changeset 0:2f59c6239f25 draft default tip

"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e-dirty"
author bgruening
date Sat, 10 Oct 2020 09:43:40 +0000
parents
children
files chembl.py chembl_structure_pipeline.xml structure_pipeline.py test-data/10mol.sdf test-data/check.mol test-data/in1.smi test-data/o_molblock.mol test-data/out1.smi test-data/out2.smi test-data/out3.smi test-data/out4.smi test-data/parent_molblock.mol test-data/pipeline_multi.sdf test-data/std_molblock.mol
diffstat 14 files changed, 1922 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chembl.py	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,118 @@
+import argparse
+
+from chembl_webresource_client.new_client import new_client
+from chembl_webresource_client.settings import Settings
+
+Settings.Instance().CACHING = False
+
+
+def open_file(filename):
+    with open(filename) as f:
+        return f.readline().split()[0]
+
+
+def get_smiles(res):
+    """
+    Get a list of SMILES from function results
+    """
+    smiles = set()
+    for smi in res:
+        try:
+            smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id']))
+        except TypeError:
+            continue
+    return smiles
+
+
+def sim_search(smiles, tanimoto):
+    """
+    Return compounds which are within a Tanimoto range of the SMILES input
+    """
+    similarity = new_client.similarity
+    return similarity.filter(smiles=smiles, similarity=tanimoto).only(['molecule_structures', 'molecule_chembl_id'])
+
+
+def substr_search(smiles):
+    """
+    Return compounds which contain the SMILES substructure input
+    """
+    substructure = new_client.substructure
+    return substructure.filter(smiles=smiles).only(['molecule_structures', 'molecule_chembl_id'])
+
+
+def filter_drugs(mols):
+    """
+    Return only compounds which are approved drugs
+    """
+    return mols.filter(max_phase=4)
+
+
+def filter_biotherapeutic(mols):
+    """
+    Return only biotherapeutic molecules
+    """
+    return mols.filter(biotherapeutic__isnull=False)
+
+
+def filter_nat_prod(mols):
+    """
+    Return only natural products
+    """
+    return mols.filter(natural_product=1)
+
+
+def filter_ro5(mols):
+    """
+    Return only compounds with no RO5 violations
+    """
+    return mols.filter(molecule_properties__num_ro5_violations=0)
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
+    parser.add_argument('-i', '--input', help='SMILES input')
+    parser.add_argument('-f', '--file', help='SMILES input as file')
+    parser.add_argument('-o', '--output', help="SMILES output")
+    parser.add_argument('-t', '--tanimoto', type=int, help='Tanimoto similarity score')
+    parser.add_argument('-s', '--substructure', action='store_true', help='Substructure search using the SMILES input.')
+    parser.add_argument('-d', '--drugs', action='store_true', help='Filter approved drugs')
+    parser.add_argument('-b', '--biotherapeutic', action='store_true', help='Filter biotherapeutic molecules')
+    parser.add_argument('-n', '--nat-prod', action='store_true', help='Filter natural products')
+    parser.add_argument('-r', '--ro5', action='store_true', help='Filter compounds that pass Lipinski RO5')
+
+    args = parser.parse_args()
+
+    if args.file:  # get SMILES from file rather than -i option
+        args.input = open_file(args.file)
+
+    if len(args.input) < 5:
+        raise IOError('SMILES must be at least 5 characters long.')
+
+    if args.substructure:  # specify search type: substructure or similarity
+        mols = substr_search(args.input)
+    else:
+        mols = sim_search(args.input, args.tanimoto)
+
+    # filter options:
+    if args.drugs:
+        mols = filter_drugs(mols)
+
+    if args.biotherapeutic:
+        mols = filter_biotherapeutic(mols)
+
+    if args.nat_prod:
+        mols = filter_nat_prod(mols)
+
+    if args.ro5:
+        mols = filter_ro5(mols)
+
+    # get SMILES from search output
+    mols = get_smiles(mols)
+
+    # write to file
+    with open(args.output, 'w') as f:
+        f.write('\n'.join(mols))
+
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chembl_structure_pipeline.xml	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,85 @@
+<tool id="chembl_structure_pipeline" name="ChEMBL structure pipeline" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>for curation and standardizing of molecular structures</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">chembl_structure_pipeline</requirement>
+    </requirements>  
+    <command><![CDATA[
+        python '$__tool_directory__/structure_pipeline.py' 
+            --input '$input'
+            --output '$output'
+            $standardize
+            $get_parent
+            $check
+]]>
+    </command>
+    <inputs>
+        <param label="SDF/MOL input" type="data" name="input" format="sdf,mol" argument="--input"/>
+        <param label="Standardize" checked="false" type="boolean" name="standardize" argument="--standardize" truevalue="--standardize" falsevalue="" help="Apply the 'Standardize' pipeline component"/>
+        <param label="Get parent" checked="false" type="boolean" name="get_parent" argument="--get_parent" truevalue="--get_parent" falsevalue="" help="Apply the 'GetParent' pipeline component"/>
+        <param label="Check" checked="false" type="boolean" name="check" argument="--check" truevalue="--check" falsevalue="" help="Apply the 'Check' pipeline component"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="sdf" label="Processed molecules"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="o_molblock.mol" />
+            <param name="standardize" value="true" />
+            <output name="output" value="std_molblock.mol"/>
+        </test>
+        <test>
+            <param name="input" value="o_molblock.mol" ftype="mol" />
+            <param name="get_parent" value="true" />
+            <output name="output" value="parent_molblock.mol"/>
+        </test>
+        <test>
+            <param name="input" value="o_molblock.mol" ftype="mol" />
+            <param name="check" value="true" />
+            <output name="output" value="check.mol"/>
+        </test>
+        <test>
+            <param name="input" value="10mol.sdf" ftype="sdf" />
+            <param name="standardize" value="true" />
+            <param name="get_parent" value="true" />
+            <param name="check" value="true" />
+            <output name="output" value="pipeline_multi.sdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Apply the ChEMBL chemical curation pipeline to a set of chemical structures in SDF
+format. The pipeline is described in detail in the citation provided (Bento et al.,
+2020).
