Merge branch 'CAselect'

CHRIS.py

@@ -1,7 +1,7 @@
 from flask import Flask, render_template
 
 app = Flask(__name__)
-app.debug = False
+app.debug = True
 
 from color_module import blueprint
 app.register_blueprint(blueprint)

ChemID.py

@@ -1,4 +1,6 @@
 import sys,os,glob,re,string
+from collections import Counter
+from operator import itemgetter
 import nltk
 import pandas as pd
 import numpy as np

color2_module/colors.py

@@ -1,13 +1,28 @@
 from flask import Flask, render_template, request
 import numpy as np
-from functions import SigFigs, Piringer, WilkeChang, SheetRelease
+from functions import SigFigs, Piringer, WilkeChang, SheetRelease, SheetRates, RatePlot
 from functions import Piecewise, PowerLaw
 from . import blueprint
 from polymers import Polymers, Polymers2
+from ChemID import ResolveChemical, ImageFromSmiles, Imageto64
+import rdkit
+from rdkit.Chem import AllChem as Chem
+
+# 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
 
 # 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()
@@ -15,22 +30,21 @@ else:
     polymers, categories, params = Polymers2()
 
 # Named color additives, TI values, and Mw
-nCA = 14
-caData = np.zeros((nCA,), dtype=[('name', 'a75'), ('TI', 'd'), ('MW', 'd')])
-caData[0] = ('Titanium dioxide (CAS#:13463-67-7)', 1.0, 1100.)
-caData[1] = ('Carbon black (CAS#:1333-86-4)', 2.0, 1100.)
-caData[2] = ('Pigment brown 24 (CAS#:68186-90-3)', 0.5, 1100.)
-caData[3] = ('Zinc Oxide (CAS#:1314-13-2)', 0.05, 1100.)
-caData[4] = ('Pigment Red 101 (CAS#: 1309-37-1)', 1.0, 1100.)
-caData[5] = ('Solvent violet 13 (CAS#:81-48-1)', 0.0013, 319.4)
-caData[6] = ('Manganese phthalocyanine (CAS#:14325-24-7)', 0.15, 567.5)
-caData[7] = ('Pigment blue 15 (CAS#:147-14-8)', 0.15, 576.1)
-caData[8] = ('Phthalocyanine green (CAS#:1326-53-6)', 0.15, 1092.8)
-caData[9] = ('Ultramarine blue (CAS#:57445-37-5)', 3.3, 1100.)
-caData[10] = ('Pigment Yellow 138 (CAS#:30125-47-4)', 1.0, 693.96)
-caData[11] = ('Other metal oxide color additive', 1.0, 1100.0)
-caData[12] = ('Other non-metal oxide color additive', 1.0, 1100.0)
-caData[13] = ('Other color additive associated compound', 1.0, 1100.0)
+nCA = 13
+caData = np.zeros((nCA,), dtype=[('name', 'a75'), ('TI', 'd'), ('MW', 'd'),('CAS', 'a75')])
+caData[0] = ('Titanium dioxide (CAS#:13463-67-7)', 1.0, 1100., '13463-67-7')
+caData[1] = ('Carbon black (CAS#:1333-86-4)', 2.0, 1100., '1333-86-4')
+caData[2] = ('Pigment brown 24 (CAS#:68186-90-3)', 0.5, 1100., '68186-90-3')
+caData[3] = ('Zinc Oxide (CAS#:1314-13-2)', 0.05, 1100., '1314-13-2')
+caData[4] = ('Pigment Red 101 (CAS#: 1309-37-1)', 1.0, 1100., '1309-37-1')
+caData[5] = ('Solvent violet 13 (CAS#:81-48-1)', 0.0013, 319.4, '81-48-1')
+caData[6] = ('Manganese phthalocyanine (CAS#:14325-24-7)', 0.15, 567.5, '14325-24-7')
+caData[7] = ('Pigment blue 15 (CAS#:147-14-8)', 0.15, 576.1, '147-14-8')
+caData[8] = ('Phthalocyanine green (CAS#:1328-53-6)', 0.15, 1092.8, '1328-53-6')
+caData[9] = ('Ultramarine blue (CAS#:57455-37-5)', 3.3, 1100., '57455-37-5')
+caData[10] = ('Pigment Yellow 138 (CAS#:30125-47-4)', 1.0, 693.96, '30125-47-4')
+caData[11] = ('Other color additive', 1.0, 1100.0, ' ')
+caData[12] = ('Other color additive associated compound', 1.0, 1100.0, ' ')
 
