added basic LogP calculation w/ rdkit

ChemID.py

@@ -12,21 +12,24 @@ import base64
 
 import rdkit
 from rdkit.Chem import AllChem as Chem
-from rdkit.Chem import Descriptors,Descriptors3D, Draw
+from rdkit.Chem import Descriptors,Descriptors3D,Draw,Crippen
 
 def ResolveChemical(chemName, IDtype):
 
+    LogP_func = Crippen.MolLogP
+    
     if IDtype == 'CAS':
         cas = chemName
         smiles = None
         name = None
         Mw = None
+        LogP = None
         im64 = None
         error = 0
 
         if not is_cas(cas):
             error = 3 #invalid cas
-            return (name, cas, smiles, Mw, im64, error)
+            return (name, cas, smiles, Mw, LogP, im64, error)
 
         smiles = cas2smiles(cas)
 
@@ -38,6 +41,7 @@ def ResolveChemical(chemName, IDtype):
                 error = 2 #invalid smiles
             if mol:
                 Mw = Descriptors.MolWt(mol)
+                LogP = LogP_func(mol)
                 im = ImageFromSmiles(smiles)
                 im64 = Imageto64(im)
             else:
@@ -49,6 +53,7 @@ def ResolveChemical(chemName, IDtype):
         cas = None
         name = None
         Mw = None
+        LogP = None
         im64 = None
         error = 0
 
@@ -62,6 +67,7 @@ def ResolveChemical(chemName, IDtype):
             error = 2
         if mol:
             Mw = Descriptors.MolWt(mol)
+            LogP = LogP_func(mol)
             im = ImageFromSmiles(smiles)
             im64 = Imageto64(im)
         else:
@@ -71,6 +77,7 @@ def ResolveChemical(chemName, IDtype):
         smiles = None
         cas = None
         Mw = None
+        LogP = None
         im64 = None
         error = 0
 
@@ -84,6 +91,7 @@ def ResolveChemical(chemName, IDtype):
                 error = 2
             if mol:
                 Mw = Descriptors.MolWt(mol)
+                LogP = LogP_func(mol)
                 im = ImageFromSmiles(smiles)
                 im64 = Imageto64(im)
             else:
@@ -96,6 +104,7 @@ def ResolveChemical(chemName, IDtype):
         smiles = None
         cas = None
         Mw = None
+        LogP = None
         im64 = None
         error = 4 # invalid IDtype selection, probably not possible
 
@@ -106,7 +115,7 @@ def ResolveChemical(chemName, IDtype):
         if not cas:
             cas = 'Not found'
 
-    return (name, cas, smiles, Mw, im64, error)
+    return (name, cas, smiles, Mw, LogP, im64, error)
 
 #Generates an image of the molecule represented by the SMILES code given.
 #Returns None if the image cannot be generated. From https://github.com/ronaldo-prata/flask-test/blob/master/functions.py

exposure_module/exposure.py

@@ -21,7 +21,7 @@ def exp_post():
     chemName = request.form["chemName"]
     IDtype = request.form["IDtype"]
 
-    iupac, cas, smiles, MW, molImage, error = ResolveChemical(chemName, IDtype)
+    iupac, cas, smiles, MW, LogP, molImage, error = ResolveChemical(chemName, IDtype)
 
     if error > 0:
         return render_template('chemError.html')
@@ -62,6 +62,7 @@ def exp_post():
     MOS = SigFigs(MOS, 2)
     diff = SigFigs(diff, 2)
     MW = SigFigs(MW, 6)
+    LogP = SigFigs(LogP, 6)
 
     # Generate the rate plot using matplotlib
     tarray = np.arange(1., 31., 1.)
@@ -70,4 +71,4 @@ def exp_post():
 
     return render_template('exposure_report.html', polymers=polymers, pIndex=pIndex, release=release,
                            assume=assume, area=area, vol=vol, amount=amount, diff=diff, time=time, exposure=exposure, TTC=TTC,
-                           MOS=MOS, chemName=chemName, image=pngImageB64String, MW=MW, iupac=iupac, cas=cas, smiles=smiles, molImage=molImage)
+                           MOS=MOS, chemName=chemName, image=pngImageB64String, MW=MW, LogP=LogP, iupac=iupac, cas=cas, smiles=smiles, molImage=molImage)

exposure_module/templates/exposure_report.html

@@ -53,6 +53,7 @@
       IUPAC Name ::  {{iupac}} <br> <br>
       CAS ::  {{cas}} <br> <br>
       Molecular weight :: {{MW}} <br> <br>
+      LogKow :: {{LogP}} <br> <br>
       SMILES :: {{smiles}}
   </div>
   <div class="column">