+
+The pipeline consists of three components:
+ - a Standardizer which formats compounds according to defined rules and conventions, based mostly on FDA/IUPAC guidelines.
+ - a GetParent component that removes any salts and solvents from the compound to create its parent.
+ - a Checker to test the validity of chemical structures and flag any serious errors. Errors are given a code from 0 (least serious) to 10 (most serious), the highest of which is stored in the SDF field `<MaxPenaltyScore>`. A list of all errors encountered is recorded under `<IssueMessages>`.
+
+Either one or more of these protocols can be applied in a single Galaxy job.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+One or more molecules in MOL/SDF format.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+A MOL/SD-file containing the processed molecules.
+
+]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13321-020-00456-1</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/structure_pipeline.py	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,59 @@
+import argparse
+
+from chembl_structure_pipeline import checker, standardizer
+
+
+def load_mols(input_file):
+    """
+    Returns a list of strings, each a molblock
+    """
+    with open(input_file) as f:
+        mols = [''.join(('\n', mol.strip())) for mol in f.read().strip().split('$$$$\n')]
+    return mols
+
+
+def write_mols(mols, output_file):
+    """
+    Writes a list of molblocks to an SDF
+    """
+    with open(output_file, 'w') as f:
+        f.write('\n$$$$'.join(mols))
+
+
+def standardize_molblock(mol):
+    return standardizer.standardize_molblock(mol)
+
+
+def get_parent_molblock(mol):
+    return standardizer.get_parent_molblock(mol)[0]
+
+
+def check_molblock(mol):
+    issues = checker.check_molblock(mol)
+    max_penalty_score = str(max([issue[0] for issue in issues])) if issues else '0'
+    message = '; '.join([issue[1] for issue in issues])
+    mol_with_issues = '\n'.join((mol, '> <MaxPenaltyScore>', max_penalty_score, '> <IssueMessages>', message))
+    return mol_with_issues
+
+
+def main():
+    parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
+    parser.add_argument('-i', '--input', help='SDF/MOL input')
+    parser.add_argument('-o', '--output', help="Standardized output")
+    parser.add_argument('--standardize', action='store_true', help="Standardize molblock")
+    parser.add_argument('--get_parent', action='store_true', help="Get parent molblock.")
+    parser.add_argument('--check', action='store_true', help="Check molblock")
+    args = parser.parse_args()
+
+    mols = load_mols(args.input)
+    if args.standardize:
+        mols = [standardize_molblock(mol) for mol in mols]
+    if args.get_parent:
+        mols = [get_parent_molblock(mol) for mol in mols]
+    if args.check:
+        mols = [check_molblock(mol) for mol in mols]
+    write_mols(mols, args.output)
+
+
+if __name__ == "__main__":
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/10mol.sdf	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,759 @@
+
+  SciTegic01171120562D
+
+ 26 30  0  0  0  0            999 V2000
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+  1  2  1  0
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+  8 26  2  0
+M  END
+> <mr_id>
+4358263
+
+> <SMI>
+Oc1cccc(c1)c2nc(N3CCOCC3)c4oc5ncccc5c4n2
+
+$$$$
+
+  SciTegic01171120562D
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+M  END
+> <mr_id>
+8573
+
+> <SMI>
+CO[C@@H]1[C@@H](C[C@H]2O[C@]1(C)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35)N(C)C(=O)c9ccccc9
+
+$$$$
+
+  SciTegic01171120562D
+
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+M  END
+> <mr_id>
+4027
+
+> <SMI>
+Clc1ccc(Nc2nnc(Cc3ccncc3)c4ccccc24)cc1
+
+$$$$
+
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+ 20 21  1  0
+ 21 22  1  0
+ 22 23  1  0
+ 22 24  1  0
+ 21 25  1  0
+ 18 25  2  0
+ 25 26  1  0
+  7 26  2  0
+M  END
+> <mr_id>
+600
+
+> <SMI>
+CC[C@H](CO)Nc1nc(NCc2ccccc2)c3ncn(C(C)C)c3n1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 25 28  0  0  0  0            999 V2000
+    2.3383   -1.3500    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 C   0  0
