added standardize module

Author: tdudgeon

Dockerfile-rdkit

@@ -1,4 +1,4 @@
-FROM informaticsmatters/rdkit-python-debian:Release_2018_03_01
+FROM informaticsmatters/rdkit-python-debian:Release_2018_09_1
 LABEL maintainer="Tim Dudgeon<[email protected]>"
 
 USER root

src/python/pipelines/rdkit/standardize.py

@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+# Copyright 2018 Informatics Matters Ltd.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import argparse
+
+from rdkit import DataStructs, rdBase
+from rdkit.Chem.MolStandardize import rdMolStandardize
+
+from pipelines_utils import parameter_utils, utils
+from pipelines_utils_rdkit import rdkit_utils, mol_utils
+
+
+### functions #########################################
+
+#lfc = rdMolStandardize.LargestFragmentChooser()
+uncharger = rdMolStandardize.Uncharger()
+
+
+def standardize(mol, neutralise, fragment):
+    """
+
+    :param mol: The molecule to standardize
+    :param neutralise: Boolean for whether to neutralise the molecule
+    :param fragment: The approach for choosing the largest fragment. Either 'hac' or 'mw'. If not specified the whole
+    molecule is used.
+    :return: The standardized molecule
+    """
+    mol = rdMolStandardize.Cleanup(mol)
+    #mol = lfc.choose(mol)
+    # We use our own largest fragment picker as the RDKit one behaves slightly differently
+    if fragment:
+        mol = mol_utils.fragment(mol, fragment)
+    if neutralise:
+        mol = uncharger.uncharge(mol)
+    return mol
+
+
+### start main execution #########################################
+
+def main():
+
+    ### command line args definitions #########################################
+
+    parser = argparse.ArgumentParser(description='RDKit Standardize')
+    parser.add_argument('--fragment-method', choices=['hac', 'mw'], help='Approach to find biggest fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight)')
+    parser.add_argument('--neutralise', action='store_true', help='Neutralise the molecule')
+
+    parameter_utils.add_default_io_args(parser)
+    parser.add_argument('-q', '--quiet', action='store_true', help='Quiet mode')
+    parser.add_argument('--thin', action='store_true', help='Thin output mode')
+
+    args = parser.parse_args()
+    utils.log("Standardize Args: ", args)
+
+    # handle metadata
+    source = "standardize.py"
+    datasetMetaProps = {"source":source, "description": "Standardize using RDKit " + rdBase.rdkitVersion}
+    clsMappings = {}
+    fieldMetaProps = []
+
+
+    input,output,suppl,writer,output_base = rdkit_utils.\
+        default_open_input_output(args.input, args.informat, args.output,
+                                  'standardize', args.outformat,
+                                  thinOutput=False, valueClassMappings=clsMappings,
+                                  datasetMetaProps=datasetMetaProps,
+                                  fieldMetaProps=fieldMetaProps)
+    i = 0
+    total = 0
+    for mol in suppl:
+        if mol is None:
+            i += 1
+            continue
+        m = standardize(mol, args.neutralise, args.fragment_method)
+        writer.write(m)
+        total += 1
+
+    input.close()
+    writer.flush()
+    writer.close()
+    output.close()
+
+    if args.meta:
+        utils.write_metrics(output_base, {'__InputCount__':i, '__OutputCount__':total, 'RDKitStandardize':i})
+
+if __name__ == "__main__":
+    main()
+