Added submodule for querying info by SMILES from chemical databases

polymerist/rdutils/smileslib/chemdbqueries.py

@@ -0,0 +1,31 @@
+'''For querying chemical databases for information about molecules specified by SMILES string and other structures'''
+
+import logging
+LOGGER  = logging.getLogger(__name__)
+
+import cirpy
+import pubchempy as pcp
+from typing import Optional
+
+
+def get_property_from_smiles(smiles : str, prop_name : str='iupac_name') -> Optional[str]: # TODO: abstract each query method via Strategy pattern
+    '''Takes the SMILES string representing a molecule and attempts to fetch its IUPAC name from NIH CACTUS and/or PubChem
+    Returns the fetched IUPAC name as a str, or NoneType if both queries fail'''
+    # Open with NIH query (fastest method), return name if found...
+    LOGGER.debug(f'Attempting query of property "{prop_name}" from NIH CACTUS')
+    iupac_name = cirpy.resolve(smiles, prop_name)
+    if iupac_name is not None:
+        if isinstance(iupac_name, list):
+            return iupac_name.pop()
+        return iupac_name 
+
+    # ...otherwise, search through PubChem Compound queries for a matching results
+    pc_prop_name = pcp.PROPERTY_MAP.get(prop_name, prop_name)
+    LOGGER.debug(f'Attempting query of property "{pc_prop_name}" from PubChem PUGREST')
+    for prop_query in pcp.get_properties(pc_prop_name, smiles, namespace='smiles'):
+        if pc_prop_name in prop_query:
+            return prop_query[pc_prop_name]
+    else:
+        return None 
+
+    # TODO : add ChemSpider once I can obtain an API key (https://chemspipy.readthedocs.io/en/latest/guide/intro.html#apikey)