+   -2.5987    1.5004    0.0000 C   0  0
+   -2.7390    2.9810    0.0000 N   0  0
+   -4.2067    3.2905    0.0000 C   0  0
+   -4.9546    1.9903    0.0000 C   0  0
+   -3.9492    0.8772    0.0000 N   0  0
+   -6.4469    1.8311    0.0000 C   0  0
+   -7.4153    2.9701    0.0000 C   0  0
+   -8.8906    2.6991    0.0000 C   0  0
+   -9.3937    1.2860    0.0000 N   0  0
+   -8.4213    0.1438    0.0000 C   0  0
+   -6.9460    0.4147    0.0000 C   0  0
+   -4.8193    4.6606    0.0000 C   0  0
+   -4.0353    5.9336    0.0000 C   0  0
+   -4.7489    7.2530    0.0000 C   0  0
+   -6.2483    7.2947    0.0000 C   0  0
+   -6.8192    8.3502    0.0000 F   0  0
+   -7.0341    6.0170    0.0000 C   0  0
+   -6.3205    4.6976    0.0000 C   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  2  7  2  0
+  5  8  1  0
+  8  9  2  0
+  9 10  1  0
+ 10 11  2  0
+ 11 12  1  0
+  8 12  1  0
+ 11 13  1  0
+ 13 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 13 18  2  0
+ 10 19  1  0
+ 19 20  1  0
+ 20 21  2  0
+ 21 22  1  0
+ 22 23  1  0
+ 22 24  2  0
+ 24 25  1  0
+ 19 25  2  0
+M  END
+> <mr_id>
+8393
+
+> <SMI>
+Oc1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 27 30  0  0  0  0            999 V2000
+    3.6375   -0.9049    0.0000 C   0  0
+    2.5973   -1.5031    0.0000 S   0  0
+    2.5956   -2.7031    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 C   0  0
+   -2.5987    1.5004    0.0000 C   0  0
+   -2.7390    2.9810    0.0000 N   0  0
+   -4.2067    3.2905    0.0000 C   0  0
+   -4.9546    1.9903    0.0000 C   0  0
+   -3.9492    0.8772    0.0000 N   0  0
+   -6.4469    1.8311    0.0000 C   0  0
+   -7.4153    2.9701    0.0000 C   0  0
+   -8.8906    2.6991    0.0000 C   0  0
+   -9.3937    1.2860    0.0000 N   0  0
+   -8.4213    0.1438    0.0000 C   0  0
+   -6.9460    0.4147    0.0000 C   0  0
+   -4.8193    4.6606    0.0000 C   0  0
+   -4.0353    5.9336    0.0000 C   0  0
+   -4.7489    7.2530    0.0000 C   0  0
+   -6.2483    7.2947    0.0000 C   0  0
+   -6.8192    8.3502    0.0000 F   0  0
+   -7.0341    6.0170    0.0000 C   0  0
+   -6.3205    4.6976    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  8  9  1  0
+  4  9  2  0
+  7 10  1  0
+ 10 11  2  0
+ 11 12  1  0
+ 12 13  2  0
+ 13 14  1  0
+ 10 14  1  0
+ 13 15  1  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 18 19  2  0
+ 19 20  1  0
+ 15 20  2  0
+ 12 21  1  0
+ 21 22  1  0
+ 22 23  2  0
+ 23 24  1  0
+ 24 25  1  0
+ 24 26  2  0
+ 26 27  1  0
+ 21 27  2  0
+M  END
+> <mr_id>
+3250
+
+> <SMI>
+CS(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccncc3)c4ccc(F)cc4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 29 33  0  0  0  0            999 V2000
+  -12.5295    0.6317    0.0000 N   0  0
+  -11.9608    1.6884    0.0000 C   0  0
+  -12.5918    2.7091    0.0000 O   0  0
+  -10.4606    1.7327    0.0000 C   0  0
+   -9.6699    0.4580    0.0000 C   0  0
+   -8.1707    0.5054    0.0000 C   0  0
+   -7.4652    1.8235    0.0000 C   0  0
+   -8.2527    3.1022    0.0000 C   0  0
+   -9.7520    3.0548    0.0000 C   0  0
+   -5.9730    1.9836    0.0000 C   0  0
+   -4.9669    0.8711    0.0000 N   0  0
+   -3.6168    1.4950    0.0000 C   0  0
+   -3.7580    2.9756    0.0000 C   0  0
+   -5.2259    3.2843    0.0000 N   0  0
+   -2.6389    3.9757    0.0000 C   0  0
+   -1.1867    3.6217    0.0000 C   0  0
+   -0.1511    4.7069    0.0000 C   0  0
+   -0.5731    6.1463    0.0000 C   0  0
+   -2.0307    6.5006    0.0000 C   0  0
+   -3.0662    5.4154    0.0000 N   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 O   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    1.7138    1.2033    0.0000 O   0  0
+    0.2917    0.7475    0.0000 C   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+  1  2  1  0
+  2  3  2  0
+  2  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  8  9  1  0
+  4  9  2  0
+  7 10  1  0
+ 10 11  2  0
+ 11 12  1  0
+ 12 13  2  0
+ 13 14  1  0
+ 10 14  1  0
+ 13 15  1  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 18 19  2  0
+ 19 20  1  0
+ 15 20  2  0
+ 12 21  1  0
+ 21 22  1  0
+ 22 23  2  0
+ 23 24  1  0
+ 24 25  1  0
+ 25 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 24 28  2  0
+ 28 29  1  0
