many updates to v3 modules

ChemID.py

@@ -1054,7 +1054,13 @@ def string2mp(name):
 
 def smiles2mp(smiles):
     try:
-        mp = compute_phys_properties(smiles)
+        SUPPORTED_ATOM_SET = {6, 7, 8, 9, 16, 17, 35, 53}
+        m = Chem.MolFromSmiles(str(smiles))
+        atom_num_set = set([a.GetAtomicNum() for a in m.GetAtoms()])
+        if atom_num_set.issubset(SUPPORTED_ATOM_SET):
+            mp = compute_phys_properties(smiles)
+        else:
+            mp = None
     except:
         mp = None
     return mp

PHYSPROP_MP_data.tsv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:de7f31b05ea0a60d15aa7aa35185e7639d19f1beba66680dab7b1d3c7d70997e
-size 131480
+oid sha256:2e252b39db1b977593a0f26113d6848526f5d70c94ccfeb0d3d78727799419e9
+size 131497

color3_module/colors.py

@@ -3,6 +3,7 @@ from flask import Flask, render_template, request
 import numpy as np
 from functions import SigFigs, Piringer, WilkeChang, SheetRelease, SheetRates, RatePlot
 from functions import Piecewise, PowerLaw
+from qrf_functions import QRF_Apply, QRF_Ceramic
 from . import blueprint
 from polymers import Polymers, Polymers3
 from ChemID import ResolveChemical, ImageFromSmiles, Imageto64
@@ -60,15 +61,15 @@ def colors():
 @blueprint.route('/color3', methods=['POST'])
 def app_post():
 
-    amount = float(request.form["amount"])
-    mass = float(request.form["mass"])
-    density = float(request.form["density"])
+    amount = float(request.form['amount'])
+    mass = float(request.form['mass'])
+    density = float(request.form['density'])
     vol = mass / density
-    polymer = request.form["polymer"]
+    polymer = request.form['polymer']
     pIndex = (np.where(polymers == polymer)[0])[0]
-    area = float(request.form["area"])
-    exposure = request.form["exposure"]
-    CA = request.form["CA"]
+    area = float(request.form['area'])
+    exposure = request.form['exposure']
+    CA = request.form['CA']
     caIndex = (np.where(CAs == CA)[0])[0]
 
     TI = caData[caIndex][1]
@@ -79,16 +80,16 @@ def app_post():
     if caIndex <= 10:
         IDtype = 'CAS'
         chemName = caData[caIndex][3].decode('UTF-8')
-        impurity = float(request.form["impurity"]) * amount * 1e-2
+        impurity = float(request.form['impurity']) * amount * 1e-2
         # problems:
-        # o C.I. Pigment Brown 24 = 68186-90-3, kludge "works"
-        # o Manganese(II) phthalocyanine = 14325-24-7, kludge "works"
+        # o C.I. Pigment Brown 24 = 68186-90-3, kludge 'works'
+        # o Manganese(II) phthalocyanine = 14325-24-7, kludge 'works'
         # o Phthalocyanine green = 1326-53-6 -> 1328-53-6, corrected CAS works
         # o Ultramarine blue = 57445-37-5 -> 57455-37-5, corrected CAS works
     if caIndex > 10:
-        chemName = request.form["chemName"]
-        IDtype = request.form["IDtype"]
-        impurity = float(request.form["impurity"]) * amount * 1e-2
+        chemName = request.form['chemName']
+        IDtype = request.form['IDtype']
+        impurity = float(request.form['impurity']) * amount * 1e-2
     if caIndex == 12:
         isCA = False
 
@@ -117,19 +118,20 @@ def app_post():
             ceramic = True
 
     # Exposure type
-    if exposure != "limited":
+    if exposure != 'limited':
         time = 24.
     else:
-        time = float(request.form["exptime"])
+        time = float(request.form['exptime'])
 
-    if exposure != "long-term":
+    if exposure != 'long-term':
         TTC = 0.12
     else:
         TTC = 0.0015
 
