <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight )"> + <option value="hac">Biggest by heavy atom count</option> + <option value="mw">Biggest by molecular weight</option> + </param> + <param name="hac_min" type="integer" optional="true" label="Minimum heavy atom count" help="Minimum number of heavy atoms for a candidate to pass screening"/> + <param name="hac_max" type="integer" optional="true" label="Maximum heavy atom count" help="Maximum number of heavy atoms for a candidate to pass screening"/> + <param name="mw_min" type="float" optional="true" label="Minimum molecular weight" help="Minimum molecular weight for a candidate to pass screening"/> + <param name="mw_max" type="float" optional="true" label="Maximum molecular weight" help="Maximum molecular weight for a candidate to pass screening"/> + </inputs> + + <expand macro="outputs" /> + + <tests> + <test> + <param name='comparator_opts' value="str"/> + <param name="input" value="C1N=C(C2=CC=CC=C2)C2=CC=CC=C2C2=C1C=NC(NC1=CC=CC=C1)=N2"/> + <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/> + <param name="descriptor_opts" value="rdkit" /> + <param name="metric_opts" value="tanimoto" /> + <param name="sim_min" value="0.45" /> + <param name="sim_max" value="1.0" /> + <output name="outfile" ftype='sdf' file="screen_output1.sdf"/> + </test> + <test> + <param name='comparator_opts' value="file"/> + <param name="input" value="pyrimethamine.mol" ftype="mol"/> + <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/> + <param name="descriptor_opts" value="rdkit" /> + <param name="metric_opts" value="tanimoto" /> + <param name="sim_min" value="0.7" /> + <param name="sim_max" value="0.8" /> + <output name="outfile" ftype='sdf' file="screen_output2.sdf"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What this tool does** + +Screen a library against a compound, filtering by fingerprint similarity and a number of other properties. + +.. class:: infomark + +**Input** + +| - Compound library in `SDF Format`_ +| - Compound to screen against in `SMILES`_ or `SDF Format`_ +| - Type of fingerprint +| - Required molecular weight and heavy atom count + +.. _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 screened compounds, with new 'Similarity' property. + +]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 2c11d1f9e00b test-data/Kinase_inhibs.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Kinase_inhibs.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,2823 @@\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 26 30 0 0 0 0 999 V2000\r\n+ -8.6396 0.9568 0.0000 O 0 0\r\n+ -7.6023 1.5602 0.0000 C 0 0\r\n+ -7.6071 3.0602 0.0000 C 0 0\r\n+ -6.3104 3.8143 0.0000 C 0 0\r\n+ -5.0090 3.0685 0.0000 C 0 0\r\n+ -5.0040 1.5682 0.0000 C 0 0\r\n+ -6.3008 0.8143 0.0000 C 0 0\r\n+ -3.7006 0.8244 0.0000 C 0 0\r\n+ -3.7006 -0.6045 0.0000 N 0 0\r\n+ -2.4915 -1.3190 0.0000 C 0 0\r\n+ -2.5059 -2.8197 0.0000 N 0 0\r\n+ -1.2156 -3.5847 0.0000 C 0 0\r\n+ -1.2329 -5.0846 0.0000 C 0 0\r\n+ -2.5404 -5.8196 0.0000 O 0 0\r\n+ -3.8308 -5.0547 0.0000 C 0 0\r\n+ -3.8135 -3.5548 0.0000 C 0 0\r\n+ -1.2274 -0.6045 0.0000 C 0 0\r\n+ 0.0000 -1.3190 0.0000 O 0 0\r\n+ 1.2274 -0.6045 0.0000 C 0 0\r\n+ 2.4732 -1.3190 0.0000 N 0 0\r\n+ 3.7372 -0.6045 0.0000 C 0 0\r\n+ 3.7372 0.8244 0.0000 C 0 0\r\n+ 2.4732 1.5389 0.0000 C 0 0\r\n+ 1.2274 0.8244 0.0000 C 0 0\r\n+ -1.2274 0.8244 0.0000 C 0 0\r\n+ -2.4915 1.5389 0.0000 N 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 2 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 2 7 2 0\r\n+ 6 8 1 0\r\n+ 8 9 1 0\r\n+ 9 10 2 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 1 0\r\n+ 15 16 1 0\r\n+ 11 16 1 0\r\n+ 10 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 2 0\r\n+ 20 21 1 0\r\n+ 21 22 2 0\r\n+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 19 24 1 0\r\n+ 24 25 1 0\r\n+ 17 25 2 0\r\n+ 25 26 1 0\r\n+ 8 26 2 0\r\n+M END\r\n+> <mr_id>\r\n+4358263\r\n+\r\n+> <SMI>\r\n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\r\n+\r\n+$$$$\r\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 43 51 0 0 1 0 999 V2000\r\n+ -4.7204 3.3431 0.0000 C 0 0\r\n+ -4.1471 2.2890 0.0000 O 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -1.8100 3.5000 0.0000 C 0 0 1 0 0 0\r\n+ -0.2400 3.5200 0.0000 C 0 0\r\n+ 0.5000 2.1800 0.0000 C 0 0 1 0 0 0\r\n+ -1.0600 2.1800 0.0000 O 0 0\r\n+ -1.8300 0.9300 0.0000 C 0 0 1 0 0 0\r\n+ -3.0300 0.9300 0.0000 C 0 0\r\n+ -0.9800 -0.7800 0.0000 N 0 0\r\n+ -2.1300 -1.4600 0.0000 C 0 0\r\n+ -3.3200 -0.7600 0.0000 C 0 0\r\n+ -4.5500 -1.4800 0.0000 C 0 0\r\n+ -4.5800 -2.7700 0.0000 C 0 0\r\n+ -3.3400 -3.4700 0.0000 C 0 0\r\n+ -2.1300 -2.7900 0.0000 C 0 0\r\n+ 0.2400 -2.7700 0.0000 C 0 0\r\n+ 1.4300 -3.4700 0.0000 C 0 0\r\n+ 1.7600 -4.9700 0.0000 C 0 0\r\n+ 3.2600 -5.0800 0.0000 N 0 0\r\n+ 3.8500 -3.6300 0.0000 C 0 0\r\n+ 4.9971 -3.2777 0.0000 O 0 0\r\n+ 2.6600 -2.7500 0.0000 C 0 0\r\n+ 2.6800 -1.4600 0.0000 C 0 0\r\n+ 3.7900 0.5600 0.0000 C 0 0\r\n+ 4.9600 1.2800 0.0000 C 0 0\r\n+ 4.9600 2.6300 0.0000 C 0 0\r\n+ 3.8100 3.2900 0.0000 C 0 0\r\n+ 2.6400 2.5900 0.0000 C 0 0\r\n+ 2.6400 1.2400 0.0000 C 0 0\r\n+ 1.4900 0.5400 0.0000 N 0 0\r\n+ 1.4500 -0.7600 0.0000 C 0 0\r\n+ 0.2400 -1.4400 0.0000 C 0 0\r\n+ -2.5511 4.8030 0.0000 N 0 0\r\n+ -1.9442 5.8382 0.0000 C 0 0\r\n+ -4.0519 4.8135 0.0000 C 0 0\r\n+ -4.6588 3.7783 0.0000 O 0 0\r\n+ -4.7941 6.1180 0.0000 C 0 0\r\n+ -6.2940 6.1306 0.0000 C 0 0\r\n+ -7.0331 7.4359 0.0000 C 0 0\r\n+ -6.2722 8.7286 0.0000 C 0 0\r\n+ -4.7723 8.7160 0.0000 C 0 0\r\n+ -4.0332 7.4108 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 6 5 1 6\r\n+ 6 7 1 0\r\n+ 7 8 1 0\r\n+ 3 8 1 0\r\n+ 8 9 1 1\r\n+ 8 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 1 0\r\n+ 12 13 2 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 11 16 2 0\r\n+ 16 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 2 '..b' N 0 0\r\n+ -6.5005 -7.5101 0.0000 C 0 0\r\n+ -7.7994 -8.2603 0.0000 C 0 0\r\n+ -9.0986 -7.5105 0.0000 C 0 0\r\n+ -9.0988 -6.0105 0.0000 C 0 0\r\n+ -7.7999 -5.2603 0.0000 C 0 0\r\n+ 1.2964 2.9980 0.0000 N 0 0\r\n+ 2.5942 3.7503 0.0000 C 0 0\r\n+ 2.5918 5.2503 0.0000 C 0 0\r\n+ 1.2915 5.9981 0.0000 N 0 0\r\n+ -0.0063 5.2460 0.0000 C 0 0\r\n+ -0.0038 3.7460 0.0000 C 0 0\r\n+ 1.2859 7.4990 0.0000 C 0 0\r\n+ 2.3231 8.1025 0.0000 O 0 0\r\n+ -0.0161 8.2454 0.0000 N 0 0\r\n+ -0.0217 9.7462 0.0000 C 0 0\r\n+ -1.3220 10.4941 0.0000 C 0 0\r\n+ -1.3245 11.9941 0.0000 C 0 0\r\n+ -0.0267 12.7463 0.0000 C 0 0\r\n+ -0.0261 14.2471 0.0000 O 0 0\r\n+ 1.2735 14.9979 0.0000 C 0 0\r\n+ 1.2739 16.1979 0.0000 C 0 0\r\n+ 2.3127 14.3978 0.0000 C 0 0\r\n+ 1.2736 11.9985 0.0000 C 0 0\r\n+ 1.2761 10.4985 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 1 0\r\n+ 4 5 2 0\r\n+ 5 6 1 0\r\n+ 6 7 2 0\r\n+ 7 8 1 0\r\n+ 8 9 2 0\r\n+ 9 10 1 0\r\n+ 5 10 1 0\r\n+ 10 11 2 0\r\n+ 11 12 1 0\r\n+ 3 12 2 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 1 0\r\n+ 15 16 1 0\r\n+ 16 17 1 0\r\n+ 17 18 1 0\r\n+ 18 19 1 0\r\n+ 19 20 1 0\r\n+ 20 21 1 0\r\n+ 21 22 1 0\r\n+ 17 22 1 0\r\n+ 6 23 1 0\r\n+ 23 24 1 0\r\n+ 24 25 1 0\r\n+ 25 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 23 28 1 0\r\n+ 26 29 1 0\r\n+ 29 30 2 0\r\n+ 29 31 1 0\r\n+ 31 32 1 0\r\n+ 32 33 1 0\r\n+ 33 34 2 0\r\n+ 34 35 1 0\r\n+ 35 36 1 0\r\n+ 36 37 1 0\r\n+ 37 38 1 0\r\n+ 37 39 1 0\r\n+ 35 40 2 0\r\n+ 40 41 1 0\r\n+ 32 41 2 0\r\n+M END\r\n+> <mr_id>\r\n+4291116\r\n+\r\n+> <SMI>\r\n+COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5\r\n+\r\n+$$$$\r\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 34 38 0 0 0 0 999 V2000\r\n+ -5.7794 -9.7727 0.0000 O 0 0\r\n+ -4.8342 -9.0333 0.0000 C 0 0\r\n+ -3.7215 -9.4825 0.0000 O 0 0\r\n+ -5.0445 -7.5473 0.0000 C 0 0\r\n+ -6.4347 -6.9838 0.0000 C 0 0\r\n+ -6.6418 -5.4982 0.0000 C 0 0\r\n+ -5.4588 -4.5759 0.0000 C 0 0\r\n+ -5.6629 -3.0890 0.0000 N 0 0\r\n+ -4.4777 -2.1678 0.0000 C 0 0\r\n+ -4.6909 -0.7107 0.0000 N 0 0\r\n+ -3.5360 0.2310 0.0000 C 0 0\r\n+ -2.1322 -0.3021 0.0000 C 0 0\r\n+ -1.1017 0.7996 0.0000 C 0 0\r\n+ 0.4087 0.6930 0.0000 N 0 0\r\n+ 1.2438 -0.5686 0.0000 C 0 0\r\n+ 2.7297 -0.3578 0.0000 C 0 0\r\n+ 3.5918 -1.5905 0.0000 C 0 0\r\n+ 3.0835 -2.6775 0.0000 F 0 0\r\n+ 5.0862 -1.4619 0.0000 C 0 0\r\n+ 5.7221 -0.1033 0.0000 C 0 0\r\n+ 4.8635 1.1267 0.0000 C 0 0\r\n+ 3.3690 0.9981 0.0000 C 0 0\r\n+ 2.6835 1.9830 0.0000 F 0 0\r\n+ 0.7996 -1.9901 0.0000 C 0 0\r\n+ 1.9546 -2.9496 0.0000 C 0 0\r\n+ 1.7236 -4.4422 0.0000 C 0 0\r\n+ 2.6594 -5.1934 0.0000 Cl 0 0\r\n+ 0.3554 -4.9752 0.0000 C 0 0\r\n+ -0.8174 -3.9980 0.0000 C 0 0\r\n+ -0.5686 -2.5587 0.0000 C 0 0\r\n+ -1.8835 -1.8124 0.0000 C 0 0\r\n+ -3.0918 -2.7364 0.0000 N 0 0\r\n+ -4.0686 -5.1394 0.0000 C 0 0\r\n+ -3.8615 -6.6251 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 2 3 2 0\r\n+ 2 4 1 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 7 8 1 0\r\n+ 8 9 1 0\r\n+ 9 10 1 0\r\n+ 10 11 2 0\r\n+ 11 12 1 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 14 15 2 0\r\n+ 15 16 1 0\r\n+ 16 17 1 0\r\n+ 17 18 1 0\r\n+ 17 19 2 0\r\n+ 19 20 1 0\r\n+ 20 21 2 0\r\n+ 21 22 1 0\r\n+ 16 22 2 0\r\n+ 22 23 1 0\r\n+ 15 24 1 0\r\n+ 24 25 2 0\r\n+ 25 26 1 0\r\n+ 26 27 1 0\r\n+ 26 28 2 0\r\n+ 28 29 1 0\r\n+ 29 30 2 0\r\n+ 24 30 1 0\r\n+ 30 31 1 0\r\n+ 12 31 2 0\r\n+ 31 32 1 0\r\n+ 9 32 2 0\r\n+ 7 33 2 0\r\n+ 33 34 1 0\r\n+ 4 34 2 0\r\n+M END\r\n+> <mr_id>\r\n+4297285\r\n+\r\n+> <SMI>\r\n+OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1\r\n+\r\n+$$$$\r\n' |
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| diff -r 000000000000 -r 2c11d1f9e00b test-data/XChemReactionMaker1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/XChemReactionMaker1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,5393 @@\n+\n+ CDK 0228171352\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ -6.8855 0.7072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.9293 -0.4485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.4503 -0.1983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9276 1.2077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4486 1.4579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.4924 0.3022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0134 0.5525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5094 1.9584 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.9428 -0.6032 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4218 -0.3530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3780 -1.5087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8570 -1.2585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3797 0.1475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8587 0.3977 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4235 1.3032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9445 1.0530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0152 -1.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0590 -2.2594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.4941 -1.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 3 4 2 0 0 0 0 \n+ 4 5 1 0 0 0 0 \n+ 5 6 2 0 0 0 0 \n+ 6 7 1 0 0 0 0 \n+ 7 8 2 0 0 0 0 \n+ 7 9 1 0 0 0 0 \n+ 9 10 1 0 0 0 0 \n+ 10 11 2 0 0 0 0 \n+ 11 12 1 0 0 0 0 \n+ 12 13 2 0 0 0 0 \n+ 13 14 1 0 0 0 0 \n+ 13 15 1 0 0 0 0 \n+ 15 16 2 0 0 0 0 \n+ 6 17 1 0 0 0 0 \n+ 17 18 1 0 0 0 0 \n+ 17 19 2 0 0 0 0 \n+ 19 3 1 0 0 0 0 \n+ 16 10 1 0 0 0 0 \n+M END\n+> <reactant_uuid>\n+df65c0e8-c7dd-492f-b1ee-c58c7e484dda\n+\n+> <source_uuid>\n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+$$$$\n+\n+ CDK 0228171352\n+\n+ 20 21 0 0 0 0 0 0 0 0999 V2000\n+ 0.1344 2.1395 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.3643 0.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6115 -0.4144 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0860 -0.1389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0618 -1.2781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.5363 -1.0027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0350 0.4120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.5095 0.6875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0592 1.5512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5847 1.2758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8388 0.4494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8146 1.5886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.2891 1.3131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.2649 2.4523 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.7878 -0.1015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8120 -1.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.3375 -0.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.3617 -2.1045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.1128 -1.8290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8604 -3.5192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 3 4 1 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+ 6 7 2 0 0 0 0 \n+ 7 8 1 0 0 0 0 \n+ 7 9 1 0 0 0 0 \n+ 9 10 2 0 0 0 0 \n+ 2 11 1 0 0 0 0 \n+ 11 12 2 0 0 0 0 \n+ 12 13 1 0 0 0 0 \n+ 13 14 1 0 0 0 0 \n+ 13 15 2 0 0 0 0 \n+ 15 16 1 0 0 0 0 \n+ 16 17 2 0 0 0 0 \n+ 17 18 1 0 0 0 0 \n+ 18 19 2 0 0 0 0 \n+ 18 20 1 0 0 0 0 \n+ 10 4 1 '..b'3 -2.1380 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9723 -0.8465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7093 0.4600 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.2092 0.