tweak to ceramics logic, added picture of pigment brown

color2_module/colors.py

@@ -4,7 +4,7 @@ from functions import SigFigs, Piringer, WilkeChang, SheetRelease, SheetRates, R
 from functions import Piecewise, PowerLaw
 from . import blueprint
 from polymers import Polymers, Polymers2
-from ChemID import ResolveChemical
+from ChemID import ResolveChemical, ImageFromSmiles, Imageto64
 import rdkit
 from rdkit.Chem import AllChem as Chem
 
@@ -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()
@@ -99,7 +102,10 @@ def app_post():
         #IDtype = 'SMILES'
         #chemName = 'O=[Ti]=O.O=[Sb]O[Sb](=O)=O.O=[Cr]O[Cr]=O'
         #iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)
-        iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = None, chemName, 'O=[Ti]=O.O=[Sb]O[Sb](=O)=O.O=[Cr]O[Cr]=O', 1100, None, None, 1001, None, 0
+        iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = None, chemName, 'O=[Ti]=O.O=[Sb]O[Sb]=O.O=[Cr]O[Cr]=O', 1100, None, None, 1001, None, 0
+        im = ImageFromSmiles(smiles)
+        im64 = Imageto64(im)
+        molImage = im64
     elif chemName == '14325-24-7':
         IDtype = 'SMILES'
         chemName = 'C1=CC=C2C(=C1)C3=NC4=NC(=NC5=C6C=CC=CC6=C([N-]5)N=C7C8=CC=CC=C8C(=N7)N=C2[N-]3)C9=CC=CC=C94.[Mn+2]'
@@ -111,8 +117,6 @@ def app_post():
     #    iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)
     else:
         iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)
-        ## XXX
-        #print(iupac, cas, smiles, MW, LogP, rho, mp, error)
 
     if error > 0:
         # TODO output more useful info
@@ -120,22 +124,23 @@ def app_post():
 
     # 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]
+    #mol = Chem.AddHs(mol)
+    #natoms = mol.GetNumAtoms()
     ceramic = False
-    if all(a.GetAtomicNum() in metal_nums for a in mol.GetAtoms()):
+    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
-    #if natoms == 1 and smiles != '[C]':
-        # only one atom, except for carbon -> assumed metal
-        # return render_template('chemError.html')
         return render_template('metalError.html', show_properties=show_properties, chemName=chemName, MW=MW,
                                LogP=LogP, rho=rho, mp=mp, iupac=iupac,
                                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.:
-            # if not a metal but melting point > 1000, assume ceramic
+        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
             MW = 1100.
             ceramic = True