made ceramics logic consistent, changed ceramic MP cutoff to 700 C (to catch salts like NaCl)

ChemID.py

@@ -58,6 +58,9 @@ def ResolveChemical(chemName, IDtype, debug=False, get_properties=['logp','rho',
     #LogP_func = Crippen.MolLogP
     LogP_func = getLogP
     
+    # remove excess whitespace
+    chemName = chemName.strip()
+    
     name = None
     smiles = None
     cas = None

color2_module/colors.py

@@ -123,15 +123,14 @@ def app_post():
         return render_template('chemError.html')
 
     # metals/ceramics logic
+    ceramic = False
     mol = Chem.MolFromSmiles(smiles)
     #mol = Chem.AddHs(mol)
     #natoms = mol.GetNumAtoms()
-    ceramic = False
     atom_num_list = [a.GetAtomicNum() for a in mol.GetAtoms()]
     is_metal = set(atom_num_list) <= METAL_ATOM_SET
     #is_metal = all(a.GetAtomicNum() in metal_nums for a in mol.GetAtoms())
     #is_organic = set(atom_num_list) <= ORGANIC_ATOM_SET
-    num_CC_bonds = sum([1 if b.GetBeginAtom().GetAtomicNum() == 6 and b.GetEndAtom().GetAtomicNum() == 6 else 0 for b in mol.GetBonds()])
     if is_metal:
         # if all atoms are metals -> this is a metal
         return render_template('metalError.html', show_properties=show_properties, chemName=chemName, MW=MW,
@@ -139,8 +138,10 @@ def app_post():
                                cas=cas, smiles=smiles, molImage=molImage)
                                #LogP_origin=LogP_origin, rho_origin=rho_origin, mp_origin=mp_origin)
     else:
-        if not num_CC_bonds and (type(mp) is float or type(mp) is int) and mp > 1000.:
-            # if not a metal and no carbon-carbon bonds but melting point > 1000, assume ceramic
+        # get number of carbon-carbon bonds
+        num_CC_bonds = sum([1 if b.GetBeginAtom().GetAtomicNum() == 6 and b.GetEndAtom().GetAtomicNum() == 6 else 0 for b in mol.GetBonds()])
+        if not num_CC_bonds and (type(mp) is float or type(mp) is int) and mp > 700.:
+            # if not a metal, no C-C bonds, and mp > 700 (sodium chloride has mp ~ 800), assume ceramic...
             MW = 1100.
             ceramic = True
 

custom_chemicals_db.tsv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c46fe917b6bf96481b6d3dfd4613b60103affab34ede2863ecf16b8425385316
-size 7805
+oid sha256:e35d86380fe9a5ea099f0d8734762670c57e9437ead36b02ba9e1ce06fc6de41
+size 10174

exposure2_module/exposure.py

@@ -20,6 +20,9 @@ debug = False
 # flag for testing new polymer categories
 use_new = True
 
+ORGANIC_ATOM_SET = {5, 6, 7, 8, 9, 15, 16, 17, 35, 53}
+METAL_ATOM_SET = set([3,4,11,12,13] + list(range(19,31+1)) + list(range(37,50+1)) + list(range(55,84+1)) + list(range(87,114+1)) + [116])
+
 # load polymer data including Ap values
 if not use_new:
     polymers, Ap = Polymers()
@@ -69,12 +72,12 @@ def exp_post():
         mp = 'Not found'
 
     # metals/ceramics logic
-    mol = Chem.MolFromSmiles(smiles)
-    mol = Chem.AddHs(mol)
-    #natoms = mol.GetNumAtoms()
-    metal_nums = [3,4,11,12,13] + list(range(19,31+1)) + list(range(37,50+1)) + list(range(55,84+1)) + list(range(87,114+1)) + [116]
     ceramic = False
-    if all(a.GetAtomicNum() in metal_nums for a in mol.GetAtoms()):
+    mol = Chem.MolFromSmiles(smiles)
+    #mol = Chem.AddHs(mol)
+    atom_num_list = [a.GetAtomicNum() for a in mol.GetAtoms()]
+    is_metal = set(atom_num_list) <= METAL_ATOM_SET
+    if is_metal:
         # if all atoms are metals -> this is a metal
     #if natoms == 1 and smiles != '[C]':
         # only one atom, except for carbon -> assumed metal
@@ -83,7 +86,11 @@ def exp_post():
                                cas=cas, smiles=smiles, molImage=molImage,
                                LogP_origin=LogP_origin, rho_origin=rho_origin, mp_origin=mp_origin)
     else:
-        if (type(mp) is float or type(mp) is int) and mp > 1000.:
+        # get number of carbon-carbon bonds
+        num_CC_bonds = sum([1 if b.GetBeginAtom().GetAtomicNum() == 6 and b.GetEndAtom().GetAtomicNum() == 6 else 0 for b in mol.GetBonds()])
+        if not num_CC_bonds and (type(mp) is float or type(mp) is int) and mp > 700.:
+            # if not a metal, and mp > 700 (sodium chloride has mp ~ 800), and no C-C bonds, assume ceramic...
+        #if (type(mp) is float or type(mp) is int) and mp > 1000.:
             # if not a metal but melting point > 1000, assume ceramic
             MW = 1100.
             ceramic = True