+ 21 29  2  0
+M  END
+> <mr_id>
+4347423
+
+> <SMI>
+NC(=O)c1ccc(cc1)c2nc(c([nH]2)c3ccccn3)c4ccc5OCOc5c4
+
+$$$$
+
+  SciTegic01171120562D
+
+ 32 34  0  0  0  0            999 V2000
+    3.6331   -3.6060    0.0000 C   0  0
+    2.5951   -3.0039    0.0000 N   0  0
+    2.5973   -1.5031    0.0000 C   0  0
+    3.6375   -0.9049    0.0000 O   0  0
+    1.2990   -0.7500    0.0000 C   0  0
+    1.2990    0.7500    0.0000 C   0  0
+    0.0000    1.5000    0.0000 C   0  0
+   -0.0031    3.0008    0.0000 O   0  0
+   -1.3039    3.7494    0.0000 C   0  0
+   -1.3092    5.2494    0.0000 C   0  0
+   -2.6108    5.9949    0.0000 C   0  0
+   -3.9073    5.2404    0.0000 C   0  0
+   -5.2112    5.9836    0.0000 N   0  0
+   -6.5072    5.2269    0.0000 C   0  0
+   -6.5010    4.0269    0.0000 O   0  0
+   -7.8111    5.9701    0.0000 N   0  0
+   -9.1072    5.2134    0.0000 C   0  0
+  -10.4114    5.9543    0.0000 C   0  0
+  -11.7053    5.1953    0.0000 C   0  0
+  -11.6949    3.6953    0.0000 C   0  0
+  -12.7299    3.0882    0.0000 Cl  0  0
+  -10.3907    2.9543    0.0000 C   0  0
+   -9.0969    3.7133    0.0000 C   0  0
+  -10.3803    1.4536    0.0000 C   0  0
+  -11.4150    0.8457    0.0000 F   0  0
+   -9.3367    0.8611    0.0000 F   0  0
+  -10.3714    0.2536    0.0000 F   0  0
+   -3.9021    3.7404    0.0000 C   0  0
+   -2.6005    2.9949    0.0000 C   0  0
+   -1.2990    0.7500    0.0000 C   0  0
+   -1.2990   -0.7500    0.0000 C   0  0
+    0.0000   -1.5000    0.0000 N   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  3  5  1  0
+  5  6  1  0
+  6  7  2  0
+  7  8  1  0
+  8  9  1  0
+  9 10  1  0
+ 10 11  2  0
+ 11 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  2  0
+ 14 16  1  0
+ 16 17  1  0
+ 17 18  1  0
+ 18 19  2  0
+ 19 20  1  0
+ 20 21  1  0
+ 20 22  2  0
+ 22 23  1  0
+ 17 23  2  0
+ 22 24  1  0
+ 24 25  1  0
+ 24 26  1  0
+ 24 27  1  0
+ 12 28  2  0
+ 28 29  1  0
+  9 29  2  0
+  7 30  1  0
+ 30 31  2  0
+ 31 32  1  0
+  5 32  2  0
+M  END
+> <mr_id>
+4255941
+
+> <SMI>
+CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
+
+$$$$
+
+  SciTegic01171120562D
+
+ 35 42  0  0  1  0            999 V2000
+   -1.9455    5.8387    0.0000 C   0  0
+   -2.5513    4.8029    0.0000 N   0  0
+   -1.8100    3.5000    0.0000 C   0  0  2  0  0  0
+   -0.2400    3.5200    0.0000 C   0  0
+    0.5000    2.1800    0.0000 C   0  0  1  0  0  0
+   -1.0600    2.1800    0.0000 O   0  0
+   -1.8300    0.9300    0.0000 C   0  0  1  0  0  0
+   -3.0300    0.9300    0.0000 C   0  0
+   -2.6500    2.2500    0.0000 C   0  0  2  0  0  0
+   -4.1471    2.2892    0.0000 O   0  0
+   -4.7748    1.2665    0.0000 C   0  0
+   -0.9800   -0.7800    0.0000 N   0  0
+   -2.1300   -1.4600    0.0000 C   0  0
+   -3.3200   -0.7600    0.0000 C   0  0
+   -4.5500   -1.4800    0.0000 C   0  0
+   -4.5800   -2.7700    0.0000 C   0  0
+   -3.3400   -3.4700    0.0000 C   0  0
+   -2.1300   -2.7900    0.0000 C   0  0
+    0.2400   -2.7700    0.0000 C   0  0
+    1.4300   -3.4700    0.0000 C   0  0
+    1.7600   -4.9700    0.0000 C   0  0
+    3.2600   -5.0800    0.0000 N   0  0
+    3.8500   -3.6300    0.0000 C   0  0
+    4.9971   -3.2777    0.0000 O   0  0
+    2.6600   -2.7500    0.0000 C   0  0
+    2.6800   -1.4600    0.0000 C   0  0
+    3.7900    0.5600    0.0000 C   0  0
+    4.9600    1.2800    0.0000 C   0  0
+    4.9600    2.6300    0.0000 C   0  0
+    3.8100    3.2900    0.0000 C   0  0
+    2.6400    2.5900    0.0000 C   0  0
+    2.6400    1.2400    0.0000 C   0  0
+    1.4900    0.5400    0.0000 N   0  0
+    1.4500   -0.7600    0.0000 C   0  0
+    0.2400   -1.4400    0.0000 C   0  0
+  1  2  1  0
+  3  2  1  6
+  3  4  1  0
+  5  4  1  6
+  5  6  1  0
+  6  7  1  0
+  7  8  1  1
+  7  9  1  0
+  3  9  1  0
+  9 10  1  6
+ 10 11  1  0
+  7 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 16 17  2  0
+ 17 18  1  0
+ 13 18  2  0
+ 18 19  1  0
+ 19 20  1  0
+ 20 21  1  0
+ 21 22  1  0
+ 22 23  1  0
+ 23 24  2  0
+ 23 25  1  0
+ 20 25  2  0
+ 25 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  2  0
+ 29 30  1  0
+ 30 31  2  0
+ 31 32  1  0
+ 27 32  2  0
+ 32 33  1  0
+  5 33  1  0
+ 33 34  1  0
+ 26 34  2  0