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9462 1.7815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4461 1.7965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.2091 0.5050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.7090 0.5201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4721 -0.8014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9722 -0.8165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5276 -0.8615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2645 -2.1680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7645 -2.1830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5274 -0.8915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.9977 -0.5944 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1694 0.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4759 1.6327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7674 0.8697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8053 1.5195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7905 0.4149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2906 0.4300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 3 4 1 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+ 6 7 2 0 0 0 0 \n+ 7 8 1 0 0 0 0 \n+ 7 9 1 0 0 0 0 \n+ 9 10 2 0 0 0 0 \n+ 2 11 1 0 0 0 0 \n+ 11 12 2 0 0 0 0 \n+ 12 13 1 0 0 0 0 \n+ 13 14 2 0 0 0 0 \n+ 14 15 1 0 0 0 0 \n+ 15 16 1 0 0 0 0 \n+ 16 17 1 0 0 0 0 \n+ 17 18 1 0 0 0 0 \n+ 16 19 2 0 0 0 0 \n+ 19 20 1 0 0 0 0 \n+ 20 21 2 0 0 0 0 \n+ 10 4 1 0 0 0 0 \n+ 21 11 1 0 0 0 0 \n+ 20 14 1 0 0 0 0 \n+M END\n+> <reactant_uuid>\n+ad46f59c-f66e-4fd9-a871-bd2efc6f7a1d\n+\n+> <source_uuid>\n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+$$$$\n+\n+ CDK 0228171352\n+\n+ 17 18 0 0 0 0 0 0 0 0999 V2000\n+ 0.0570 1.8667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.4770 0.4650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4699 -0.6983 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9508 -0.4599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8978 -1.6232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3787 -1.3848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.9127 0.0169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3936 0.2553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9658 1.1802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4848 0.9418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.9580 0.2266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.9049 1.3899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.3858 1.1515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.9198 -0.2503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.4008 -0.4887 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9729 -1.4136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4920 -1.1752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 3 4 1 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+ 6 7 2 0 0 0 0 \n+ 7 8 1 0 0 0 0 \n+ 7 9 1 0 0 0 0 \n+ 9 10 2 0 0 0 0 \n+ 2 11 1 0 0 0 0 \n+ 11 12 2 0 0 0 0 \n+ 12 13 1 0 0 0 0 \n+ 13 14 2 0 0 0 0 \n+ 14 15 1 0 0 0 0 \n+ 14 16 1 0 0 0 0 \n+ 16 17 2 0 0 0 0 \n+ 10 4 1 0 0 0 0 \n+ 17 11 1 0 0 0 0 \n+M END\n+> <reactant_uuid>\n+9750a3fa-97eb-444a-bc34-8ea1560759f4\n+\n+> <source_uuid>\n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/cluster_butina_matrix_output1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_butina_matrix_output1.tsv Tue Jul 21 05:22:46 2020 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/cluster_butina_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster_butina_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,2931 @@\n+\n+ RDKit 2D\n+\n+ 26 30 0 0 0 0 0 0 0 0999 V2000\n+ -8.6396 0.9568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6023 1.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6071 3.0602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3104 3.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0040 1.5682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3008 0.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 -0.6045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 -1.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5059 -2.8197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2156 -3.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2329 -5.0846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5404 -5.8196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8308 -5.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8135 -3.5548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 -1.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 -1.3190 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 1.5389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 2 7 1 0\n+ 6 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 11 16 1 0\n+ 10 17 2 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 22 23 1 0\n+ 23 24 2 0\n+ 19 24 1 0\n+ 24 25 1 0\n+ 17 25 1 0\n+ 25 26 2 0\n+ 8 26 1 0\n+M END\n+> <mr_id> (1) \n+4358263\n+\n+> <SMI> (1) \n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\n+\n+> <Cluster> (1) \n+29\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 43 51 0 0 1 0 0 0 0 0999 V2000\n+ -4.7204 3.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.1471 2.2890 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6500 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8100 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.2400 3.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5000 2.1800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0600 2.1800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9800 -0.7800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -1.4600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3200 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5500 -1.4800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5800 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3400 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -2.7900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2400 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.4300 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7600 -4.9700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.2600 -5.0800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8500 -3.6300 0.'..b'85 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 5 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 3 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 16 17 1 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 21 22 1 0\n+ 17 22 1 0\n+ 6 23 1 0\n+ 23 24 1 0\n+ 24 25 1 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 23 28 1 0\n+ 26 29 1 0\n+ 29 30 2 0\n+ 29 31 1 0\n+ 31 32 1 0\n+ 32 33 2 0\n+ 33 34 1 0\n+ 34 35 2 0\n+ 35 36 1 0\n+ 36 37 1 0\n+ 37 38 1 0\n+ 37 39 1 0\n+ 35 40 1 0\n+ 40 41 2 0\n+ 32 41 1 0\n+M END\n+> <mr_id> (35) \n+4291116\n+\n+> <SMI> (35) \n+COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5\n+\n+> <Cluster> (35) \n+5\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 34 38 0 0 0 0 0 0 0 0999 V2000\n+ -5.7794 -9.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.8342 -9.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7215 -9.4825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0445 -7.5473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.4347 -6.9838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.6418 -5.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4588 -4.5759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.6629 -3.0890 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.4777 -2.1678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.6909 -0.7107 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5360 0.2310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1322 -0.3021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1017 0.7996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4087 0.6930 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2438 -0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7297 -0.3578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5918 -1.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0835 -2.6775 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0862 -1.4619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7221 -0.1033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8635 1.1267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3690 0.9981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6835 1.9830 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7996 -1.9901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9546 -2.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7236 -4.4422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6594 -5.1934 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3554 -4.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8174 -3.9980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5686 -2.5587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8835 -1.8124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0918 -2.7364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0686 -5.1394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8615 -6.6251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 17 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 16 22 1 0\n+ 22 23 1 0\n+ 15 24 1 0\n+ 24 25 2 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 26 28 2 0\n+ 28 29 1 0\n+ 29 30 2 0\n+ 24 30 1 0\n+ 30 31 1 0\n+ 12 31 1 0\n+ 31 32 2 0\n+ 9 32 1 0\n+ 7 33 1 0\n+ 33 34 2 0\n+ 4 34 1 0\n+M END\n+> <mr_id> (36) \n+4297285\n+\n+> <SMI> (36) \n+OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1\n+\n+> <Cluster> (36) \n+4\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/constrained_conf_gen_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constrained_conf_gen_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,12550 @@\n+\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ 9.1252 0.5350 1.2654 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.1887 -0.3817 0.7086 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8030 -0.1676 0.6608 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2021 0.9979 1.1671 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8167 1.1629 1.0998 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0017 0.1666 0.5346 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5365 0.3642 0.4841 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0623 1.5348 0.4824 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6533 -0.7523 0.6559 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2537 -0.6268 0.4089 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1922 -0.0627 -0.7897 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5070 0.3799 -0.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4163 0.0957 0.1308 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6858 0.6629 0.1319 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0268 -0.7174 1.1999 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6792 -1.0451 1.3647 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6065 -0.9937 0.0066 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8341 -1.9757 -0.6142 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9978 -1.1539 0.0831 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 9 1 0\n+ 9 10 1 0\n+ 10 11 2 0\n+ 11 12 1 0\n+ 12 13 2 0\n+ 13 14 1 0\n+ 13 15 1 0\n+ 15 16 2 0\n+ 6 17 1 0\n+ 17 18 1 0\n+ 17 19 2 0\n+ 19 3 1 0\n+ 16 10 1 0\n+M END\n+> <reactant_uuid> (1) \n+df65c0e8-c7dd-492f-b1ee-c58c7e484dda\n+\n+> <source_uuid> (1) \n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+> <EmbedRMS> (1) \n+0.09745244728532461\n+\n+> <SourceMolNum> (1) \n+1\n+\n+> <ConformerNum> (1) \n+1\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ 9.1252 0.5350 1.2654 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.1887 -0.3817 0.7086 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8030 -0.1676 0.6608 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2021 0.9979 1.1671 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8167 1.1629 1.0998 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0017 0.1666 0.5346 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5365 0.3642 0.4841 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0623 1.5348 0.4824 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6533 -0.7523 0.6559 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2537 -0.6268 0.4089 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1922 -0.0627 -0.7897 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5070 0.3799 -0.