refactor lookup from name

ChemID.py

@@ -50,7 +50,8 @@ def ResolveChemical(chemName, IDtype):
         error = 0
 
         name = smiles2name(smiles)
-        cas = name2cas(name)
+        if name:
+            cas = name2cas(name)
 
         try:
             mol = Chem.MolFromSmiles(smiles)
@@ -67,10 +68,10 @@ def ResolveChemical(chemName, IDtype):
         im64 = None
         error = 0
 
-        cas = name2cas(name)
-        smiles = cas2smiles(cas)
+        smiles = name2smiles(name)
 
         if smiles:
+            cas = name2cas(name)
             try:
                 mol = Chem.MolFromSmiles(smiles)
                 Mw = Descriptors.MolWt(mol)
@@ -350,6 +351,59 @@ def name2cas(name):
             cas = None
     return cas
 
+# function to convert name to SMILES
+def name2smiles(name):
+    smiles = None
+    # first try chemicals package
+    try:
+        cm = chemicals.search_chemical(name)
+        smiles = cm.smiles
+    except:
+        smiles = None
+    # then try pubchem for compounds
+    if not smiles:
+        try:
+            compounds = pcp.get_compounds(name, namespace='name')
+            c = compounds[0]
+            smiles = c.isomeric_smiles
+        except:
+            smiles = None
+    # next try cirpy
+    if not smiles:
+        try:
+            smiles = cirpy.resolve(name, 'smiles')
+        except:
+            smiles = None
+    if type(smiles) is list:
+        smiles = smiles[0]
+    # then try it as a pubchem substance
+    if not smiles:
+        try:
+            compounds = pcp.get_substances(name, namespace='name')
+            # sometimes there are multiple substances, and multiple synonyms per substance
+            allsyns = [syn for c in compounds for syn in c.isomeric_smiles if name not in syn]
+            # choose the most common synonym
+            fd = nltk.FreqDist(allsyns)
+            smiles = fd.most_common(1)[0][0]
+        except:
+            smiles = None
+    # finally try to resolve SMILES from name using OPSIN
+    #if not smiles:
+    #    try:
+    #        with open('opsin.tmp.1', 'w') as fp:
+    #            fp.write(name)
+    #        os.system('java -jar /Users/robert.elder/software/utils/opsin-2.4.0-jar-with-dependencies.jar -osmi opsin.tmp.1 opsin.tmp.2 &> /dev/null')
+    #        with open('opsin.tmp.2') as fp:
+    #            smiles = fp.read()
+    #        if smiles == '\n':
+    #            smiles = None
+    #        smiles = smiles.strip() #remove trailing newline
+    #    except KeyboardInterrupt:
+    #        raise
+    #    except:
+    #        smiles = None
+    return smiles
+
 def check_cas(cas):
     n1,n2,n3 = cas.split('-')
     # combine and flip first 2 numbers