+ 34 35  1  0
+ 12 35  1  0
+ 19 35  2  0
+M  END
+> <mr_id>
+66
+
+> <SMI>
+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35
+
+$$$$
+
+  SciTegic01171120562D
+
+ 32 35  0  0  1  0            999 V2000
+    7.1381   -2.1568    0.0000 C   0  0
+    6.0456   -2.6531    0.0000 C   0  0
+    4.7409   -1.9129    0.0000 N   0  0
+    3.6552   -2.9294    0.0000 C   0  0
+    2.1855   -2.6254    0.0000 C   0  0
+    1.7138   -1.2033    0.0000 C   0  0
+    2.5889    0.0182    0.0000 C   0  0
+    3.7889    0.0269    0.0000 O   0  0
+    1.7138    1.2033    0.0000 N   0  0
+    0.2917    0.7475    0.0000 C   0  0
+   -1.0028    1.5132    0.0000 C   0  0
+   -2.3155    0.7475    0.0000 C   0  0
+   -2.3155   -0.7475    0.0000 C   0  0
+   -3.3560   -1.3452    0.0000 F   0  0
+   -1.0028   -1.5132    0.0000 C   0  0
+    0.2917   -0.7475    0.0000 C   0  0
+    4.2542   -4.2907    0.0000 C   0  0
+    3.6559   -5.3308    0.0000 C   0  0
+    5.7448   -4.1226    0.0000 C   0  0
+    6.7580   -5.2264    0.0000 C   0  0
+    6.3978   -6.3710    0.0000 O   0  0
+    8.2231   -4.9012    0.0000 N   0  0
+    9.2380   -6.0068    0.0000 C   0  0
+   10.7032   -5.6816    0.0000 C   0  0  2  0  0  0
+   11.0634   -4.5369    0.0000 O   0  0
+   11.7181   -6.7872    0.0000 C   0  0
+   13.1833   -6.4620    0.0000 N   0  0
+   14.1993   -7.5656    0.0000 C   0  0
+   15.6630   -7.2376    0.0000 C   0  0
+   16.1108   -5.8060    0.0000 O   0  0
+   15.0949   -4.7024    0.0000 C   0  0
+   13.6312   -5.0304    0.0000 C   0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  7  9  1  0
+  9 10  1  0
+ 10 11  1  0
+ 11 12  2  0
+ 12 13  1  0
+ 13 14  1  0
+ 13 15  2  0
+ 15 16  1  0
+  6 16  1  0
+ 10 16  2  0
+  4 17  2  0
+ 17 18  1  0
+ 17 19  1  0
+  2 19  2  0
+ 19 20  1  0
+ 20 21  2  0
+ 20 22  1  0
+ 22 23  1  0
+ 23 24  1  0
+ 24 25  1  6
+ 24 26  1  0
+ 26 27  1  0
+ 27 28  1  0
+ 28 29  1  0
+ 29 30  1  0
+ 30 31  1  0
+ 31 32  1  0
+ 27 32  1  0
+M  END
+> <mr_id>
+4362206
+
+> <SMI>
+Cc1[nH]c(/C=C/2\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4
+
+$$$$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check.mol	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,17 @@
+
+Mrv1810 07121910172D          
+
+  4  3  0  0  0  0            999 V2000
+   -2.5038    0.4060    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+   -2.5038    1.2310    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+   -3.2182   -0.0065    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
+   -1.7893   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  4  0  0  0
+M  CHG  2   2  -1   3   1
+M  END
+> <MaxPenaltyScore>
+5
+> <IssueMessages>
+molecule has a bond with an illegal stereo flag; InChI: Proton(s) added/removed; InChI: Omitted undefined stereo
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in1.smi	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,1 @@
+CN1CCC[C@H]1c2cccnc2	test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/o_molblock.mol	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,13 @@
+
+  Mrv1810 07121910172D          
+
+  4  3  0  0  0  0            999 V2000
+   -2.5038    0.4060    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+   -2.5038    1.2310    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+   -3.2182   -0.0065    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
+   -1.7893   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  4  0  0  0
+M  CHG  2   2  -1   3   1
+M  END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out1.smi	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,47 @@
+CN1CCCC1c2ccc(Cl)cc2	CHEMBL279352
+CCCC[C@H]1CC[C@H](N1C)c2cccnc2	CHEMBL119581
+CN1CCCC1c2ccc(F)nc2	CHEMBL72470
+C[C@H]1CC[C@H](N1C)c2cccnc2	CHEMBL116645
+CCCC[C@@H]1CC[C@H](N1C)c2cccnc2	CHEMBL119574
+CN1CCCC1c2ccc(CCc3ccc(Cl)cc3)nc2	CHEMBL189470
+CN1CCC[C@H]1c2cccnc2	CHEMBL3
+CN1CCCC1c2cncc(Cl)c2	CHEMBL61013
+CCCCCc1ccc(cn1)C2CCCN2C	CHEMBL103566
+CN1CCCC1c2cccnc2	CHEMBL440464
+CN1CCCC1c2ccc(nc2)c3ccccc3	CHEMBL350748
+CN1CCCC1c2cnccc2N	CHEMBL193763
+C(N1CCCC1c2cccnc2)c3ccccc3	CHEMBL163552
+COCC1CCN(C)[C@@H]1c2cccnc2	CHEMBL119020
+CN1CCCC1c2ccc(C)nc2	CHEMBL294757