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4163 0.0957 0.1308 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6858 0.6629 0.1319 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0268 -0.7174 1.1999 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6792 -1.0451 1.3647 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6065 -0.9937 0.0066 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8341 -1.9757 -0.6142 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9978 -1.1539 0.0831 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 9 1 0\n+ 9 10 1 0\n+ 10 11 2 0\n+ 11 12 1 0\n+ 12 13 2 0\n+ 13 14 1 0\n+ 13 15 1 0\n+ 15 16 2 0\n+ 6 17 1 0\n+ 17 18 1 0\n+ 17 19 2 0\n+ 19 3 1 0\n+ 16 10 1 0\n+M END\n+> <reactant_uuid> (2) \n+df65c0e8-c7dd-492f-b1ee-c58c7e484dda\n+\n+> <source_uuid> (2) \n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+> <EmbedRMS> (2) \n+0.09745244728532461\n+\n+> <SourceMolNum> (2) \n+1\n+\n+> <ConformerNum> (2) \n+2\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 20 21 0 0 0 0 0 0 0 0999 V2000\n+ 2.0651 1.5'..b'6 1 0\n+ 16 17 1 0\n+ 17 18 1 0\n+ 16 19 2 0\n+ 19 20 1 0\n+ 20 21 2 0\n+ 10 4 1 0\n+ 21 11 1 0\n+ 20 14 1 0\n+M END\n+> <reactant_uuid> (198) \n+ad46f59c-f66e-4fd9-a871-bd2efc6f7a1d\n+\n+> <source_uuid> (198) \n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+> <EmbedRMS> (198) \n+0.0991211499751241\n+\n+> <SourceMolNum> (198) \n+99\n+\n+> <ConformerNum> (198) \n+2\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 17 18 0 0 0 0 0 0 0 0999 V2000\n+ 2.0615 1.5275 0.4718 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5393 0.3584 0.4994 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6515 -0.7609 0.6458 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2524 -0.6236 0.4084 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1965 -0.0586 -0.7883 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5126 0.3816 -0.8888 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4183 0.0942 0.1356 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6842 0.6691 0.1207 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0248 -0.7216 1.2041 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6766 -1.0463 1.3651 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0084 0.1801 0.5357 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6142 -0.8950 1.2155 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0062 -1.0299 1.2299 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8131 -0.0929 0.5734 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2003 -0.2197 0.5810 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2217 0.9827 -0.0934 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8309 1.1223 -0.1094 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 7 9 1 0\n+ 9 10 2 0\n+ 2 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 14 15 1 0\n+ 14 16 1 0\n+ 16 17 2 0\n+ 10 4 1 0\n+ 17 11 1 0\n+M END\n+> <reactant_uuid> (199) \n+9750a3fa-97eb-444a-bc34-8ea1560759f4\n+\n+> <source_uuid> (199) \n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+> <EmbedRMS> (199) \n+0.10259243646429834\n+\n+> <SourceMolNum> (199) \n+100\n+\n+> <ConformerNum> (199) \n+1\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 17 18 0 0 0 0 0 0 0 0999 V2000\n+ 2.0615 1.5275 0.4718 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5393 0.3584 0.4994 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6515 -0.7609 0.6458 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2524 -0.6236 0.4084 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1965 -0.0586 -0.7883 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5126 0.3816 -0.8888 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4183 0.0942 0.1356 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6842 0.6691 0.1207 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0248 -0.7216 1.2041 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6766 -1.0463 1.3651 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0084 0.1801 0.5357 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6142 -0.8950 1.2155 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0062 -1.0299 1.2299 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8131 -0.0929 0.5734 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2003 -0.2197 0.5810 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2217 0.9827 -0.0934 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8309 1.1223 -0.1094 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 7 9 1 0\n+ 9 10 2 0\n+ 2 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 14 15 1 0\n+ 14 16 1 0\n+ 16 17 2 0\n+ 10 4 1 0\n+ 17 11 1 0\n+M END\n+> <reactant_uuid> (200) \n+9750a3fa-97eb-444a-bc34-8ea1560759f4\n+\n+> <source_uuid> (200) \n+33509b1f-56f4-4a43-bc9f-5aea174b9dad\n+\n+> <EmbedRMS> (200) \n+0.10259243646429834\n+\n+> <SourceMolNum> (200) \n+100\n+\n+> <ConformerNum> (200) \n+2\n+\n+$$$$\n+\n+gzip: outp.sdf.gz: unexpected end of file\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/dhfr_3d.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dhfr_3d.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,83921 @@\n+1-pyrimethamine\n+ Cerius2 12180216023D 1 1.00000 \n+ Structure written by MMmdl.\n+ 30 31 0 0 0 0 0 0 0 0999 V2000\n+ -2.8357 0.2028 0.4209 N 0 0 0 0 0 0\n+ -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0\n+ -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0\n+ -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0\n+ -0.4439 0.2086 0.1358 C 0 0 0 0 0 0\n+ -1.6550 0.8467 0.4052 C 0 0 0 0 0 0\n+ 0.8362 0.9302 0.0951 C 0 0 0 0 0 0\n+ 1.6327 1.0444 1.2466 C 0 0 0 0 0 0\n+ 2.8536 1.7244 1.2069 C 0 0 0 0 0 0\n+ 3.2885 2.2979 0.0146 C 0 0 0 0 0 0\n+ 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0\n+ 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0\n+ -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0\n+ -1.7348 2.2137 0.6034 N 0 0 0 0 0 0\n+ 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0\n+ 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0\n+ 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0\n+ 1.3065 0.6014 2.1872 H 0 0 0 0 0 0\n+ 3.4548 1.8000 2.1100 H 0 0 0 0 0 0\n+ 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0\n+ 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0\n+ -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0\n+ -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0\n+ -0.9674 2.6820 1.0738 H 0 0 0 0 0 0\n+ -2.6605 2.5780 0.8038 H 0 0 0 0 0 0\n+ 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0\n+ -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0\n+ -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0\n+ 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0\n+ 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0\n+ 1 2 2 0 0 0\n+ 1 6 1 0 0 0\n+ 2 3 1 0 0 0\n+ 2 13 1 0 0 0\n+ 3 4 2 0 0 0\n+ 4 5 1 0 0 0\n+ 4 17 1 0 0 0\n+ 5 6 2 0 0 0\n+ 5 7 1 0 0 0\n+ 6 14 1 0 0 0\n+ 7 8 2 0 0 0\n+ 7 12 1 0 0 0\n+ 8 9 1 0 0 0\n+ 8 18 1 0 0 0\n+ 9 10 2 0 0 0\n+ 9 19 1 0 0 0\n+ 10 11 1 0 0 0\n+ 10 15 1 0 0 0\n+ 11 12 2 0 0 0\n+ 11 20 1 0 0 0\n+ 12 21 1 0 0 0\n+ 13 22 1 0 0 0\n+ 13 23 1 0 0 0\n+ 14 24 1 0 0 0\n+ 14 25 1 0 0 0\n+ 16 17 1 0 0 0\n+ 16 26 1 0 0 0\n+ 16 27 1 0 0 0\n+ 16 28 1 0 0 0\n+ 17 29 1 0 0 0\n+ 17 30 1 0 0 0\n+M END\n+> <Name>\n+1-pyrimethamine\n+\n+> <Family>\n+A\n+\n+> <PC_uM>\n+3.7\n+\n+> <TG_uM>\n+0.39\n+\n+> <RL_uM>\n+2.3\n+\n+> <set>\n+1\n+\n+$$$$\n+1-3062\n+ Cerius2 12180216023D 1 1.00000 \n+ Structure written by MMmdl.\n+ 30 31 0 0 0 0 0 0 0 0999 V2000\n+ -2.8168 0.2065 0.4735 N 0 0 0 0 0 0\n+ -2.8206 -1.1045 0.2371 C 0 0 0 0 0 0\n+ -1.7327 -1.8208 -0.0438 N 0 0 0 0 0 0\n+ -0.5439 -1.1720 -0.0988 C 0 0 0 0 0 0\n+ -0.4317 0.1989 0.1374 C 0 0 0 0 0 0\n+ -1.6324 0.8424 0.4390 C 0 0 0 0 0 0\n+ 0.8521 0.9130 0.0752 C 0 0 0 0 0 0\n+ 1.6858 0.9917 1.2029 C 0 0 0 0 0 0\n+ 2.9119 1.6650 1.1430 C 0 0 0 0 0 0\n+ 3.3184 2.2713 -0.0498 C 0 0 0 0 0 0\n+ 2.4965 2.2018 -1.1763 C 0 0 0 0 0 0\n+ 1.2730 1.5284 -1.1135 C 0 0 0 0 0 0\n+ -4.0128 -1.7579 0.2830 N 0 0 0 0 0 0\n+ -1.6980 2.2076 0.6534 N 0 0 0 0 0 0\n+ 4.8189 3.1175 -0.1945 Cl 0 0 0 0 0 0\n+ 0.3929 -3.4780 -0.7058 C 0 0 0 0 0 0\n+ 0.6782 -2.0057 -0.4320 C 0 0 0 0 0 0\n+ 3.8777 1.7088 2.5773 Cl 0 0 0 0 0 0\n+ 1.3763 0.5224 2.1357 H 0 0 0 0 0 0\n+ 2.7982 2.6697 -2.1110 H 0 0 0 0 0 0\n+ 0.6467 1.4886 -2.0046 H 0 0 0 0 0 0\n+ -4.0437 -2.7510 0.1067 H 0 0 0 0 0 0\n+ -4.8568 -1.2458 0.4914 H 0 0 0 0 0 0\n+ -0.9218 2.6660 1.1184 H 0 0 0 0 0 0\n+ -2.6181 2.5747 0.8742 H 0 0 0 0 0 0\n+ 1.3238 -4.0'..b'-0.2684 0.5909 H 0 0 0 0 0 0\n+ 1 2 2 0 0 0\n+ 1 6 1 0 0 0\n+ 2 3 1 0 0 0\n+ 2 12 1 0 0 0\n+ 3 4 2 0 0 0\n+ 4 5 1 0 0 0\n+ 4 7 1 0 0 0\n+ 5 6 2 0 0 0\n+ 5 10 1 0 0 0\n+ 6 11 1 0 0 0\n+ 7 8 2 0 0 0\n+ 8 9 1 0 0 0\n+ 8 14 1 0 0 0\n+ 9 10 2 0 0 0\n+ 9 13 1 0 0 0\n+ 10 21 1 0 0 0\n+ 11 22 1 0 0 0\n+ 11 23 1 0 0 0\n+ 12 24 1 0 0 0\n+ 12 25 1 0 0 0\n+ 13 16 2 0 0 0\n+ 13 26 1 0 0 0\n+ 14 15 2 0 0 0\n+ 14 17 1 0 0 0\n+ 15 16 1 0 0 0\n+ 15 20 1 0 0 0\n+ 16 27 1 0 0 0\n+ 17 18 2 0 0 0\n+ 17 28 1 0 0 0\n+ 18 19 1 0 0 0\n+ 18 29 1 0 0 0\n+ 19 20 2 0 0 0\n+ 19 30 1 0 0 0\n+ 20 31 1 0 0 0\n+M END\n+> <Name>\n+51-10\n+\n+> <Family>\n+misc\n+\n+> <PC_uM>\n+>0.4\n+\n+> <TG_uM>\n+0.460000\n+\n+> <RL_uM>\n+2.400000\n+\n+> <set>\n+0\n+\n+$$$$\n+46-210057\n+ Cerius2 12180216033D 1 1.00000 \n+ Structure written by MMmdl.\n+ 39 40 0 0 0 0 0 0 0 0999 V2000\n+ -2.8284 1.2604 3.3541 N 0 0 0 0 0 0\n+ -3.3955 0.5713 2.3605 C 0 0 0 0 0 0\n+ -2.7309 -0.2154 1.5116 N 0 0 0 0 0 0\n+ -1.3931 -0.3178 1.6803 C 0 0 0 0 0 0\n+ -0.7313 0.3607 2.6834 C 0 0 0 0 0 0\n+ -1.4984 1.1631 3.4943 C 0 0 0 0 0 0\n+ -0.2665 0.2739 -1.2642 C 0 0 0 0 0 0\n+ 0.2828 -0.4834 -0.2178 C 0 0 0 0 0 0\n+ 1.6783 -0.5254 -0.0902 C 0 0 0 0 0 0\n+ 2.4961 0.2194 -0.9566 C 0 0 0 0 0 0\n+ 1.9388 0.9519 -2.0165 C 0 0 0 0 0 0\n+ 0.5504 0.9772 -2.1574 C 0 0 0 0 0 0\n+ -0.9276 1.8480 4.5468 N 0 0 0 0 0 0\n+ -4.7431 0.6724 2.2021 N 0 0 0 0 0 0\n+ 2.8258 1.6039 -2.8335 O 0 0 0 0 0 0\n+ 2.2831 2.2818 -3.9652 C 0 0 0 0 0 0\n+ 2.2308 -1.2525 0.9358 O 0 0 0 0 0 0\n+ 2.7540 -2.4925 0.4421 C 0 0 0 0 0 0\n+ -0.6386 -1.2208 0.7310 C 0 0 0 0 0 0\n+ 3.8646 0.1924 -0.8111 O 0 0 0 0 0 0\n+ 4.2687 1.1510 0.1733 C 0 0 0 0 0 0\n+ 0.3381 0.2663 2.8272 H 0 0 0 0 0 0\n+ -1.3481 0.3205 -1.3942 H 0 0 0 0 0 0\n+ 0.0624 1.5420 -2.9475 H 0 0 0 0 0 0\n+ 0.0083 2.2253 4.4316 H 0 0 0 0 0 0\n+ -1.5604 2.4228 5.0949 H 0 0 0 0 0 0\n+ -5.1972 0.1572 1.4626 H 0 0 0 0 0 0\n+ -5.2778 1.2590 2.8250 H 0 0 0 0 0 0\n+ 3.1194 2.6902 -4.5405 H 0 0 0 0 0 0\n+ 1.6515 3.1195 -3.6519 H 0 0 0 0 0 0\n+ 1.7367 1.5911 -4.6162 H 0 0 0 0 0 0\n+ 2.9877 -3.1204 1.3068 H 0 0 0 0 0 0\n+ 3.6786 -2.3337 -0.1215 H 0 0 0 0 0 0\n+ 2.0183 -3.0230 -0.1733 H 0 0 0 0 0 0\n+ -1.3546 -1.7999 0.1320 H 0 0 0 0 0 0\n+ -0.0955 -1.9685 1.3200 H 0 0 0 0 0 0\n+ 5.3622 1.1855 0.1766 H 0 0 0 0 0 0\n+ 3.9368 0.8516 1.1729 H 0 0 0 0 0 0\n+ 3.8982 2.1539 -0.0672 H 0 0 0 0 0 0\n+ 1 2 2 0 0 0\n+ 1 6 1 0 0 0\n+ 2 3 1 0 0 0\n+ 2 14 1 0 0 0\n+ 3 4 2 0 0 0\n+ 4 5 1 0 0 0\n+ 4 19 1 0 0 0\n+ 5 6 2 0 0 0\n+ 5 22 1 0 0 0\n+ 6 13 1 0 0 0\n+ 7 8 2 0 0 0\n+ 7 12 1 0 0 0\n+ 7 23 1 0 0 0\n+ 8 9 1 0 0 0\n+ 8 19 1 0 0 0\n+ 9 10 2 0 0 0\n+ 9 17 1 0 0 0\n+ 10 11 1 0 0 0\n+ 10 20 1 0 0 0\n+ 11 12 2 0 0 0\n+ 11 15 1 0 0 0\n+ 12 24 1 0 0 0\n+ 13 25 1 0 0 0\n+ 13 26 1 0 0 0\n+ 14 27 1 0 0 0\n+ 14 28 1 0 0 0\n+ 15 16 1 0 0 0\n+ 16 29 1 0 0 0\n+ 16 30 1 0 0 0\n+ 16 31 1 0 0 0\n+ 17 18 1 0 0 0\n+ 18 32 1 0 0 0\n+ 18 33 1 0 0 0\n+ 18 34 1 0 0 0\n+ 19 35 1 0 0 0\n+ 19 36 1 0 0 0\n+ 20 21 1 0 0 0\n+ 21 37 1 0 0 0\n+ 21 38 1 0 0 0\n+ 21 39 1 0 0 0\n+M END\n+> <Name>\n+46-210057\n+\n+> <Family>\n+misc\n+\n+> <PC_uM>\n+>30\n+\n+> <TG_uM>\n+N/A\n+\n+> <RL_uM>\n+N/A\n+\n+> <set>\n+2\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/hits-17.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hits-17.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,602 @@\n+Mpro-x0072_0\n+ RDKit 3D\n+\n+ 13 13 0 0 0 0 0 0 0 0999 V2000\n+ 9.8790 -5.4960 26.1730 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4790 -4.3410 26.0680 S 0 0 1 0 0 0 0 0 0 0 0 0\n+ 7.1910 -5.0190 26.2290 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4340 -3.4430 27.2120 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4960 -3.4980 24.5920 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7540 -3.0340 24.0580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5680 -1.8260 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8760 -1.0500 23.1440 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9060 -1.4610 22.3160 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1060 -0.7790 22.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.2770 0.3180 23.1500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2420 0.7320 23.9810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0390 0.0410 23.9830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2 1 1 1\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 8 13 1 0\n+ 9 10 1 0\n+ 13 12 2 0\n+ 10 11 2 0\n+ 11 12 1 0\n+M END\n+$$$$\n+Mpro-x0104_0\n+ RDKit 3D\n+\n+ 16 17 0 0 0 0 0 0 0 0999 V2000\n+ 9.5220 5.3850 22.9640 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.6910 5.7360 23.8810 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.4660 6.3160 24.8740 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0740 5.3880 23.6220 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.4920 4.6500 22.4510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1760 3.3750 22.9180 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2100 2.3170 23.4570 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.1390 2.4870 24.3210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5720 1.3010 24.5250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.2360 0.3380 23.8210 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0300 -1.0620 23.6930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.8800 -1.8120 22.8830 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.9290 -1.1860 22.1980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1280 0.1820 22.3230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2670 0.9460 23.1470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.7690 -1.8980 21.4040 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 15 1 0\n+ 8 9 1 0\n+ 15 10 2 0\n+ 15 14 1 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 13 16 1 0\n+M END\n+$$$$\n+Mpro-x0107_0\n+ RDKit 3D\n+\n+ 11 11 0 0 0 0 0 0 0 0999 V2000\n+ 10.1640 -0.7840 22.5400 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.2630 -0.1570 21.4780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5870 0.8590 20.9670 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.0140 -0.7980 21.1040 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.1560 -0.2070 20.0890 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5230 -0.2650 18.7510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7670 0.2590 17.8050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6370 0.8610 18.1030 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.1890 0.9760 19.4120 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9640 0.4250 20.4340 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5280 0.5220 21.