added get_properties option to ResolveChemical and exposure.py to only get some properties like MP, and added show_properties flag to exposure.py to show/hide properties

ChemID.py

@@ -51,7 +51,7 @@ dfmp_expt = pd.read_csv('PHYSPROP_MP_data.tsv', sep='\t')
 #df_pred = pd.read_excel('Comptox_pred_data.xlsx')
 df_pred = pd.read_csv('Comptox_pred_data.tsv', sep='\t')
 
-def ResolveChemical(chemName, IDtype, debug=False):
+def ResolveChemical(chemName, IDtype, debug=False, get_properties=['logp','rho','mp']):
 
     #LogP_func = Crippen.MolLogP
     LogP_func = getLogP
@@ -80,9 +80,11 @@ def ResolveChemical(chemName, IDtype, debug=False):
 
         if smiles:
             name = cas2name(cas)
-            rho, rho_origin = string2density(cas)
-            mp, mp_origin = mol2mp(cas, name, smiles)
-            if pd.isna(rho) and name:
+            if 'rho' in get_properties:
+                rho, rho_origin = string2density(cas)
+            if 'mp' in get_properties:
+                mp, mp_origin = mol2mp(cas, name, smiles)
+            if 'rho' in get_properties and pd.isna(rho) and name:
                 rho, rho_origin = string2density(name)
             try:
                 mol = Chem.MolFromSmiles(smiles)
@@ -90,7 +92,8 @@ def ResolveChemical(chemName, IDtype, debug=False):
                 error = 2 #invalid smiles
             if mol:
                 Mw = Descriptors.MolWt(mol)
-                LogP, LogP_origin = LogP_func(cas, mol)
+                if 'logp' in get_properties:
+                    LogP, LogP_origin = LogP_func(cas, mol)
                 im = ImageFromSmiles(smiles)
                 im64 = Imageto64(im)
             else:
@@ -103,11 +106,13 @@ def ResolveChemical(chemName, IDtype, debug=False):
         name = smiles2name(smiles)
         if name:
             cas = name2cas(name)
-            rho, rho_origin = string2density(name)
-        if pd.isna(rho) and cas:
+            if 'rho' in get_properties:
+                rho, rho_origin = string2density(name)
+        if 'rho' in get_properties and pd.isna(rho) and cas:
             rho, rho_origin = string2density(cas)
 
-        mp, mp_origin = mol2mp(cas, name, smiles)
+        if 'mp' in get_properties:
+            mp, mp_origin = mol2mp(cas, name, smiles)
 
         try:
             mol = Chem.MolFromSmiles(smiles)
@@ -115,7 +120,8 @@ def ResolveChemical(chemName, IDtype, debug=False):
             error = 2
         if mol:
             Mw = Descriptors.MolWt(mol)
-            LogP, LogP_origin = LogP_func(cas, mol)
+            if 'logp' in get_properties:
+                LogP, LogP_origin = LogP_func(cas, mol)
             im = ImageFromSmiles(smiles)
             im64 = Imageto64(im)
         else:
@@ -129,23 +135,25 @@ def ResolveChemical(chemName, IDtype, debug=False):
         if not smiles:
             smiles = cas2smiles(cas)
 
-        if pd.isna(rho) and cas:
+        if 'rho' in get_properties and pd.isna(rho) and cas:
             rho, rho_origin = string2density(cas)
-        if pd.isna(rho):
+        if 'rho' in get_properties and pd.isna(rho):
             rho, rho_origin = string2density(name)
-        if pd.isna(rho):
+        if 'rho' in get_properties and pd.isna(rho):
             # try this because sometimes iupac names don't work
             rho, rho_origin = string2density(chemName)
 
         if smiles:
-            mp, mp_origin = mol2mp(cas, name, smiles)
+            if 'mp' in get_properties:
+                mp, mp_origin = mol2mp(cas, name, smiles)
             try:
                 mol = Chem.MolFromSmiles(smiles)
             except:
                 error = 2
             if mol:
                 Mw = Descriptors.MolWt(mol)
-                LogP, LogP_origin = LogP_func(cas, mol)
+                if 'logp' in get_properties:
+                    LogP, LogP_origin = LogP_func(cas, mol)
                 im = ImageFromSmiles(smiles)
                 im64 = Imageto64(im)
             else:

exposure_module/exposure.py

@@ -11,7 +11,13 @@ from rdkit.Chem import AllChem as Chem
 # load polymer data including Ap values
 polymers, Ap = Polymers()
 
-# output additional info
+# get additional physical properties, options are: logp, rho, mp
+#get_properties = [] # don't get any; this breaks ceramics logic
+#get_properties = ['logp','rho','mp'] # get all three
+get_properties = ['mp'] # only get mp
+# show additional physical properties
+show_properties = False
+# output additional info for physical properties
 debug = False
 
 # load the index page for the exposure module
@@ -28,26 +34,32 @@ def exp_post():
     IDtype = request.form["IDtype"]
 
     if debug:
-        iupac, cas, smiles, MW, LogP, LogP_origin, rho, rho_origin, mp, mp_origin, molImage, error = ResolveChemical(chemName, IDtype, debug=debug)
+        iupac, cas, smiles, MW, LogP, LogP_origin, rho, rho_origin, mp, mp_origin, molImage, error = ResolveChemical(chemName, IDtype, debug=debug, get_properties=['logp','rho','mp'])
         LogP_origin, rho_origin, mp_origin = f' ({LogP_origin})', f' ({rho_origin})', f' ({mp_origin})', 
     else:
         LogP_origin, rho_origin, mp_origin = '','',''
-        iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype)
+        iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)
 
     if error > 0:
         # TODO output more useful info
         return render_template('chemError.html')
 
