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Changeset 6:a57de37f12c2 (2020-10-07)

Previous changeset 5:1ade252ebe08 (2020-07-28) Next changeset 7:1d6fb7967ae9 (2020-10-10)

Commit message:
"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e"

modified:
chembl.py
chembl.xml

added:
chembl_structure_pipeline.xml
structure_pipeline.py
test-data/10mol.sdf
test-data/check.mol
test-data/o_molblock.mol
test-data/parent_molblock.mol
test-data/pipeline_multi.sdf
test-data/std_molblock.mol

diff -r 1ade252ebe08 -r a57de37f12c2 chembl.py
--- a/chembl.py Tue Jul 28 08:20:47 2020 -0400
+++ b/chembl.py Wed Oct 07 09:31:40 2020 +0000

[

@@ -1,62 +1,73 @@
+import argparse
+
+from chembl_webresource_client.new_client import new_client
from chembl_webresource_client.settings import Settings
+
Settings.Instance().CACHING = False
-from chembl_webresource_client.new_client import new_client
-import argparse
+

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:
+    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')
@@ -101,7 +112,7 @@
     # write to file
     with open(args.output, 'w') as f:
         f.write('\n'.join(mols))
-
+

if __name__ == "__main__":
     main()

diff -r 1ade252ebe08 -r a57de37f12c2 chembl.xml
--- a/chembl.xml Tue Jul 28 08:20:47 2020 -0400
+++ b/chembl.xml Wed Oct 07 09:31:40 2020 +0000

@@ -1,9 +1,9 @@
<tool id="chembl" name="Search ChEMBL database" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>for compounds which are similar to a SMILES string</description>
     <macros>
         <token name="@TOOL_VERSION@">0.10.1</token>
         <token name="@GALAXY_VERSION@">2</token>
     </macros>
-    <description>for compounds which are similar to a SMILES string</description>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">chembl_webresource_client</requirement>
     </requirements>

diff -r 1ade252ebe08 -r a57de37f12c2 chembl_structure_pipeline.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chembl_structure_pipeline.xml Wed Oct 07 09:31:40 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>

diff -r 1ade252ebe08 -r a57de37f12c2 structure_pipeline.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/structure_pipeline.py Wed Oct 07 09:31:40 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()

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/10mol.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/10mol.sdf Wed Oct 07 09:31:40 2020 +0000