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 7 1 0\n+ 10 9 2 0\n+ 10 11 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+M END\n+$$$$\n+Mpro-x0161_0\n+ RDKit 3D\n+\n+ 14 14 0 0 0 0 0 0 0 0999 V2000\n+ 11.6590 -1.5020 21.8060 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3210 -1.6370 23.0350 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.0730 -0.5250 23.4440 C 0 0 0 0 0 0 0 0 '..b'0 0 0 0 0 0 0 0 0 0\n+ 9.9550 -5.4170 24.6470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.9660 -5.9220 23.5900 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5010 -5.7070 24.0110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.3510 -4.8000 26.2520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7670 -4.2080 26.4740 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 3 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 4 6 1 0\n+ 3 13 1 0\n+ 3 14 1 0\n+ 13 12 1 0\n+ 14 15 1 0\n+ 5 10 1 0\n+ 6 8 2 0\n+ 10 9 2 0\n+ 8 9 1 0\n+ 7 9 1 0\n+ 7 11 1 0\n+ 7 15 1 0\n+ 11 12 1 0\n+M END\n+$$$$\n+Mpro-x1093_0\n+ RDKit 3D\n+\n+ 19 21 0 0 0 0 0 0 0 0999 V2000\n+ 13.9130 -1.2590 23.2230 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5110 -0.9700 23.5310 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1000 1.2550 21.1530 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.6150 -1.9330 22.8770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9240 -0.2280 22.6330 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.1650 -1.5840 23.1190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7830 0.2880 17.8390 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7420 0.7360 23.3590 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7860 1.4690 18.5050 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.1970 0.4050 23.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.1590 0.1020 21.5780 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.3780 -1.0090 20.8940 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5260 -0.4030 19.8320 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7680 -0.4040 18.4910 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8860 0.7470 18.7550 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0720 1.8050 19.5870 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4050 1.4630 20.8980 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5480 0.7300 21.1350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3230 0.3480 20.0330 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 4 1 0\n+ 2 10 1 0\n+ 4 6 1 0\n+ 10 8 1 0\n+ 3 11 2 0\n+ 11 5 1 0\n+ 11 12 1 0\n+ 6 5 1 0\n+ 5 8 1 0\n+ 7 14 1 0\n+ 7 15 1 0\n+ 14 13 2 0\n+ 15 9 2 0\n+ 15 19 1 0\n+ 9 16 1 0\n+ 16 17 2 0\n+ 12 13 1 0\n+ 13 19 1 0\n+ 19 18 2 0\n+ 17 18 1 0\n+M END\n+$$$$\n+Mpro-x1249_0\n+ RDKit 3D\n+\n+ 18 19 0 0 0 0 0 0 0 0999 V2000\n+ 8.5420 0.5850 24.9250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.7940 1.3450 24.0240 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2640 2.3450 23.4580 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.9260 0.9180 25.2490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.0600 -1.8530 20.5550 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5640 0.9570 23.6730 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8450 0.2990 24.2350 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.4250 0.8450 23.8150 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.0070 0.9620 23.8500 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.8550 0.3860 22.9070 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.5210 -0.8490 22.3430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.3580 -1.4190 21.3580 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.3630 -1.5210 22.7290 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.5270 -0.9460 23.6770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.5720 0.7280 25.0430 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.1400 0.2280 24.7420 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3070 0.9270 22.4720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7020 1.5370 22.7150 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 4 1 0\n+ 2 3 2 0\n+ 2 8 1 0\n+ 4 7 1 0\n+ 8 15 1 0\n+ 8 18 1 0\n+ 7 9 2 0\n+ 7 14 1 0\n+ 5 12 3 0\n+ 12 11 1 0\n+ 6 16 1 0\n+ 6 17 1 0\n+ 16 15 1 0\n+ 17 18 1 0\n+ 9 10 1 0\n+ 14 13 2 0\n+ 10 11 2 0\n+ 11 13 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/pbf_ev_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pbf_ev_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,3237 @@\n+\n+ RDKit 3D\n+\n+ 26 30 0 0 0 0 0 0 0 0999 V2000\n+ 5.7817 1.5920 -0.5649 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.9278 0.4991 -0.5167 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.4650 -0.7807 -0.6164 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6765 -1.9128 -0.5762 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3109 -1.7100 -0.4304 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7551 -0.4588 -0.3298 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5583 0.6333 -0.3729 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2948 -0.3479 -0.1776 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6925 0.8501 -0.0742 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6362 0.9861 0.0656 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2747 2.2538 0.1751 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0536 2.6449 1.3105 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.9622 4.1038 1.6190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8706 4.9014 0.4861 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.7722 4.5334 -0.3110 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1254 3.1921 -0.9211 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.4436 -0.1323 0.1082 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.7386 -0.3125 0.2333 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0401 -1.5886 0.2190 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.2003 -2.2657 0.3130 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.2497 -3.6098 0.2706 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0694 -4.3313 0.1253 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8731 -3.6491 0.0278 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8453 -2.2882 0.0729 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8276 -1.3623 0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5199 -1.4398 -0.1374 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 2 7 1 0\n+ 6 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 11 16 1 0\n+ 10 17 2 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 22 23 1 0\n+ 23 24 2 0\n+ 19 24 1 0\n+ 24 25 1 0\n+ 17 25 1 0\n+ 25 26 2 0\n+ 8 26 1 0\n+M END\n+> <mr_id> (1) \n+4358263\n+\n+> <SMI> (1) \n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\n+\n+> <distance> (1) \n+0.18727589657179827\n+\n+> <angle_0> (1) \n+0.3065745189323571\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 43 51 0 0 1 0 0 0 0 0999 V2000\n+ 3.0698 -2.4381 -0.8707 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7802 -1.9263 -1.0276 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.8267 -0.5773 -1.5059 C 0 0 2 0 0 0 0 0 0 0 0 0\n+ 2.3349 0.3742 -0.2318 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 0.9082 0.3792 0.5488 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4679 1.8098 -0.2452 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 0.1482 1.1942 -1.5901 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3346 -0.1141 -1.6460 C 0 0 1 0 0 0 0 0 0 0 0 0\n+ 0.1897 -0.2808 -3.2054 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.6902 -0.9567 -1.1938 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0083 -2.2050 -1.5534 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.3526 -3.1055 -2.3683 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9113 -4.3607 -2.5797 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1143 -4.7117 -1.9791 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.7438 -3.7769 -1.1628 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.2078 -2.5308 -0.9425 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6293 -1.4463 -0.1865 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7508 -1.1917 0.5937 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.9203 -2.0218 0.9397 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.7688 -1.2292 1.7724 N 0 '..b'17 1 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 21 22 1 0\n+ 17 22 1 0\n+ 6 23 1 0\n+ 23 24 1 0\n+ 24 25 1 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 23 28 1 0\n+ 26 29 1 0\n+ 29 30 2 0\n+ 29 31 1 0\n+ 31 32 1 0\n+ 32 33 2 0\n+ 33 34 1 0\n+ 34 35 2 0\n+ 35 36 1 0\n+ 36 37 1 0\n+ 37 38 1 0\n+ 37 39 1 0\n+ 35 40 1 0\n+ 40 41 2 0\n+ 32 41 1 0\n+M END\n+> <mr_id> (35) \n+4291116\n+\n+> <SMI> (35) \n+COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5\n+\n+> <distance> (35) \n+0.77266088281599687\n+\n+> <angle_0> (35) \n+14.150100561002294\n+\n+> <angle_1> (35) \n+21.93457092002464\n+\n+$$$$\n+\n+ RDKit 3D\n+\n+ 34 38 0 0 0 0 0 0 0 0999 V2000\n+ 9.3174 0.9176 0.3373 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2908 0.0883 0.7567 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5738 -0.8433 1.5441 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.9440 0.3428 0.2623 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.6626 1.3776 -0.6049 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3851 1.6113 -1.0679 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3233 0.8193 -0.6853 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0030 1.0718 -1.1724 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9554 0.2063 -0.7294 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.1670 -0.8075 0.1060 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2102 -1.6548 0.5545 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0790 -1.4067 0.0772 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0958 -2.3698 0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.3017 -1.7656 1.0625 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0542 -0.8083 0.5414 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.2149 -0.4492 1.3300 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0625 0.5652 1.0989 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.7731 1.5182 0.1721 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.2421 0.7671 1.8522 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.5408 -0.1056 2.8695 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.6782 -1.1445 3.1161 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5380 -1.3384 2.3843 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6994 -2.3809 2.6529 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8154 -0.2252 -0.7646 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9573 0.0968 -1.4467 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8266 0.6502 -2.7027 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.2457 1.0998 -3.6617 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5957 0.8950 -3.3058 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.4373 0.5654 -2.6115 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5831 0.0137 -1.3616 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.2702 -0.3359 -0.7975 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7122 0.4729 -1.2105 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.5935 -0.2185 0.1817 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.8728 -0.4491 0.6427 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 17 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 16 22 1 0\n+ 22 23 1 0\n+ 15 24 1 0\n+ 24 25 2 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 26 28 2 0\n+ 28 29 1 0\n+ 29 30 2 0\n+ 24 30 1 0\n+ 30 31 1 0\n+ 12 31 1 0\n+ 31 32 2 0\n+ 9 32 1 0\n+ 7 33 1 0\n+ 33 34 2 0\n+ 4 34 1 0\n+M END\n+> <mr_id> (36) \n+4297285\n+\n+> <SMI> (36) \n+OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1\n+\n+> <distance> (36) \n+0.64716140861609839\n+\n+> <angle_0> (36) \n+2.6924651290610671\n+\n+> <angle_1> (36) \n+22.520493131956616\n+\n+> <angle_2> (36) \n+39.845642308232193\n+\n+> <angle_3> (36) \n+2.3384482013466448\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/poses.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/poses.