+    polytg = ''
     use_qrf = False
-    if polymer == "Other polymer":
-        polytg = request.form["polytg"]
+    if polymer == 'Other polymer':
+        polytg = request.form['polytg']
         if polytg == '':
             # left blank, use old default (Wilke Chang), which is taken care of by pIndex
             pass
@@ -140,16 +142,25 @@ def app_post():
 
     if use_qrf:
         #print('using qrf', file=sys.stderr)
+        method = 'qrf'
         if ceramic:
             diff,domain_extrap = QRF_Ceramic(density, polytg, quantiles=[0.03,0.5,0.97])
         else:
             diff,domain_extrap = QRF_Apply(density, polytg, smiles, quantiles=[0.03,0.5,0.97])
         diff = diff[2] # upper bound
+        if domain_extrap:
+            # outside training domain, default to Wilke-Chang
+            diff = Piecewise(MW, params[None])
+            method = 'qrf/wc'
     else:
         ## use categories
         category = categories[pIndex]
         diff = Piecewise(MW, params[category])
         domain_extrap = False
+        if category:
+            method = 'category'
+        else:
+            method = 'wc'
 
     release = SheetRelease(amount, vol, area, time, diff)
 
@@ -174,5 +185,5 @@ def app_post():
     return render_template('color3_report.html', caIndex=caIndex, TI=TI, isCA=isCA, show_properties=show_properties, polymers=polymers, pIndex=pIndex, release=release,
                            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,
-                           ceramic=ceramic, impurity=impurity, iMOS=iMOS, domain_extrap=domain_extrap)
+                           ceramic=ceramic, impurity=impurity, iMOS=iMOS, methods=[method,polytg,density])
 

color3_module/templates/color3_report.html

@@ -66,15 +66,22 @@
 </div>
 </div>
 
-{% if domain_extrap %}
-<font color="red"> Warning: This polymer/solute combination is outside the model's training domain, so the predicted diffusion coefficient may not be accurate. <br> </font>
-{% endif %}
-
 <h2>Exposure </h2>
 
 <p>
+{% if methods[0]=="category" %}
 <u> Diffusion calculation for leaching from {{polymers[pIndex]}} estimates a worst case single day
     exposure = {{release}} mg. </u>
+{% elif methods[0]=="wc" %}
+<u> Diffusion calculation for leaching from the polymer (with worst-case diffusion in water assumed because no T<sub>g</sub> was specified) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% elif methods[0]=="qrf" %}
+<u> Diffusion calculation for leaching from the polymer (with density = {{methods[2]}} g/cm<sup>3</sup> and T<sub>g</sub> = {{methods[1]}} &deg;C) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% elif methods[0]=="qrf/wc" %}
+<u> Diffusion calculation for leaching from the polymer (with worst-case diffusion in water assumed because this system is outside the model training domain) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% endif %}
 <p>
 
 <p>
@@ -126,7 +133,7 @@ The threshold for toxicological concern (TTC) for {{exposure}} contact is {{TTC}
 </p>
 
 <p>
-<font color="red"> *Note*: This assessment assumes that {{chemName}} is not in the cohort of concern. </font>
+<font color="red"> *Note*: This assessment assumes that the chemical is not in the cohort of concern. </font>
 </p>
 
 {% else %}

exposure3_module/exposure.py

@@ -7,7 +7,6 @@ from qrf_functions import QRF_Apply, QRF_Ceramic
 from . import blueprint
 from polymers import Polymers, Polymers3
 from ChemID import ResolveChemical
-
 import rdkit
 from rdkit.Chem import AllChem as Chem
 
@@ -38,8 +37,8 @@ def exposure():
 @blueprint.route('/exposure3', methods=['POST'])
 def exp_post():
 
-    chemName = request.form["chemName"]
-    IDtype = request.form["IDtype"]
+    chemName = request.form['chemName']
+    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, get_properties=['logp','rho','mp'])
@@ -89,29 +88,30 @@ def exp_post():
             MW = 1100.
             ceramic = True
 