[

b'@@ -0,0 +1,759 @@\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' 0.0000 C 0 0\r\n+ -2.6500 2.2500 0.0000 C 0 0 2 0 0 0\r\n+ -4.1471 2.2892 0.0000 O 0 0\r\n+ -4.7748 1.2665 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+ 1 2 1 0\r\n+ 3 2 1 6\r\n+ 3 4 1 0\r\n+ 5 4 1 6\r\n+ 5 6 1 0\r\n+ 6 7 1 0\r\n+ 7 8 1 1\r\n+ 7 9 1 0\r\n+ 3 9 1 0\r\n+ 9 10 1 6\r\n+ 10 11 1 0\r\n+ 7 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 2 0\r\n+ 17 18 1 0\r\n+ 13 18 2 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+ 22 23 1 0\r\n+ 23 24 2 0\r\n+ 23 25 1 0\r\n+ 20 25 2 0\r\n+ 25 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 2 0\r\n+ 29 30 1 0\r\n+ 30 31 2 0\r\n+ 31 32 1 0\r\n+ 27 32 2 0\r\n+ 32 33 1 0\r\n+ 5 33 1 0\r\n+ 33 34 1 0\r\n+ 26 34 2 0\r\n+ 34 35 1 0\r\n+ 12 35 1 0\r\n+ 19 35 2 0\r\n+M END\r\n+> <mr_id>\r\n+66\r\n+\r\n+> <SMI>\r\n+CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n3c4ccccc4c5c6CNC(=O)c6c7c8ccccc8n2c7c35\r\n+\r\n+$$$$\r\n+\r\n+ SciTegic01171120562D\r\n+\r\n+ 32 35 0 0 1 0 999 V2000\r\n+ 7.1381 -2.1568 0.0000 C 0 0\r\n+ 6.0456 -2.6531 0.0000 C 0 0\r\n+ 4.7409 -1.9129 0.0000 N 0 0\r\n+ 3.6552 -2.9294 0.0000 C 0 0\r\n+ 2.1855 -2.6254 0.0000 C 0 0\r\n+ 1.7138 -1.2033 0.0000 C 0 0\r\n+ 2.5889 0.0182 0.0000 C 0 0\r\n+ 3.7889 0.0269 0.0000 O 0 0\r\n+ 1.7138 1.2033 0.0000 N 0 0\r\n+ 0.2917 0.7475 0.0000 C 0 0\r\n+ -1.0028 1.5132 0.0000 C 0 0\r\n+ -2.3155 0.7475 0.0000 C 0 0\r\n+ -2.3155 -0.7475 0.0000 C 0 0\r\n+ -3.3560 -1.3452 0.0000 F 0 0\r\n+ -1.0028 -1.5132 0.0000 C 0 0\r\n+ 0.2917 -0.7475 0.0000 C 0 0\r\n+ 4.2542 -4.2907 0.0000 C 0 0\r\n+ 3.6559 -5.3308 0.0000 C 0 0\r\n+ 5.7448 -4.1226 0.0000 C 0 0\r\n+ 6.7580 -5.2264 0.0000 C 0 0\r\n+ 6.3978 -6.3710 0.0000 O 0 0\r\n+ 8.2231 -4.9012 0.0000 N 0 0\r\n+ 9.2380 -6.0068 0.0000 C 0 0\r\n+ 10.7032 -5.6816 0.0000 C 0 0 2 0 0 0\r\n+ 11.0634 -4.5369 0.0000 O 0 0\r\n+ 11.7181 -6.7872 0.0000 C 0 0\r\n+ 13.1833 -6.4620 0.0000 N 0 0\r\n+ 14.1993 -7.5656 0.0000 C 0 0\r\n+ 15.6630 -7.2376 0.0000 C 0 0\r\n+ 16.1108 -5.8060 0.0000 O 0 0\r\n+ 15.0949 -4.7024 0.0000 C 0 0\r\n+ 13.6312 -5.0304 0.0000 C 0 0\r\n+ 1 2 1 0\r\n+ 2 3 1 0\r\n+ 3 4 1 0\r\n+ 4 5 1 0\r\n+ 5 6 2 0\r\n+ 6 7 1 0\r\n+ 7 8 2 0\r\n+ 7 9 1 0\r\n+ 9 10 1 0\r\n+ 10 11 1 0\r\n+ 11 12 2 0\r\n+ 12 13 1 0\r\n+ 13 14 1 0\r\n+ 13 15 2 0\r\n+ 15 16 1 0\r\n+ 6 16 1 0\r\n+ 10 16 2 0\r\n+ 4 17 2 0\r\n+ 17 18 1 0\r\n+ 17 19 1 0\r\n+ 2 19 2 0\r\n+ 19 20 1 0\r\n+ 20 21 2 0\r\n+ 20 22 1 0\r\n+ 22 23 1 0\r\n+ 23 24 1 0\r\n+ 24 25 1 6\r\n+ 24 26 1 0\r\n+ 26 27 1 0\r\n+ 27 28 1 0\r\n+ 28 29 1 0\r\n+ 29 30 1 0\r\n+ 30 31 1 0\r\n+ 31 32 1 0\r\n+ 27 32 1 0\r\n+M END\r\n+> <mr_id>\r\n+4362206\r\n+\r\n+> <SMI>\r\n+Cc1[nH]c(/C=C/2\\C(=O)Nc3ccc(F)cc23)c(C)c1C(=O)NC[C@H](O)CN4CCOCC4\r\n+\r\n+$$$$\r\n'

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/check.mol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/check.mol Wed Oct 07 09:31:40 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

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/o_molblock.mol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/o_molblock.mol Wed Oct 07 09:31:40 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

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/parent_molblock.mol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parent_molblock.mol Wed Oct 07 09:31:40 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

