Merge remote-tracking branch 'origin/smiles' into smiles

ChemID.py

@@ -81,6 +81,7 @@ def ResolveChemical(chemName, IDtype):
         im64 = None
         error = 0
 
+        name, name_origin = name2iupac(name)
         smiles = name2smiles(name)
 
         if smiles:
@@ -155,10 +156,10 @@ def smiles2name(smiles):
     # first try chemicals package
     try:
         cm = chemicals.search_chemical(smiles)
-        if cm.common_name:
-            name = cm.common_name
-        elif cm.iupac_name:
+        if cm.iupac_name:
             name = cm.iupac_name
+        elif cm.common_name:
+            name = cm.common_name
     except:
         name = None
     # then try pubchem for compounds
@@ -167,6 +168,9 @@ def smiles2name(smiles):
             compounds = pcp.get_compounds(smiles, namespace='smiles')
             c = compounds[0]
             name = c.iupac_name
+            if not name:
+                # have seen empty iupac_name before, try synonyms if this happens
+                name = c.synonyms[0]
         except:
             name = None
     # next try cirpy
@@ -234,12 +238,14 @@ def cas2name(cas):
     #if not is_cas(cas):
     #    name = 'INVALID CAS'
     # first try chemicals package
-    if not name:
-        try:
-            cm = chemicals.search_chemical(cas)
+    try:
+        cm = chemicals.search_chemical(cas)
+        if cm.iupac_name:
+            name = cm.iupac_name
+        elif cm.common_name:
             name = cm.common_name
-        except:
-            name = None
+    except:
+        name = None
     # then try cirpy
     if not name:
         try:
@@ -261,14 +267,17 @@ def cas2name(cas):
             name = None
     return name
 
-# function to convert chemical entity string to iupac name
-def string2name(string):
+# function to convert chemical name to iupac name
+def name2iupac(string):
     name = None
     origin = None
     # try chemicals package
     try:
         cm = chemicals.search_chemical(string)
-        name = cm.common_name
+        if cm.iupac_name:
+            name = cm.iupac_name
+        elif cm.common_name:
+            name = cm.common_name
         origin = 'chemicals'
     except KeyboardInterrupt:
         raise
@@ -280,10 +289,10 @@ def string2name(string):
         try:
             compounds = pcp.get_compounds(string, namespace='name')
             c = compounds[0]
-            #name = c.iupac_name
-            #if not name:
-            # have seen empty iupac_name before, try synonyms if this happens
-            name = c.synonyms[0]
+            name = c.iupac_name
+            if not name:
+                # have seen empty iupac_name before, try synonyms if this happens
+                name = c.synonyms[0]
             origin = 'PubChem'
         except:
             name = None
@@ -291,8 +300,8 @@ def string2name(string):
     # next try cirpy
     if not name:
         try:
-            name = cirpy.resolve(string, 'names')
-            #name = cirpy.resolve(string, 'iupac_name')
+            #name = cirpy.resolve(string, 'names')
+            name = cirpy.resolve(string, 'iupac_name')
             if name: origin = 'CIRPY'
         except:
             name = None
@@ -319,8 +328,10 @@ def string2name(string):
         try:
             compounds = pcp.get_compounds(string_strip, namespace='name')
             c = compounds[0]
-            name = c.synonyms[0]
-            #name = c.iupac_name
+            name = c.iupac_name
+            if not name:
+                # have seen empty iupac_name before, try synonyms if this happens
+                name = c.synonyms[0]
             origin = 'PubChem'
         except:
             name = None
@@ -328,7 +339,8 @@ def string2name(string):
         # next try cirpy
         if not name:
             try:
-                name = cirpy.resolve(string_strip, 'names')
+                #name = cirpy.resolve(string_strip, 'names')
+                name = cirpy.resolve(string, 'iupac_name')
                 if name: origin = 'CIRPY'
             except:
                 name = None

exposure_module/templates/exposure_report.html

@@ -50,6 +50,7 @@
 <div class="container">
 <div class="row">
   <div class="column">
+      Input ::  {{chemName}} <br> <br>
       IUPAC Name ::  {{iupac}} <br> <br>
       CAS ::  {{cas}} <br> <br>
       Molecular weight :: {{MW}} <br> <br>