-    MW = SigFigs(MW, 6)
-    if LogP is np.nan or LogP is None:
+    #MW = SigFigs(MW, 6)
+    if 'logp' not in get_properties:
+        LogP = 'Not searched'
+    elif LogP is np.nan or LogP is None:
         LogP = 'Not found'
     else:
-        LogP = SigFigs(LogP, 6)
-    if rho is np.nan or rho is None:
+        LogP = SigFigs(LogP, 4)
+    if 'rho' not in get_properties:
+        rho = 'Not searched'
+    elif rho is np.nan or rho is None:
         rho = 'Not found'
     else:
         rho = SigFigs(rho, 4)
-    if mp is np.nan or mp is None:
+    if 'mp' not in get_properties:
+        mp = 'Not searched'
+    elif mp is np.nan or mp is None:
         mp = 'Not found'
 
     # metals/ceramics logic
@@ -58,7 +70,7 @@ def exp_post():
 
         # only one atom, except for carbon -> assumed metal
         # return render_template('chemError.html')
-        return render_template('metalError.html', chemName=chemName, MW=MW, LogP=LogP, rho=rho, mp=mp, iupac=iupac,
+        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:
@@ -72,7 +84,7 @@ def exp_post():
             ceramic = True
 
     if MW < 100.:
-        return render_template('MwError.html', chemName=chemName, MW=MW, LogP=LogP, rho=rho, mp=mp, iupac=iupac, cas=cas, smiles=smiles, molImage=molImage, 
+        return render_template('MwError.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)
 
     amount = float(request.form["amount"])
@@ -116,7 +128,7 @@ def exp_post():
     rates = SheetRates(amount, vol, area, tarray, diff)
     pngImageB64String = RatePlot(tarray, rates)
 
-    return render_template('exposure_report.html', polymers=polymers, pIndex=pIndex, release=release,
+    return render_template('exposure_report.html', show_properties=show_properties, 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, 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, ceramic=ceramic)

exposure_module/templates/MwError.html

@@ -45,10 +45,12 @@
       Input ::  {{chemName}} <br> <br>
       IUPAC Name ::  {{iupac}} <br> <br>
       CAS ::  {{cas}} <br> <br>
-      Molecular weight (g/mol) :: {{MW}} <br> <br>
-      LogKow :: {{'%0.2f'%LogP|float}}{{LogP_origin}} <br> <br>
+      Molecular weight (g/mol) :: {{'%0.4f'%MW|float}} <br> <br>
+      {% if show_properties %} 
+      LogKow :: {{LogP}}{{LogP_origin}} <br> <br>
       Density (g/cm<sup>3</sup>) :: {{rho}}{{rho_origin}} <br> <br>
-      Melting point (&deg;C) :: {{'%0.1f'%mp|float}}{{mp_origin}} <br> <br>
+      Melting point (&deg;C) :: {{mp}}{{mp_origin}} <br> <br>
+      {% endif %}
       SMILES :: {{smiles}}
   </div>
   <div class="column">

exposure_module/templates/exposure_report.html

@@ -53,14 +53,14 @@
       Input ::  {{chemName}} <br> <br>
       IUPAC Name ::  {{iupac}} <br> <br>
       CAS ::  {{cas}} <br> <br>
-      Molecular weight (g/mol) :: {{MW}}
+      Molecular weight (g/mol) :: {{'%0.4f'%MW|float}}
       {% if ceramic %} :: ceramic detected, assume maximum Mw {% endif %}
       <br> <br>
-      <!--
-      LogKow :: {{'%0.2f'%LogP|float}}{{LogP_origin}}<br> <br>
+      {% if show_properties %} 
+      LogKow :: {{LogP}}{{LogP_origin}}<br> <br>
       Density (g/cm<sup>3</sup>) :: {{rho}}{{rho_origin}}<br> <br>
-      Melting point (&deg;C) :: {{'%0.1f'%mp|float}}{{mp_origin}}<br> <br>
-      -->
+      Melting point (&deg;C) :: {{mp}}{{mp_origin}}<br> <br>
+      {% endif %}
       SMILES :: {{smiles}}
   </div>
   <div class="column">

exposure_module/templates/metalError.html

@@ -45,10 +45,12 @@
       Input ::  {{chemName}} <br> <br>
       IUPAC Name ::  {{iupac}} <br> <br>
       CAS ::  {{cas}} <br> <br>
-      Molecular weight (g/mol) :: {{MW}} <br> <br>
-      LogKow :: {{'%0.2f'%LogP|float}}{{LogP_origin}} <br> <br>
+      Molecular weight (g/mol) :: {{'%0.4f'%MW|float}} <br> <br>
+      {% if show_properties %} 
+      LogKow :: {{LogP}}{{LogP_origin}} <br> <br>
       Density (g/cm<sup>3</sup>) :: {{rho}}{{rho_origin}} <br> <br>
-      Melting point (&deg;C) :: {{'%0.1f'%mp|float}}{{mp_origin}} <br> <br>
+      Melting point (&deg;C) :: {{mp}}{{mp_origin}} <br> <br>
+      {% endif %}
       SMILES :: {{smiles}}
   </div>
   <div class="column">