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,964 @@\n+CCOC(=O)c1ccccc1\n+ RDKit 3D\n+\n+ 21 21 0 0 0 0 0 0 0 0999 V2000\n+ 6.3781 -1.3795 25.0647 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.2779 -2.0723 24.0541 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5337 -1.4039 23.9972 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5716 -1.8142 23.1534 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.4148 -2.8154 22.4008 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8522 -1.0709 23.1463 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9075 -1.4723 22.3079 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1179 -0.7755 22.3131 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.2869 0.3279 23.1510 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2452 0.7375 23.9854 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0327 0.0425 23.9858 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.2136 -0.3230 24.7644 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3975 -1.8984 25.1116 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.8482 -1.4040 26.0706 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.4291 -3.1299 24.3613 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7938 -2.0478 23.0537 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.7998 -2.3259 21.6505 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.9263 -1.0913 21.6663 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.2257 0.8667 23.1533 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3778 1.5937 24.6343 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2396 0.3761 24.6432 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 4 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 2 0\n+ 11 6 1 0\n+ 1 12 1 0\n+ 1 13 1 0\n+ 1 14 1 0\n+ 2 15 1 0\n+ 2 16 1 0\n+ 7 17 1 0\n+ 8 18 1 0\n+ 9 19 1 0\n+ 10 20 1 0\n+ 11 21 1 0\n+M END\n+> <EmbedRMS> (1)\n+0.016243762993699434\n+\n+> <Hit> (1)\n+1\n+\n+> <TETHERED ATOMS> (1)\n+4,6,7,8,9,10,11\n+\n+$$$$\n+COc1ccc(CCNS(C)(=O)=O)cc1\n+ RDKit 3D\n+\n+ 29 29 0 0 0 0 0 0 0 0999 V2000\n+ 15.6468 0.7693 22.4057 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.4981 1.0647 23.1936 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.2995 0.3369 23.1508 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1226 -0.7755 22.3075 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9106 -1.4669 22.3010 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8580 -1.0534 23.1266 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5855 -1.8494 23.1794 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7474 -3.0138 24.1604 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4297 -3.5052 24.5470 N 0 0 0 0 0 2 0 0 0 0 0 0\n+ 8.4630 -4.3499 26.0676 S 0 0 0 0 0 6 0 0 0 0 0 0\n+ 9.8448 -5.4799 26.1663 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.1796 -5.1104 26.2026 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5187 -3.3734 27.2038 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0382 0.0458 23.9791 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.2493 0.7390 23.9829 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 16.0196 -0.2499 22.6413 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 16.4454 1.5026 22.6399 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 15.3991 0.8459 21.3259 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.9170 -1.1160 21.6576 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.7953 -2.3308 21.6579 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.3289 -2.2403 22.1705 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7483 -1.1923 23.5044 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2948 -2.6558 25.0623 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.3297 -3.8334 23.6867 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7602 -6.0885 27.0901 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7964 -4.9103 26.1916 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.8389 -6.1503 25.2824 H 0 0 0 0 '..b' 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.8389 -6.1503 25.2824 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7964 -4.9103 26.1916 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7602 -6.0885 27.0901 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2947 -2.6556 25.0623 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.3297 -3.8335 23.6870 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.3292 -2.2408 22.1702 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7481 -1.1927 23.5037 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.7954 -2.3307 21.6582 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.9196 -1.1138 21.6587 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3604 1.5876 24.6487 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2432 0.3597 24.6446 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 2 0\n+ 11 12 1 0\n+ 12 13 2 0\n+ 12 14 1 0\n+ 11 15 1 0\n+ 15 16 2 0\n+ 16 8 1 0\n+ 1 17 1 0\n+ 1 18 1 0\n+ 1 19 1 0\n+ 6 20 1 0\n+ 6 21 1 0\n+ 7 22 1 0\n+ 7 23 1 0\n+ 9 24 1 0\n+ 10 25 1 0\n+ 15 26 1 0\n+ 16 27 1 0\n+M CHG 2 5 -1 14 -1\n+M END\n+> <EmbedRMS> (13)\n+0.058548333509641205\n+\n+> <Hit> (13)\n+1\n+\n+> <TETHERED ATOMS> (13)\n+1,2,3,4,5,6,7,8,9,10,11,15,16\n+\n+$$$$\n+CS(=O)(=O)NCCc1ccc(C(=O)O)cc1\n+ RDKit 3D\n+\n+ 28 28 0 0 0 0 0 0 0 0999 V2000\n+ 9.8444 -5.4803 26.1661 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4617 -4.3513 26.0680 S 0 0 0 0 0 6 0 0 0 0 0 0\n+ 7.1785 -5.1119 26.2062 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.5189 -3.3740 27.2034 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.4280 -3.5065 24.5472 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7477 -3.0117 24.1608 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.5866 -1.8490 23.1770 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.8584 -1.0528 23.1254 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.9111 -1.4662 22.3008 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1227 -0.7748 22.3083 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.3028 0.3368 23.1490 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.5865 1.0726 23.1607 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 15.5371 0.7148 22.4152 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.7618 2.1705 23.9953 O 0 0 0 0 0 1 0 0 0 0 0 0\n+ 12.2483 0.7401 23.9845 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0378 0.0456 23.9784 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.8378 -6.1513 25.2827 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7956 -4.9099 26.1896 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.7613 -6.0882 27.0905 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.1092 -4.1867 23.8190 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2855 -2.6444 25.0647 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.3518 -3.8250 23.6990 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.7479 -1.1923 23.4991 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.3325 -2.2424 22.1685 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.7964 -2.3301 21.6576 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.9206 -1.1134 21.6591 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 12.3604 1.5876 24.6490 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.2430 0.3597 24.6438 H 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 2 0\n+ 11 12 1 0\n+ 12 13 2 0\n+ 12 14 1 0\n+ 11 15 1 0\n+ 15 16 2 0\n+ 16 8 1 0\n+ 1 17 1 0\n+ 1 18 1 0\n+ 1 19 1 0\n+ 5 20 1 0\n+ 6 21 1 0\n+ 6 22 1 0\n+ 7 23 1 0\n+ 7 24 1 0\n+ 9 25 1 0\n+ 10 26 1 0\n+ 15 27 1 0\n+ 16 28 1 0\n+M CHG 1 14 -1\n+M END\n+> <EmbedRMS> (14)\n+0.05891078568463065\n+\n+> <Hit> (14)\n+1\n+\n+> <TETHERED ATOMS> (14)\n+1,2,3,4,5,6,7,8,9,10,11,15,16\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/pyrimethamine.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pyrimethamine.mol Tue Jul 21 05:22:46 2020 -0400 |
| b |
| @@ -0,0 +1,66 @@ +1-pyrimethamine + Cerius2 12180216023D 1 1.00000 + Structure written by MMmdl. + 30 31 0 0 0 0 0 0 0 0999 V2000 + -2.8357 0.2028 0.4209 N 0 0 0 0 0 0 + -2.8255 -1.1104 0.1969 C 0 0 0 0 0 0 + -1.7271 -1.8218 -0.0537 N 0 0 0 0 0 0 + -0.5417 -1.1654 -0.0884 C 0 0 0 0 0 0 + -0.4439 0.2086 0.1358 C 0 0 0 0 0 0 + -1.6550 0.8467 0.4052 C 0 0 0 0 0 0 + 0.8362 0.9302 0.0951 C 0 0 0 0 0 0 + 1.6327 1.0444 1.2466 C 0 0 0 0 0 0 + 2.8536 1.7244 1.2069 C 0 0 0 0 0 0 + 3.2885 2.2979 0.0146 C 0 0 0 0 0 0 + 2.5126 2.1980 -1.1375 C 0 0 0 0 0 0 + 1.2918 1.5178 -1.0966 C 0 0 0 0 0 0 + -4.0141 -1.7715 0.2232 N 0 0 0 0 0 0 + -1.7348 2.2137 0.6034 N 0 0 0 0 0 0 + 4.7918 3.1344 -0.0351 Cl 0 0 0 0 0 0 + 0.4261 -3.4744 -0.6318 C 0 0 0 0 0 0 + 0.6932 -1.9936 -0.3864 C 0 0 0 0 0 0 + 1.3065 0.6014 2.1872 H 0 0 0 0 0 0 + 3.4548 1.8000 2.1100 H 0 0 0 0 0 0 + 2.8462 2.6451 -2.0710 H 0 0 0 0 0 0 + 0.6948 1.4500 -2.0056 H 0 0 0 0 0 0 + -4.0348 -2.7663 0.0556 H 0 0 0 0 0 0 + -4.8657 -1.2631 0.4089 H 0 0 0 0 0 0 + -0.9674 2.6820 1.0738 H 0 0 0 0 0 0 + -2.6605 2.5780 0.8038 H 0 0 0 0 0 0 + 1.3655 -3.9964 -0.8406 H 0 0 0 0 0 0 + -0.2391 -3.6219 -1.4893 H 0 0 0 0 0 0 + -0.0337 -3.9462 0.2432 H 0 0 0 0 0 0 + 1.3880 -1.9081 0.4572 H 0 0 0 0 0 0 + 1.1868 -1.5858 -1.2763 H 0 0 0 0 0 0 + 1 2 2 0 0 0 + 1 6 1 0 0 0 + 2 3 1 0 0 0 + 2 13 1 0 0 0 + 3 4 2 0 0 0 + 4 5 1 0 0 0 + 4 17 1 0 0 0 + 5 6 2 0 0 0 + 5 7 1 0 0 0 + 6 14 1 0 0 0 + 7 8 2 0 0 0 + 7 12 1 0 0 0 + 8 9 1 0 0 0 + 8 18 1 0 0 0 + 9 10 2 0 0 0 + 9 19 1 0 0 0 + 10 11 1 0 0 0 + 10 15 1 0 0 0 + 11 12 2 0 0 0 + 11 20 1 0 0 0 + 12 21 1 0 0 0 + 13 22 1 0 0 0 + 13 23 1 0 0 0 + 14 24 1 0 0 0 + 14 25 1 0 0 0 + 16 17 1 0 0 0 + 16 26 1 0 0 0 + 16 27 1 0 0 0 + 16 28 1 0 0 0 + 17 29 1 0 0 0 + 17 30 1 0 0 0 +M END \ No newline at end of file |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/ref_mol.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref_mol.sdf Tue Jul 21 05:22:46 2020 -0400 |
| [ |
| @@ -0,0 +1,49 @@ + + RDKit 3D + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 3.9712 0.1501 0.5844 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5166 0.3848 0.3204 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6474 -0.7021 0.6617 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2473 -0.5387 0.4677 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2286 -0.2315 -0.8004 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4500 0.4259 -0.8610 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3911 0.0755 0.0992 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0310 -0.7738 1.1372 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6867 -1.0391 1.3639 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6323 0.7131 0.1820 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0373 1.5357 0.5544 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 + 3 4 1 0 + 4 5 2 0 + 5 6 1 0 + 6 7 2 0 + 7 8 1 0 + 8 9 2 0 + 7 10 1 0 + 2 11 2 0 + 9 4 1 0 +M END +> <Amides> (1) +[{, uuid, 8239add3-47ea-40a0-a326-d93c45f9cfb2, source, CC(=O)Cl, format, smiles, }, {, uuid, 33509b1f-56f4-4a43-bc9f-5aea174b9dad, source, Nc1ccc(O)cc1, format, smiles, }] + +> <N-Alkylation> (1) +[{, uuid, c5420e1a-a5fe-4ca6-b815-0d243a87c559, source, Nc1ccc(O)cc1, format, smiles, }, {, uuid, 19252796-114d-45d3-ac6f-1e6d497314e5, source, CC(=O)Br, format, smiles, }] + +> <SNAr> (1) +[{, uuid, 1b3d2bc5-963d-482d-8b19-9af7303add11, source, CC(N)=O, format, smiles, }, {, uuid, bc66f13d-18f7-41bd-9b0f-77614ba1ecdc, source, Oc1ccc(Br)cc1, format, smiles, }] + +> <chain> (1) +A + +> <cmpd_id> (1) +CMPD_FIVE + +> <model_id> (1) +4CUT + +> <path_to_pdb> (1) +WONKA_DATA/4CUT.pdb + +$$$$ |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/rxn_maker_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rxn_maker_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,77800 @@\n+\n+ RDKit 2D\n+\n+ 14 14 0 0 0 0 0 0 0 0999 V2000\n+ 4.6954 -0.3113 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.2268 -0.0064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.2284 -1.1259 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7597 -0.8211 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4548 -2.2897 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.0646 0.6476 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.7090 -0.5162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7074 -1.6357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.1760 -1.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6464 0.0935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6480 1.2130 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1793 0.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1810 2.0277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.8174 3.1472 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 4 6 2 0\n+ 4 7 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 3 0\n+ 12 7 1 0\n+M END\n+$$$$\n+\n+ RDKit 2D\n+\n+ 23 24 0 0 0 0 0 0 0 0999 V2000\n+ -2.5634 -3.1937 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.2394 -1.8547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9155 -0.5157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4131 -0.4317 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.0892 0.9073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.2676 2.1623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7699 2.0783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0939 0.7393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5962 0.6552 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5122 2.1529 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.6803 -0.8424 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0986 0.5712 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5775 -0.7678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.2441 -2.0228 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0751 -0.8518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7512 -2.1908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2488 -2.2749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0704 -1.0199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3943 0.3191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2159 1.5741 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7136 1.4901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.5399 2.9131 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8967 0.4032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 3 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 11 2 0\n+ 9 12 1 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 13 15 1 0\n+ 15 16 2 0\n+ 16 17 1 0\n+ 17 18 2 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 20 22 1 0\n+ 19 23 2 0\n+ 8 3 1 0\n+ 23 15 1 0\n+M END\n+$$$$\n+\n+ RDKit 2D\n+\n+ 23 24 0 0 0 0 0 0 0 0999 V2000\n+ -2.3157 -3.1731 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.1865 -1.9518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0574 -0.7305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.5505 -0.8740 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.4214 0.3473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.7991 1.7121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.3060 1.8557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.4352 0.6343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.9420 0.'