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/pipeline_multi.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pipeline_multi.sdf Wed Oct 07 09:31:40 2020 +0000

b'@@ -0,0 +1,739 @@\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 1 0\n+ 3 4 2 0\n+ 4 5 1 0\n+ 5 6 2 0\n+ 6 7 1 0\n+ 2 7 2 0\n+ 6 8 1 0\n+ 8 9 1 0\n+ 9 10 2 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 1 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 2 0\n+ 25 26 1 0\n+ 8 26 2 0\n+M END\n+\n+> <MaxPenaltyScore>\n+0\n+> <IssueMessages>\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 0 0 0 0 0 0\n+ 4.9971 -3.2777 0.'..b' 0 0\n+ 3.8100 3.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6400 2.5900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.6400 1.2400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.4900 0.5400 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.4500 -0.7600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2400 -1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0\n+ 3 2 1 6\n+ 3 4 1 0\n+ 5 4 1 6\n+ 5 6 1 0\n+ 6 7 1 0\n+ 7 8 1 1\n+ 7 9 1 0\n+ 3 9 1 0\n+ 9 10 1 6\n+ 10 11 1 0\n+ 7 12 1 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+ 13 18 2 0\n+ 18 19 1 0\n+ 19 20 1 0\n+ 20 21 1 0\n+ 21 22 1 0\n+ 22 23 1 0\n+ 23 24 2 0\n+ 23 25 1 0\n+ 20 25 2 0\n+ 25 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 28 29 2 0\n+ 29 30 1 0\n+ 30 31 2 0\n+ 31 32 1 0\n+ 27 32 2 0\n+ 32 33 1 0\n+ 5 33 1 0\n+ 33 34 1 0\n+ 26 34 2 0\n+ 34 35 1 0\n+ 12 35 1 0\n+ 19 35 2 0\n+M END\n+\n+> <MaxPenaltyScore>\n+2\n+> <IssueMessages>\n+molecule has a stereo bond in a ring\n+$$$$\n+ RDKit 2D\n+\n+ 32 35 0 0 1 0 0 0 0 0999 V2000\n+ 7.1381 -2.1568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.0456 -2.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.7409 -1.9129 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.6552 -2.9294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.1855 -2.6254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7138 -1.2033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 2.5889 0.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.7889 0.0269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1.7138 1.2033 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2917 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0028 1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.3155 0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -2.3155 -0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ -3.3560 -1.3452 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n+ -1.0028 -1.5132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.2917 -0.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 4.2542 -4.2907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 3.6559 -5.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 5.7448 -4.1226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.7580 -5.2264 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 6.3978 -6.3710 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 8.2231 -4.9012 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 9.2380 -6.0068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 10.7032 -5.6816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.0634 -4.5369 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 11.7181 -6.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.1833 -6.4620 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n+ 14.1993 -7.5656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 15.6630 -7.2376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 16.1108 -5.8060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n+ 15.0949 -4.7024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 13.6312 -5.0304 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 1 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 1 0\n+ 11 12 2 0\n+ 12 13 1 0\n+ 13 14 1 0\n+ 13 15 2 0\n+ 15 16 1 0\n+ 6 16 1 0\n+ 10 16 2 0\n+ 4 17 2 0\n+ 17 18 1 0\n+ 17 19 1 0\n+ 2 19 2 0\n+ 19 20 1 0\n+ 20 21 2 0\n+ 20 22 1 0\n+ 22 23 1 0\n+ 23 24 1 0\n+ 24 25 1 6\n+ 24 26 1 0\n+ 26 27 1 0\n+ 27 28 1 0\n+ 28 29 1 0\n+ 29 30 1 0\n+ 30 31 1 0\n+ 31 32 1 0\n+ 27 32 1 0\n+M END\n+\n+> <MaxPenaltyScore>\n+0\n+> <IssueMessages>\n'

diff -r 1ade252ebe08 -r a57de37f12c2 test-data/std_molblock.mol
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/std_molblock.mol Wed Oct 07 09:31:40 2020 +0000