-    amount = float(request.form["amount"])
-    mass = float(request.form["mass"])
-    density = float(request.form["density"])
+    amount = float(request.form['amount'])
+    mass = float(request.form['mass'])
+    density = float(request.form['density'])
     vol = mass / density
-    area = float(request.form["area"])
-    exposure = request.form["exposure"]
+    area = float(request.form['area'])
+    exposure = request.form['exposure']
 
-    polymer = request.form["polymer"]
+    polymer = request.form['polymer']
     pIndex = np.argmax(polymers == polymer)
 
-    if exposure != "limited":
+    if exposure != 'limited':
         time = 24.
     else:
-        time = float(request.form["exptime"])
+        time = float(request.form['exptime'])
 
-    if exposure != "long-term":
+    if exposure != 'long-term':
         TTC = 0.12
     else:
         TTC = 0.0015
 
+    polytg = ''
     use_qrf = False
-    if polymer == "Other polymer":
-        polytg = request.form["polytg"]
+    if polymer == 'Other polymer':
+        polytg = request.form['polytg']
         if polytg == '':
             # left blank, use old default (Wilke Chang), which is taken care of by pIndex
             pass
@@ -122,16 +122,25 @@ def exp_post():
 
     if use_qrf:
         #print('using qrf', file=sys.stderr)
+        method = 'qrf'
         if ceramic:
             diff,domain_extrap = QRF_Ceramic(density, polytg, quantiles=[0.03,0.5,0.97])
         else:
             diff,domain_extrap = QRF_Apply(density, polytg, smiles, quantiles=[0.03,0.5,0.97])
         diff = diff[2] # upper bound
+        if domain_extrap:
+            # outside training domain, default to Wilke-Chang
+            diff = Piecewise(MW, params[None])
+            method = 'qrf/wc'
     else:
         ## use categories
         category = categories[pIndex]
         diff = Piecewise(MW, params[category])
         domain_extrap = False
+        if category:
+            method = 'category'
+        else:
+            method = 'wc'
 
     release = SheetRelease(amount, vol, area, time, diff)
 
@@ -149,5 +158,5 @@ def exp_post():
     return render_template('exposure3_report.html', show_properties=show_properties, polymers=polymers, pIndex=pIndex, release=release,
                            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, domain_extrap=domain_extrap)
+                           LogP_origin=LogP_origin, rho_origin=rho_origin, mp_origin=mp_origin, ceramic=ceramic, methods=[method,polytg,density])
 

exposure3_module/templates/exposure3_report.html

@@ -69,14 +69,22 @@
 </div>
 </div>
 
-{% if domain_extrap %}
-<font color="red"> Warning: This polymer/solute combination is outside the model's training domain, so the predicted diffusion coefficient may not be accurate. <br> </font>
-{% endif %}
-
 <h2> Exposure </h2>
 
 <p>
-<u> Diffusion calculation for leaching from {{polymers[pIndex]}} estimates the worst case single day exposure = {{release}} mg. </u>
+{% if methods[0]=="category" %}
+<u> Diffusion calculation for leaching from {{polymers[pIndex]}} estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% elif methods[0]=="wc" %}
+<u> Diffusion calculation for leaching from the polymer (with worst-case diffusion in water assumed because no T<sub>g</sub> was specified) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% elif methods[0]=="qrf" %}
+<u> Diffusion calculation for leaching from the polymer (with density = {{methods[2]}} g/cm<sup>3</sup> and T<sub>g</sub> = {{methods[1]}} &deg;C) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% elif methods[0]=="qrf/wc" %}
+<u> Diffusion calculation for leaching from the polymer (with worst-case diffusion in water assumed because this system is outside the model training domain) estimates a worst case single day
+    exposure = {{release}} mg. </u>
+{% endif %}
 <p>
 
 <p>