..b' 0 0 0\n+ 1.8581 0.5751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.3429 1.9946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8146 2.2845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8015 1.1549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.3167 -0.2646 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8450 -0.5545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.3603 -1.9740 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.8755 -3.3935 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 5 9 1 0\n+ 9 10 2 0\n+ 9 11 2 0\n+ 9 12 1 0\n+ 12 13 2 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 18 19 3 0\n+ 17 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 2D\n+\n+ 19 19 0 0 0 0 0 0 0 0999 V2000\n+ 8.6686 0.8376 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.5185 -0.1253 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1095 0.3892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.9594 -0.5737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5504 -0.0592 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4003 -1.0221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.9913 -0.5076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.1588 -1.4705 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5678 -0.9560 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0823 -2.3650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0532 0.4530 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.9768 -0.4414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.1269 -1.4044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.5359 -0.8898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.7948 0.5877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.6446 1.5506 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.2357 1.0361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0856 1.9990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9355 2.9619 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 11 2 0\n+ 9 12 1 0\n+ 12 13 2 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 18 19 3 0\n+ 17 12 1 0\n+M END\n+$$$$\n+\n+ RDKit 2D\n+\n+ 16 16 0 0 0 0 0 0 0 0999 V2000\n+ 3.9020 0.8100 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8432 -0.2525 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7807 0.8064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9057 -1.3113 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7844 -1.3150 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3348 -0.9292 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0509 -2.3788 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7205 0.5203 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1147 -0.5435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1736 -1.6060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.6231 -1.2203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0139 0.2279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.9551 1.2904 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.5055 0.9047 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.4467 1.9672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6121 3.0297 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 6 8 2 0\n+ 6 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 14 15 1 0\n+ 15 16 3 0\n+ 14 9 1 0\n+M END\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/screen_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,1570 @@\n+9-16b\n+ RDKit 3D\n+\n+ 21 23 0 0 0 0 0 0 0 0999 V2000\n+ -4.9867 0.1332 -0.5004 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0262 -1.1893 -0.3412 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9974 -1.9346 0.0633 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8398 -1.3126 0.3203 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6816 0.0699 0.1907 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8313 0.7559 -0.2181 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7465 -2.0680 0.7264 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5043 -1.4864 1.0050 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.3302 -0.1069 0.8851 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.4213 0.6647 0.4658 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.0121 0.5318 1.1605 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.8059 0.5464 -0.0553 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0828 1.0577 -0.1482 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7446 1.0076 -1.3839 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0410 1.5119 -1.5408 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6956 2.0777 -0.4531 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0626 2.1407 0.7836 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7648 1.6335 0.9306 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8378 2.1248 -0.4237 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.1980 -1.8263 -0.6104 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 7.2886 2.7013 -0.6366 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 20 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 7 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 19 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 11 1 0\n+ 11 12 1 0\n+ 12 13 1 0\n+ 13 14 2 0\n+ 13 18 1 0\n+ 14 15 1 0\n+ 15 16 2 0\n+ 16 17 1 0\n+ 16 21 1 0\n+ 17 18 2 0\n+M END\n+> <Name> (1) \n+9-16b\n+\n+> <Family> (1) \n+G.1\n+\n+> <PC_uM> (1) \n+0.600000\n+\n+> <TG_uM> (1) \n+0.075000\n+\n+> <RL_uM> (1) \n+0.073000\n+\n+> <set> (1) \n+0\n+\n+> <Similarity> (1) \n+0.47531572904707231\n+\n+$$$$\n+15-2\n+ RDKit 3D\n+\n+ 20 22 0 0 0 0 0 0 0 0999 V2000\n+ -3.7354 0.6372 -2.0152 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7604 -0.6645 -2.2993 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6806 -1.4420 -2.3789 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.4867 -0.8728 -2.1679 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.3382 0.4796 -1.8628 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5375 1.1964 -1.7803 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.3418 -1.6499 -2.2597 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.9396 -1.1142 -2.0599 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.1177 0.2327 -1.7566 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.0366 1.0189 -1.6674 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.3461 0.8224 -1.5623 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.9008 -0.5630 -0.2530 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8462 0.1293 0.9674 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.1163 -0.5259 2.1707 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4506 -1.8786 2.1688 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.5177 -2.5765 0.9646 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2480 -1.9226 -0.2398 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5670 2.5547 -1.5154 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.9715 -1.2419 -2.5250 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.6357 0.1474 -1.5628 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 19 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 7 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 18 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 11 1 0\n+ 11 20 1 0\n+ 12 13 2 0\n+ 12 17 1 0\n+ 12 20 1 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+M END\n+> <Name> (2) \n+15-2\n+\n+> <Family> (2) \n+G.1\n+\n+> <PC_uM'..b' -3.6410 1.9056 -0.9122 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0890 -0.6148 -0.5815 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0558 0.0708 -0.3487 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0189 1.4645 -0.2633 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1986 2.1245 -0.4356 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9045 3.2621 -0.8514 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.5701 -0.9978 -1.3728 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2433 2.2458 0.1351 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2864 -0.5998 -0.1773 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5297 0.0902 -0.1166 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5294 1.5883 -0.3520 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.3311 -2.0030 -0.0762 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5327 -2.6915 0.0967 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7368 -1.9960 0.1566 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7491 -0.6069 0.0378 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8843 0.1614 0.0464 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.1324 -0.5126 0.1985 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 12 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 7 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 11 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 8 14 1 0\n+ 9 10 2 0\n+ 9 13 1 0\n+ 13 16 1 0\n+ 14 15 2 0\n+ 14 17 1 0\n+ 15 16 1 0\n+ 15 20 1 0\n+ 17 18 2 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 1 0\n+M END\n+> <Name> (21) \n+51-9\n+\n+> <Family> (21) \n+misc\n+\n+> <PC_uM> (21) \n+8.600000\n+\n+> <TG_uM> (21) \n+0.150000\n+\n+> <RL_uM> (21) \n+0.600000\n+\n+> <set> (21) \n+0\n+\n+> <Similarity> (21) \n+0.46390374331550804\n+\n+$$$$\n+51-8\n+ RDKit 3D\n+\n+ 22 25 0 0 0 0 0 0 0 0999 V2000\n+ -4.4276 1.4179 -0.7291 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.2512 0.1010 -0.8074 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0741 -0.5114 -0.7139 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.9938 0.2359 -0.5410 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.0602 1.6174 -0.4453 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3394 2.1698 -0.5281 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8270 -0.4112 -0.4641 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3473 0.2456 -0.3130 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3523 1.6400 -0.2083 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8595 2.3291 -0.2699 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5608 3.5342 -0.4800 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.3542 -0.6735 -0.9970 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6253 2.3908 0.0947 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.5701 -0.4562 -0.2479 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8170 0.2110 -0.2748 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8536 1.7051 -0.4935 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6102 -1.8631 -0.1691 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.8170 -2.5749 -0.0969 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0308 -1.8972 -0.1167 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0255 -0.5062 -0.2154 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.2722 -2.4665 -0.0597 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.3214 -3.8885 0.0496 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 12 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 7 1 0\n+ 5 6 2 0\n+ 5 10 1 0\n+ 6 11 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 8 14 1 0\n+ 9 10 2 0\n+ 9 13 1 0\n+ 13 16 1 0\n+ 14 15 2 0\n+ 14 17 1 0\n+ 15 16 1 0\n+ 15 20 1 0\n+ 17 18 2 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 19 21 1 0\n+ 21 22 1 0\n+M END\n+> <Name> (22) \n+51-8\n+\n+> <Family> (22) \n+misc\n+\n+> <PC_uM> (22) \n+6.700000\n+\n+> <TG_uM> (22) \n+0.110000\n+\n+> <RL_uM> (22) \n+0.240000\n+\n+> <set> (22) \n+0\n+\n+> <Similarity> (22) \n+0.46159169550173013\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/screen_output2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/screen_output2.