+CN1CCCC1c2ccc(C)cc2	CHEMBL180376
+CN1CCCC[C@H]1c2cccnc2	CHEMBL3640783
+C[C@@H]1CC[C@H](N1C)c2cccnc2	CHEMBL118038
+CN1CCC[C@H]1c2ccccn2	CHEMBL2068760
+CN1CCCC1c2cccnc2C	CHEMBL160034
+CCc1ccc(cn1)C2CCCN2C	CHEMBL103225
+C[C@H]1C[C@H](N(C)C1)c2cccnc2	CHEMBL432837
+CC[C@H]1C[C@H](N(C)C1)c2cccnc2	CHEMBL115793
+CN1CCCC1c2ccccc2	CHEMBL367126
+CN1CCCC1c2ccc(CCCc3ccccc3)nc2	CHEMBL361703
+CC1CCN(C)[C@@H]1c2cccnc2	CHEMBL119019
+CN1CCCC1c2ccc(Br)nc2	CHEMBL58231
+CN1CCCCC1c2cccnc2	CHEMBL102246
+CN1CCCC1c2ccc(CCc3ccccc3)nc2	CHEMBL190295
+CN1CCC[C@H]1c2ccccc2	CHEMBL1199383
+COc1cncc(c1)C2CCCN2C	CHEMBL303530
+COc1ccc(CCc2ccc(cn2)C3CCCN3C)cc1	CHEMBL190652
+CN1CCCC1c2cncc(F)c2	CHEMBL62128
+CN1CCCC1c2cncc(C)c2	CHEMBL364003
+CN1CCC(CO)[C@H]1c2cccnc2	CHEMBL325426
+CCN1CCCC1c2cccnc2	CHEMBL163042
+COc1ccncc1C2CCCN2C	CHEMBL370168
+CCc1cncc(c1)C2CCCN2C	CHEMBL111526
+CN1CCC[C@@H]1c2cccnc2	CHEMBL9732
+CN1CCC(CF)[C@H]1c2cccnc2	CHEMBL119016
+CN1CCCC1c2ccc(Cl)nc2	CHEMBL70050
+CN1CCCC1c2cncc(Br)c2	CHEMBL61772
+CN1CCCC1c2ccc(\C=C\c3ccccc3)nc2	CHEMBL190678
+CCCc1cncc(c1)C2CCCN2C	CHEMBL382287
+CN1CCCC1c2cnc3ccccc3c2	CHEMBL161944
+CCCc1ccc(cn1)C2CCCN2C	CHEMBL103537
+CCCCc1ccc(cn1)C2CCCN2C	CHEMBL320023
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out2.smi	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,1 @@
+CN1CCC[C@H]1c2cccnc2	CHEMBL3
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out3.smi	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,55 @@
+CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O	CHEMBL1448280
+Cn1cccc1-c1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1	CHEMBL3486928
+O=C1[C@@H](NS(=O)(=O)c2ccc3cc(Cl)ccc3c2)CCCN1CC(=O)N1CCCC1c1cccnc1	CHEMBL1923459
+CN1CCCC1c1cccnc1.O=S(=O)(O)O	CHEMBL2142095
+CN1CCC[C@@H]1c1cccnc1.Cc1ccc(C(=O)OC(C(=O)O)C(OC(=O)c2ccc(C)cc2)C(=O)O)cc1	CHEMBL2448607
+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c2ccccc12	CHEMBL4095563
+O=C(NC1CCN(Cc2ccn(-c3ccc(C(F)(F)F)cc3)c2)CC1)N1CCCC1c1cccnc1	CHEMBL560283
+O=C1NC(=O)/C(=C/c2cnn3c(NC4CC4)nc(N4CCCC4c4cccnc4)nc23)N1	CHEMBL3984229
+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@H]3c3cccnc3)cccc2c1	CHEMBL3692144
+O=C(c1cc2c([nH]c1=O)CCC2)N1CCCC1c1cccnc1	CHEMBL3458802
+CC(C)C[C@H](N[C@H](CCN1C(=O)c2cc3ccccc3cc2C1=O)C(=O)O)C(=O)N1CCCC1c1cccnc1	CHEMBL158622
+c1ccc(CN2CCCC2c2cccnc2)cc1	CHEMBL163552
+Cc1ncsc1CCC(=O)N1CCCC1c1cccnc1	CHEMBL3476252
+O=C(c1cc(-c2ccc(O)cc2)n[nH]1)N1CCCC1c1cccnc1	CHEMBL3474057
+O=C(C(Nc1ccccc1F)c1cc2ccccc2s1)N1CCCC1c1cccnc1	CHEMBL2348659
+OC(COc1ccccc1-c1nc2ccccc2o1)CN1CCCC1c1cccnc1	CHEMBL608832
+O=C(Nc1ccccc1F)N1CCCC1c1cccnc1	CHEMBL1870182
+CN1CCC[C@H]1c1cccnc1.Cl	CHEMBL225057
+O=C(Nc1ccccc1C(F)(F)F)N1CCCC1c1cccnc1	CHEMBL1353542
+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@H]3[C@H](C[C@H](O)[C@@]21C)[C@@]1(C)CC[C@@H](O)C[C@H]1C[C@H]3O	CHEMBL3114538
+Cc1ccc2nc(CN3CCCC3c3cccnc3)cc(O)c2c1	CHEMBL3485916
+Cc1cc(N2CCCC2c2cccnc2)nc(C)n1	CHEMBL3454373
+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCC[C@@H]3c3cccnc3)cccc2c1	CHEMBL3682682
+CN1CCCC1c1cccnc1	CHEMBL440464
+CN1CCC[C@@H]1c1cccnc1	CHEMBL9732
+Cc1cc(N(C)C)nc(N2CCCC2c2cccnc2)n1	CHEMBL3454403
+CN1CCC[C@H]1c1cccnc1.CN1CCC[C@H]1c1cccnc1.O=S(=O)(O)O	CHEMBL3182465
+CCCc1cc(C(=O)N2CCCC2c2cccnc2)[nH]n1	CHEMBL3486295
+O=C(c1ccc(F)c(F)c1)N1CCN2C(=O)c3ccccc3[C@@]12c1ccc(N2CCC[C@H]2c2cccnc2)cc1	CHEMBL4100810
+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@@]21C	CHEMBL3114539
+CCNC(=O)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1	CHEMBL4064004
+Cc1nn(C)c(Oc2cccc(Cl)c2Cl)c1C(=O)N1CCCC1c1cccnc1	CHEMBL2336227
+CN1CCC[C@H]1c1cccnc1.C[C@H](CCC(=O)O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@@]21C	CHEMBL3114541
+CC1=C(C(=O)N2CCCC2c2cccnc2)C(c2ccc(Cl)c(Cl)c2)n2nccc2N1	CHEMBL601248
+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)nc1	CHEMBL1921840
+c1cncc(C2CCCN2c2ccnc3[nH]ncc23)c1	CHEMBL4066892
+CN1CCC[C@H]1c1cccnc1	CHEMBL3
+CCO.CN1CCC[C@H]1c1cccnc1	CHEMBL3137669
+Cc1cc(C)nc(N2CCCC2c2cccnc2)n1	CHEMBL3436596
+Cc1ccc(-c2cc(C(=O)N3CCCC3c3cccnc3)[nH]n2)o1	CHEMBL3485246
+NC(=O)c1ccc(Oc2ccc(CN3CCCC3c3cccnc3)cc2)c(Cl)c1	CHEMBL1921841
+NC(=O)c1ccc(Oc2ccc(CN3CCC[C@@H]3c3cccnc3)cc2)c(Cl)c1	CHEMBL1921843