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,2215 @@\n+1-7364\n+ RDKit 3D\n+\n+ 17 18 0 0 0 0 0 0 0 0999 V2000\n+ -2.7897 -0.3579 0.5077 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8038 -1.6260 0.0973 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7302 -2.2898 -0.3303 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5505 -1.6232 -0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.4246 -0.2980 0.0588 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.6095 0.2884 0.5017 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.8560 0.4222 0.0267 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7528 0.3416 1.1048 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9770 1.0201 1.0719 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3185 1.7913 -0.0436 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4338 1.8805 -1.1200 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2124 1.2015 -1.0843 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.9916 -2.2886 0.1130 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.6671 1.6118 0.9004 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8129 2.6537 -0.1514 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6285 -2.4088 -0.8541 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.0227 0.8619 2.4406 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 13 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 16 1 0\n+ 5 6 2 0\n+ 5 7 1 0\n+ 6 14 1 0\n+ 7 8 2 0\n+ 7 12 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 17 1 0\n+ 10 11 1 0\n+ 10 15 1 0\n+ 11 12 2 0\n+M END\n+> <Name> (1) \n+1-7364\n+\n+> <Family> (1) \n+A\n+\n+> <PC_uM> (1) \n+1.68\n+\n+> <TG_uM> (1) \n+3.7\n+\n+> <RL_uM> (1) \n+0.32\n+\n+> <set> (1) \n+1\n+\n+> <Similarity> (1) \n+0.79189944134078216\n+\n+$$$$\n+1-211804\n+ RDKit 3D\n+\n+ 19 20 0 0 0 0 0 0 0 0999 V2000\n+ -2.8152 -0.2407 0.4681 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.8282 -1.5194 0.0990 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7486 -2.1980 -0.2789 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5526 -1.5361 -0.2931 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.4375 -0.1982 0.0805 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.6336 0.4019 0.4729 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.8389 0.5312 0.0668 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6936 0.5056 1.1816 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.9081 1.1985 1.1681 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.2777 1.9275 0.0406 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4424 1.9703 -1.0727 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2282 1.2769 -1.0584 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0175 -2.1769 0.1051 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7000 1.7369 0.8267 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7721 2.7808 0.0240 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6707 -2.3199 -0.7376 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.3156 -1.7756 -1.8159 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3858 -3.6079 -1.1188 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6236 -2.4506 0.2370 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 13 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 16 1 0\n+ 5 6 2 0\n+ 5 7 1 0\n+ 6 14 1 0\n+ 7 8 2 0\n+ 7 12 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 10 15 1 0\n+ 11 12 2 0\n+ 16 17 1 0\n+ 16 18 1 0\n+ 16 19 1 0\n+M END\n+> <Name> (2) \n+1-211804\n+\n+> <Family> (2) \n+A\n+\n+> <PC_uM> (2) \n+>42\n+\n+> <TG_uM> (2) \n+>42\n+\n+> <RL_uM> (2) \n+>42\n+\n+> <set> (2) \n+2\n+\n+> <Similarity> (2) \n+0.71304347826086956\n+\n+$$$$\n+1-302325\n+ RDKit 3D\n+\n+ 20 21 0 0 0 0 0 0 0 0999 V2000\n+ -3.0757 0.2187 0.7563 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.1890 -1.0708 0.4416 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1933 -1.8189 -0.0321 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9864 -1.2284 -0.2105 '..b'N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.0178 -0.2647 -0.1932 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0815 -0.6028 0.5957 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.6156 -1.9510 0.4106 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7999 0.3621 1.4331 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7930 1.2344 0.6638 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.4207 2.1514 1.5726 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.4384 -2.1159 -0.8676 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8927 -3.4740 -0.9660 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3390 3.0019 0.8866 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.6686 -3.6694 -2.1481 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 13 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 17 1 0\n+ 5 6 2 0\n+ 5 7 1 0\n+ 6 14 1 0\n+ 7 8 2 0\n+ 7 12 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 18 1 0\n+ 10 11 1 0\n+ 10 15 1 0\n+ 11 12 2 0\n+ 16 17 1 0\n+ 18 19 2 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 20 22 1 0\n+ 21 25 1 0\n+ 22 23 1 0\n+ 23 24 1 0\n+ 24 27 1 0\n+ 25 26 1 0\n+ 26 28 1 0\n+M END\n+> <Name> (28) \n+4-10r\n+\n+> <Family> (28) \n+A\n+\n+> <PC_uM> (28) \n+0.910000\n+\n+> <TG_uM> (28) \n+N/A\n+\n+> <RL_uM> (28) \n+26.100000\n+\n+> <set> (28) \n+0\n+\n+> <Similarity> (28) \n+0.74120317820658344\n+\n+$$$$\n+4-10s\n+ RDKit 3D\n+\n+ 27 29 0 0 0 0 0 0 0 0999 V2000\n+ -5.2740 -0.1388 -1.0687 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.5487 -1.3560 -0.6024 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.7255 -2.0697 0.1643 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5306 -1.5166 0.4930 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.1456 -0.2493 0.0578 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0805 0.3962 -0.7532 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8557 0.3597 0.4106 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.7141 0.1272 -0.3764 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5373 0.6803 -0.0467 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.6241 1.5058 1.0837 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5027 1.7542 1.8720 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.7329 1.1852 1.5363 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.7477 -1.9097 -0.9269 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8723 1.6765 -1.2347 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.1148 2.2467 1.5480 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.9864 -2.1581 2.8630 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6639 -2.3693 1.3909 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.6544 0.4403 -0.8766 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9857 -0.7593 -0.8125 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0016 -1.1072 -1.6547 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.4160 -2.5004 -1.6226 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7656 -0.1476 -2.4722 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0082 0.4654 -1.7929 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.6639 1.3209 -0.6915 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7228 1.1195 0.2470 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0740 -0.3301 0.0548 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.9507 -0.5339 -1.3587 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 2 0\n+ 1 6 1 0\n+ 2 3 1 0\n+ 2 13 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 4 17 1 0\n+ 5 6 2 0\n+ 5 7 1 0\n+ 6 14 1 0\n+ 7 8 2 0\n+ 7 12 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 9 18 1 0\n+ 10 11 1 0\n+ 10 15 1 0\n+ 11 12 2 0\n+ 16 17 1 0\n+ 18 19 2 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 20 22 1 0\n+ 22 23 1 0\n+ 23 24 1 0\n+ 23 27 1 0\n+ 24 25 1 0\n+ 25 26 1 0\n+ 26 27 1 0\n+M END\n+> <Name> (29) \n+4-10s\n+\n+> <Family> (29) \n+A\n+\n+> <PC_uM> (29) \n+0.570000\n+\n+> <TG_uM> (29) \n+N/A\n+\n+> <RL_uM> (29) \n+0.500000\n+\n+> <set> (29) \n+2\n+\n+> <Similarity> (29) \n+0.70978260869565213\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/sdf-aliphatic-primary-amines-175.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sdf-aliphatic-primary-amines-175.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,71026 @@\n+292249\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 7 5 0 0 0 0 0 0 0 0999 V2000\n+ -3.3200 -1.9100 0.0000 B 0 0 0 0 0 0\n+ -2.4500 -1.4100 0.0000 F 0 0 0 0 0 0\n+ -3.3200 -2.9100 0.0000 F 0 0 0 0 0 0\n+ -4.1800 -1.4000 0.0000 F 0 0 0 0 0 0\n+ -1.2800 -0.7900 0.0000 N 0 0 0 0 0 0\n+ -0.4100 -0.2900 0.0000 C 0 0 0 0 0 0\n+ -0.4100 0.7100 0.0000 C 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 3 1 0\n+ 1 4 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+M END\n+> <BRAND> (1)\n+SIAL\n+\n+> <CAS_RN> (1)\n+75-23-0\n+\n+> <CAT_NO> (1)\n+292249\n+\n+> <FP> (1)\n+314.6\n+\n+> <FP_UOM> (1)\n+\xb0F\n+\n+> <LONGNAME> (1)\n+ethanamine compound with trifluoroborane (1:1)\n+\n+> <MDL_NO> (1)\n+MFCD00144277\n+\n+> <MF> (1)\n+C2H7BF3N\n+\n+> <MW> (1)\n+112.89\n+\n+> <NAME> (1)\n+Boron trifluoride ethylamine complex\n+\n+$$$$\n+683868\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 12 12 0 0 0 0 0 0 0 0999 V2000\n+ 1.5200 1.4500 0.0000 B 0 0 0 0 0 0\n+ 1.5200 2.4500 0.0000 O 0 0 0 0 0 0\n+ 2.3800 0.9500 0.0000 O 0 0 0 0 0 0\n+ 0.6500 0.9500 0.0000 C 0 0 0 0 0 0\n+ -0.2200 1.4500 0.0000 C 0 0 0 0 0 0\n+ -1.0800 0.9500 0.0000 C 0 0 0 0 0 0\n+ -1.0800 -0.0500 0.0000 C 0 0 0 0 0 0\n+ -0.2200 -0.5500 0.0000 C 0 0 0 0 0 0\n+ 0.6500 -0.0500 0.0000 C 0 0 0 0 0 0\n+ -1.9500 1.4500 0.0000 C 0 0 0 0 0 0\n+ -1.9400 2.4500 0.0000 O 0 0 0 0 0 0\n+ -2.8100 0.9500 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 3 1 0\n+ 1 4 1 0\n+ 4 5 1 0\n+ 4 9 2 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 6 10 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 10 11 2 0\n+ 10 12 1 0\n+M END\n+> <BRAND> (2)\n+ALDRICH\n+\n+> <CAS_RN> (2)\n+351422-73-6\n+\n+> <CAT_NO> (2)\n+683868\n+\n+> <LONGNAME> (2)\n+3-(aminocarbonyl)phenylboronic acid\n+\n+> <MDL_NO> (2)\n+MFCD03411948\n+\n+> <MF> (2)\n+C7H8BNO3\n+\n+> <MW> (2)\n+164.956\n+\n+> <NAME> (2)\n+3-Aminocarbonylphenylboronic acid\n+\n+$$$$\n+683876\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 12 12 0 0 0 0 0 0 0 0999 V2000\n+ -0.4900 2.0400 0.0000 B 0 0 0 0 0 0\n+ 0.3800 2.5300 0.0000 O 0 0 0 0 0 0\n+ -1.3500 2.5500 0.0000 O 0 0 0 0 0 0\n+ -0.4900 1.0400 0.0000 C 0 0 0 0 0 0\n+ -1.3600 0.5400 0.0000 C 0 0 0 0 0 0\n+ -1.3700 -0.4500 0.0000 C 0 0 0 0 0 0\n+ -0.5000 -0.9600 0.0000 C 0 0 0 0 0 0\n+ 0.3600 -0.4700 0.0000 C 0 0 0 0 0 0\n+ 0.3700 0.5400 0.0000 C 0 0 0 0 0 0\n+ -0.5000 -1.9600 0.0000 C 0 0 0 0 0 0\n+ 0.3600 -2.4600 0.0000 O 0 0 0 0 0 0\n+ -1.3700 -2.4600 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 1 3 1 0\n+ 1 4 1 0\n+ 4 5 1 0\n+ 4 9 2 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 7 10 1 0\n+ 8 9 1 0\n+ 10 11 2 0\n+ 10 12 1 0\n+M END\n+> <BRAND> (3)\n+ALDRICH\n+\n+> <CAS_RN> (3)\n+123088-59-5\n+\n+> <CAT_NO> (3)\n+683876\n+\n+> <LONGNAME> (3)\n+4-(aminocarbonyl)phenylboronic acid\n+\n+> <MDL_NO> (3)\n+MFCD03411940\n+\n+> <MF> (3)\n+C7H8BNO3\n+\n+> <MW> (3)\n+164.956\n+\n+> <NAME> (3)\n+4-Aminocarbonylphenylboronic acid\n+\n+$$$$\n+737488\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 6 3 0 0 0 0 0 0 0 0999 V2000\n+ 3.1500 -1.8300 0.0000 B 0 0 0 0 0 0\n+ 4.0200 -2.3300 0.0000 B 0 0 0 0 0 0\n+ 0.2500 -0.8600 0.0000 N 0 0 0 0 0 0\n+ 1.1200 -0.3600 0.0000 C 0 0 0 0 0 0\n+ 1.9800 -0.8600 0.0000 C 0 0 0 0 0 0\n+ 2.8500 -0.3600 0.0000 N 0 0 0 0 0 0\n+ 3 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+M END\n+> <BRAND> (4)\n+ALDRICH\n+\n+> <CAS_RN> (4)\n+15165-88-5\n+\n+> <CAT_NO> (4)\n+737488\n+\n+> <LONGNAME> (4)\n+1,2-ethanediamine compound with borane (1:2)\n+\n+> <MDL_NO> (4)\n+A_____737488\n+\n+> <MF'..b' -1.3600 0.5400 0.0000 C 0 0 0 0 0 0\n+ -1.3700 -0.4500 0.0000 C 0 0 0 0 0 0\n+ -0.5000 -0.9600 0.0000 C 0 0 0 0 0 0\n+ 0.3600 -0.4700 0.0000 C 0 0 0 0 0 0\n+ 0.3700 0.5400 0.0000 C 0 0 0 0 0 0\n+ -0.5100 -1.9600 0.0000 S 0 0 0 0 0 0\n+ 0.4900 -1.9600 0.0000 O 0 0 0 0 0 0\n+ -1.5100 -1.9500 0.0000 O 0 0 0 0 0 0\n+ -0.5100 -2.9600 0.0000 N 0 0 0 0 0 0\n+ -1.3800 -3.4500 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 2 7 2 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 5 8 1 0\n+ 6 7 1 0\n+ 8 9 2 0\n+ 8 10 2 0\n+ 8 11 1 0\n+ 11 12 1 0\n+M END\n+> <BRAND> (1309)\n+ALDRICH\n+\n+> <CAT_NO> (1309)\n+564397\n+\n+> <MDL_NO> (1309)\n+A_____564397\n+\n+> <MW> (1309)\n+171.2\n+\n+> <NAME> (1309)\n+Sulfonyl hydrazine, polymer-bound\n+\n+$$$$\n+472107\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 11 10 0 0 0 0 0 0 0 0999 V2000\n+ 3.4600 -0.0100 0.0000 R# 0 0 0 0 0 0\n+ 2.6000 -0.5100 0.0000 N 0 0 0 0 0 0\n+ 1.7300 0.0000 0.0000 C 0 0 0 0 0 0\n+ 0.8700 -0.5000 0.0000 C 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 N 0 0 0 0 0 0\n+ -0.8700 -0.5000 0.0000 C 0 0 0 0 0 0\n+ -1.7300 0.0000 0.0000 C 0 0 0 0 0 0\n+ -2.6000 -0.4900 0.0000 N 0 0 0 0 0 0\n+ 0.0000 1.0000 0.0000 C 0 0 0 0 0 0\n+ -0.8600 1.5000 0.0000 C 0 0 0 0 0 0\n+ -0.8600 2.5000 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 5 9 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+ 9 10 1 0\n+ 10 11 1 0\n+M END\n+> <BRAND> (1310)\n+ALDRICH\n+\n+> <CAT_NO> (1310)\n+472107\n+\n+> <MDL_NO> (1310)\n+MFCD00804324\n+\n+> <MW> (1310)\n+145.228\n+\n+> <NAME> (1310)\n+Tris(2-aminoethyl)amine, polymer-bound\n+\n+$$$$\n+657646\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 5 4 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 1.0000 0.0000 R# 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 N 0 0 0 0 0 0\n+ -0.8700 -0.5000 0.0000 C 0 0 0 0 0 0\n+ -0.8700 -1.5000 0.0000 C 0 0 0 0 0 0\n+ -1.7400 -2.0000 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 1 0\n+M END\n+> <BRAND> (1311)\n+ALDRICH\n+\n+> <CAT_NO> (1311)\n+657646\n+\n+> <MDL_NO> (1311)\n+MFCD07785596\n+\n+> <MW> (1311)\n+59.091\n+\n+> <NAME> (1311)\n+QuadraPure(R) AEA\n+\n+$$$$\n+479780\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 8 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.8700 0.5000 0.0000 R# 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 N 0 0 0 0 0 0\n+ -0.8700 0.5000 0.0000 C 0 0 0 0 0 0\n+ -1.7300 0.0000 0.0000 C 0 0 0 0 0 0\n+ -2.6000 0.5000 0.0000 N 0 0 0 0 0 0\n+ -3.4600 0.0100 0.0000 C 0 0 0 0 0 0\n+ -4.3300 0.5100 0.0000 C 0 0 0 0 0 0\n+ -5.2000 0.0100 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 1 0\n+ 4 5 1 0\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 0\n+M END\n+> <BRAND> (1312)\n+ALDRICH\n+\n+> <CAT_NO> (1312)\n+479780\n+\n+> <MDL_NO> (1312)\n+MFCD01323182\n+\n+> <MW> (1312)\n+102.159\n+\n+> <NAME> (1312)\n+Diethylenetriamine, polymer-bound\n+\n+$$$$\n+516201\n+ 10061613032D\n+http://www.chemnavigator.com\n+ 5 4 0 0 0 0 0 0 0 0999 V2000\n+ 0.8700 0.5000 0.0000 R# 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 S 0 0 0 0 0 0\n+ 0.5000 -0.8700 0.0000 O 0 0 0 0 0 0\n+ -0.5000 0.8700 0.0000 O 0 0 0 0 0 0\n+ -0.8700 -0.5000 0.0000 N 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 2 0\n+ 2 5 1 0\n+M END\n+> <BRAND> (1313)\n+ALDRICH\n+\n+> <CAS_RN> (1313)\n+135266-23-8\n+\n+> <CAT_NO> (1313)\n+516201\n+\n+> <MDL_NO> (1313)\n+MFCD04041136\n+\n+> <MW> (1313)\n+80.0874\n+\n+> <NAME> (1313)\n+Sulfonyl amide, polymer-bound\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/standardize_output1.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/standardize_output1.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,2824 @@\n+\n+ RDKit 2D\n+\n+ 26 30 0 0 0 0 0 0 0 0999 V2000\n+ -8.6396 0.9568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6023 1.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6071 3.0602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3104 3.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0040 1.5682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3008 0.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 -0.6045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 -1.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5059 -2.8197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2156 -3.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2329 -5.0846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5404 -5.8196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8308 -5.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8135 -3.5548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 -1.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 -1.3190 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 1.5389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 2 7 1 0\n+ 6 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 11 16 1 0\n+ 10 17 2 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 22 23 1 0\n+ 23 24 2 0\n+ 19 24 1 0\n+ 24 25 1 0\n+ 17 25 1 0\n+ 25 26 2 0\n+ 8 26 1 0\n+M END\n+> <mr_id> (1) \n+4358263\n+\n+> <SMI> (1) \n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 43 51 0 0 1 0 0 0 0 0999 V2000\n+ -4.7204 3.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.1471 2.2890 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6500 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8100 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.2400 3.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5000 2.1800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0600 2.1800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9800 -0.7800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -1.4600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3200 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5500 -1.4800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5800 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3400 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -2.7900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2400 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.4300 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7600 -4.9700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.2600 -5.0800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8500 -3.6300 0.0000 C 0 0 0 0 0 0 '..b' 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2761 10.4985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 5 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 3 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 16 17 1 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 21 22 1 0\n+ 17 22 1 0\n+ 6 23 1 0\n+ 23 24 1 0\n+ 24 25 1 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 23 28 1 0\n+ 26 29 1 0\n+ 29 30 2 0\n+ 29 31 1 0\n+ 31 32 1 0\n+ 32 33 2 0\n+ 33 34 1 0\n+ 34 35 2 0\n+ 35 36 1 0\n+ 36 37 1 0\n+ 37 38 1 0\n+ 37 39 1 0\n+ 35 40 1 0\n+ 40 41 2 0\n+ 32 41 1 0\n+M END\n+> <mr_id> (35) \n+4291116\n+\n+> <SMI> (35) \n+COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 34 38 0 0 0 0 0 0 0 0999 V2000\n+ -5.7794 -9.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.8342 -9.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7215 -9.4825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0445 -7.5473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.4347 -6.9838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.6418 -5.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4588 -4.5759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.6629 -3.0890 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.4777 -2.1678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.6909 -0.7107 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5360 0.2310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1322 -0.3021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1017 0.7996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4087 0.6930 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2438 -0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7297 -0.3578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5918 -1.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0835 -2.6775 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0862 -1.4619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7221 -0.1033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8635 1.1267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3690 0.9981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6835 1.9830 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7996 -1.9901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9546 -2.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7236 -4.4422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6594 -5.1934 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3554 -4.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8174 -3.9980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5686 -2.5587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8835 -1.8124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0918 -2.7364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0686 -5.1394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8615 -6.6251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 17 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 16 22 1 0\n+ 22 23 1 0\n+ 15 24 1 0\n+ 24 25 2 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 26 28 2 0\n+ 28 29 1 0\n+ 29 30 2 0\n+ 24 30 1 0\n+ 30 31 1 0\n+ 12 31 1 0\n+ 31 32 2 0\n+ 9 32 1 0\n+ 7 33 1 0\n+ 33 34 2 0\n+ 4 34 1 0\n+M END\n+> <mr_id> (36) \n+4297285\n+\n+> <SMI> (36) \n+OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/standardize_output2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/standardize_output2.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| b'@@ -0,0 +1,2824 @@\n+\n+ RDKit 2D\n+\n+ 26 30 0 0 0 0 0 0 0 0999 V2000\n+ -8.6396 0.9568 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6023 1.5602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -7.6071 3.0602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3104 3.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0040 1.5682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.3008 0.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7006 -0.6045 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 -1.3190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5059 -2.8197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2156 -3.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2329 -5.0846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.5404 -5.8196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8308 -5.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8135 -3.5548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 -1.3190 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 -1.3190 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 -0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7372 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.4732 1.5389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.2274 0.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.4915 1.5389 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 3 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 2 7 1 0\n+ 6 8 1 0\n+ 8 9 2 0\n+ 9 10 1 0\n+ 10 11 1 0\n+ 11 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 11 16 1 0\n+ 10 17 2 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 22 23 1 0\n+ 23 24 2 0\n+ 19 24 1 0\n+ 24 25 1 0\n+ 17 25 1 0\n+ 25 26 2 0\n+ 8 26 1 0\n+M END\n+> <mr_id> (1) \n+4358263\n+\n+> <SMI> (1) \n+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 43 51 0 0 1 0 0 0 0 0999 V2000\n+ -4.7204 3.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.1471 2.2890 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.6500 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8100 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.2400 3.5200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.5000 2.1800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0600 2.1800 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0300 0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.9800 -0.7800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -1.4600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3200 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5500 -1.4800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.5800 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3400 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1300 -2.7900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2400 -2.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.4300 -3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7600 -4.9700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.2600 -5.0800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.8500 -3.6300 0.0000 C 0 0 0 0 0 0 '..b' 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2761 10.4985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 7 8 2 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 5 10 1 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 3 12 1 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 1 0\n+ 15 16 1 0\n+ 16 17 1 0\n+ 17 18 1 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 21 22 1 0\n+ 17 22 1 0\n+ 6 23 1 0\n+ 23 24 1 0\n+ 24 25 1 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 23 28 1 0\n+ 26 29 1 0\n+ 29 30 2 0\n+ 29 31 1 0\n+ 31 32 1 0\n+ 32 33 2 0\n+ 33 34 1 0\n+ 34 35 2 0\n+ 35 36 1 0\n+ 36 37 1 0\n+ 37 38 1 0\n+ 37 39 1 0\n+ 35 40 1 0\n+ 40 41 2 0\n+ 32 41 1 0\n+M END\n+> <mr_id> (35) \n+4291116\n+\n+> <SMI> (35) \n+COc1cc2c(ncnc2cc1OCCCN3CCCCC3)N4CCN(CC4)C(=O)Nc5ccc(OC(C)C)cc5\n+\n+$$$$\n+\n+ RDKit 2D\n+\n+ 34 38 0 0 0 0 0 0 0 0999 V2000\n+ -5.7794 -9.7727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.8342 -9.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.7215 -9.4825 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.0445 -7.5473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.4347 -6.9838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -6.6418 -5.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.4588 -4.5759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -5.6629 -3.0890 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.4777 -2.1678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.6909 -0.7107 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.5360 0.2310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.1322 -0.3021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.1017 0.7996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.4087 0.6930 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.2438 -0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.7297 -0.3578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.5918 -1.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.0835 -2.6775 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.0862 -1.4619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7221 -0.1033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.8635 1.1267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.3690 0.9981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6835 1.9830 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.7996 -1.9901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.9546 -2.9496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7236 -4.4422 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6594 -5.1934 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.3554 -4.9752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.8174 -3.9980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -0.5686 -2.5587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.8835 -1.8124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.0918 -2.7364 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ -4.0686 -5.1394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.8615 -6.6251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 2 3 2 0\n+ 2 4 1 0\n+ 4 5 2 0\n+ 5 6 1 0\n+ 6 7 2 0\n+ 7 8 1 0\n+ 8 9 1 0\n+ 9 10 2 0\n+ 10 11 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 14 15 2 0\n+ 15 16 1 0\n+ 16 17 2 0\n+ 17 18 1 0\n+ 17 19 1 0\n+ 19 20 2 0\n+ 20 21 1 0\n+ 21 22 2 0\n+ 16 22 1 0\n+ 22 23 1 0\n+ 15 24 1 0\n+ 24 25 2 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 26 28 2 0\n+ 28 29 1 0\n+ 29 30 2 0\n+ 24 30 1 0\n+ 30 31 1 0\n+ 12 31 1 0\n+ 31 32 2 0\n+ 9 32 1 0\n+ 7 33 1 0\n+ 33 34 2 0\n+ 4 34 1 0\n+M END\n+> <mr_id> (36) \n+4297285\n+\n+> <SMI> (36) \n+OC(=O)c1ccc(Nc2ncc3CN=C(c4c(F)cccc4F)c5cc(Cl)ccc5-c3n2)cc1\n+\n+$$$$\n' |
| b |
| diff -r 000000000000 -r 2c11d1f9e00b test-data/sulfonyl_chloride.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sulfonyl_chloride.sdf Tue Jul 21 05:22:46 2020 -0400 |
| b |
| @@ -0,0 +1,30 @@ + + RDKit + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 3 0 + 2 3 1 0 + 3 4 2 0 + 4 5 1 0 + 5 6 2 0 + 6 7 1 0 + 7 8 2 0 + 8 9 1 0 + 9 10 2 0 + 9 11 2 0 + 9 12 1 0 + 8 3 1 0 +M END +$$$$ \ No newline at end of file |