+NC(=O)c1ccc(Oc2ccc(CN3CCC[C@H]3c3cccnc3)cc2)c(Cl)c1	CHEMBL1921842
+CN1CCC[C@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O	CHEMBL151515
+O=C(C(Nc1ccccc1F)c1ccc(C(F)(F)F)cc1)N1CCCC1c1cccnc1	CHEMBL2348671
+CN1CCC[C@H]1c1cccnc1.O.O.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O	CHEMBL3989563
+c1cncc(C2CCCN2C2c3ccccc3Oc3ccccc32)c1	CHEMBL278775
+CN1CCC[C@@H]1c1cccnc1.O=C(O)C(O)C(O)C(=O)O.O=C(O)C(O)C(O)C(=O)O	CHEMBL2062338
+Cn1cc(NC(=O)N2CCCC2c2cccnc2)ccc1=O	CHEMBL3453894
+CCN1CCCC1c1cccnc1	CHEMBL163042
+O=S(=O)(Nc1ncns1)c1ccc2c(N3CCCC3c3cccnc3)cccc2c1	CHEMBL3682681
+O=C(NC1COC1)c1cc2c(N3CCCC3c3cccnc3)ccnc2[nH]1	CHEMBL4083992
+O=CN1CCC[C@H]1c1cccnc1	CHEMBL3126024
+Cc1nc2ccccc2n1Cc1ccc(CNC(=O)[C@H](O)[C@@H](O)C(=O)N2CCCC2c2cccnc2)s1	CHEMBL1779603
+CC[C@H]1OC(=O)[C@H](C)[C@@H](OC(=O)N2CCC[C@@H]2c2cccnc2)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@H](N(C)C)[C@H]2O)[C@](C)(OC)C[C@@H](C)C(=O)[C@H](C)[C@H]2NC(=O)O[C@]12C	CHEMBL2338711
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out4.smi	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,4 @@
+C1CCCC1	CHEMBL1370850
+C1CCCCCCCCCCC1	CHEMBL3185808
+C1CCCCCCC1	CHEMBL452651
+C1CCCCC1	CHEMBL15980
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parent_molblock.mol	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,12 @@
+
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+   -2.5038    0.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5038    1.2310    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2182   -0.0065    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.7893   -0.0065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+M  END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pipeline_multi.sdf	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,739 @@
+
+     RDKit          2D
+
+ 26 30  0  0  0  0  0  0  0  0999 V2000
+   -8.6396    0.9568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6023    1.5602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6071    3.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3104    3.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0090    3.0685    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.0040    1.5682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.3008    0.8143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.7006   -0.6045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915   -1.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5059   -2.8197    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2156   -3.5847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2329   -5.0846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5404   -5.8196    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8308   -5.0547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.8135   -3.5548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.3190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732   -1.3190    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372   -0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7372    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4732    1.5389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2274    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4915    1.5389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  2  7  2  0
+  6  8  1  0
+  8  9  1  0
+  9 10  2  0
+ 10 11  1  0
+ 11 12  1  0
+ 12 13  1  0
+ 13 14  1  0
+ 14 15  1  0
+ 15 16  1  0
+ 11 16  1  0
+ 10 17  1  0
+ 17 18  1  0
+ 18 19  1  0
+ 19 20  2  0
+ 20 21  1  0
+ 21 22  2  0
+ 22 23  1  0
+ 23 24  2  0
+ 19 24  1  0
+ 24 25  1  0
+ 17 25  2  0
+ 25 26  1  0
+  8 26  2  0
+M  END
+
+> <MaxPenaltyScore>
+0
+> <IssueMessages>
+
+$$$$
+     RDKit          2D
+
+ 43 51  0  0  1  0  0  0  0  0999 V2000
+   -4.7204    3.3431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.1471    2.2890    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.6500    2.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8100    3.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.2400    3.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.5000    2.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0600    2.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8300    0.9300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.0300    0.9300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9800   -0.7800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.1300   -1.4600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3200   -0.7600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.5500   -1.4800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.5800   -2.7700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.3400   -3.4700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.1300   -2.7900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2400   -2.7700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4300   -3.4700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7600   -4.9700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.2600   -5.0800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.8500   -3.6300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9971   -3.2777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6600   -2.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6800   -1.4600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7900    0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9600    1.2800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9600    2.6300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.8100    3.2900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6400    2.5900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6400    1.2400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4900    0.5400    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4500   -0.7600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2400   -1.4400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5511    4.8030    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.9442    5.8382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0519    4.8135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.6588    3.7783    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7941    6.1180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2940    6.1306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.0331    7.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2722    8.7286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7723    8.7160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0332    7.4108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  3  2  1  6
+  3  4  1  0
+  4  5  1  0
+  6  5  1  6
+  6  7  1  0
+  7  8  1  0
+  3  8  1  0
+  8  9  1  1
+  8 10  1  0
+ 10 11  1  0
+ 11 12  1  0
+ 12 13  2  0
+ 13 14  1  0
+ 14 15  2  0
+ 15 16  1  0
+ 11 16  2  0
+ 16 17  1  0
+ 17 18  1  0
+ 18 19  1  0
+ 19 20  1  0
+ 20 21  1  0
+ 21 22  2  0
+ 21 23  1  0
+ 18 23  2  0
+ 23 24  1  0
+ 24 25  1  0
+ 25 26  1  0
+ 26 27  2  0
+ 27 28  1  0
+ 28 29  2  0
+ 29 30  1  0
+ 25 30  2  0
+ 30 31  1  0
+  6 31  1  0
+ 31 32  1  0
+ 24 32  2  0
+ 32 33  1  0
+ 10 33  1  0
+ 17 33  2  0
+  4 34  1  6
+ 34 35  1  0
+ 34 36  1  0
+ 36 37  2  0
+ 36 38  1  0
+ 38 39  1  0
+ 39 40  2  0
+ 40 41  1  0
+ 41 42  2  0
+ 42 43  1  0
+ 38 43  2  0
+M  END
+
+> <MaxPenaltyScore>
+2
+> <IssueMessages>
+molecule has a stereo bond in a ring
+$$$$
+     RDKit          2D
+
+ 25 28  0  0  0  0  0  0  0  0999 V2000
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+ 31 32  1  0
+  5 32  2  0
+M  END
+
+> <MaxPenaltyScore>
+0
+> <IssueMessages>
+
+$$$$
+     RDKit          2D
+
+ 35 42  0  0  1  0  0  0  0  0999 V2000
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+ 19 35  2  0
+M  END
+
+> <MaxPenaltyScore>
+2
+> <IssueMessages>
+molecule has a stereo bond in a ring
+$$$$
+     RDKit          2D
+
+ 32 35  0  0  1  0  0  0  0  0999 V2000
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+ 27 32  1  0
+M  END
+
+> <MaxPenaltyScore>
+0
+> <IssueMessages>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/std_molblock.mol	Sat Oct 10 09:43:40 2020 +0000
@@ -0,0 +1,12 @@
+
+     RDKit          2D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
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+  1  2  1  0
+  1  3  1  0
+  1  4  1  0
+M  END