 CAs = np.zeros(nCA, dtype='object')
 caMW = np.zeros(nCA, dtype='object')
@@ -50,6 +64,7 @@ def colors():
 
 @blueprint.route('/color2', methods=['POST'])
 def app_post():
+
     amount = float(request.form["amount"])
     mass = float(request.form["mass"])
     density = float(request.form["density"])
@@ -63,31 +78,73 @@ def app_post():
 
     TI = caData[caIndex][1]
     impurity = 1.
-    MW = 1100.
     isCA = True
     chemName = ''
 
-    if caIndex < 11:
-        MW = caData[caIndex][2]
-        chemName = '*' + caData[caIndex][0].decode('UTF-8') + '*'
+    if caIndex <= 10:
+        IDtype = 'CAS'
+        chemName = caData[caIndex][3].decode('UTF-8')
         impurity = float(request.form["impurity"]) * amount * 1e-2
-    if caIndex == 11:
-        MW = caData[caIndex][2]
-        chemName = request.form["chemName"] if "chemName" in request.form else "CHEMICAL NAME NOT PROVIDED"
-        chemName = '*' + chemName + '*'
+        # problems:
+        # 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
     if caIndex == 12:
-        MW = float(request.form["MW"])
-        chemName = request.form["chemName"] if "chemName" in request.form else "CHEMICAL NAME NOT PROVIDED"
-        chemName = '*' + chemName + '*'
-        impurity = float(request.form["impurity"]) * amount * 1e-2
-    if caIndex == 13:
         isCA = False
-        MW = float(request.form["MW"])
-        chemName = request.form["chemName"] if "chemName" in request.form else "CHEMICAL NAME NOT PROVIDED"
-        chemName = '*' + chemName + '*'
-        impurity = float(request.form["impurity"]) * amount * 1e-2
 
+    print(chemName)
+    if chemName == '68186-90-3':
+        #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=[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]'
+        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, '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]', 567.5, None, None, 500, None, 0
+    #elif chemName == '1326-53-6':
+    #    IDtype = 'SMILES'
+    #    chemName = 'C1=C2C(=C(C(=C1Cl)Cl)Cl)C3=NC4=NC(=NC5=NC(=NC6=C7C(=C([N-]6)N=C2[N-]3)C(=C(C(=C7Cl)Cl)Cl)Cl)C8=C5C(=C(C(=C8Cl)Cl)Cl)Cl)C9=C4C(=C(C(=C9Cl)Cl)Cl)Cl.[Cu+2]'
+    #    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)
+
+    if error > 0:
+        # TODO output more useful info
+        return render_template('chemError.html')
+
+    # metals/ceramics logic
+    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,
+                               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 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
+
+    # Exposure type
     if exposure != "limited":
         time = 24.
     else:
@@ -125,9 +182,13 @@ def app_post():
     iMOS = SigFigs(iMOS, 2)
     impurity = SigFigs(impurity, 2)
 
-    return render_template('color2_report.html', polymers=polymers, pIndex=pIndex, caIndex=caIndex, release=release,
-                           assume=assume,
-                           area=area, vol=vol, amount=amount, diff=diff, time=time, exposure=exposure, TTC=TTC,
-                           isCA=isCA, TI=TI, MOS=MOS,
-                           chemName=chemName, impurity=impurity, iMOS=iMOS)
+    # Generate the rate plot using matplotlib
+    tarray = np.arange(1., 31., 1.)
+    rates = SheetRates(amount, vol, area, tarray, diff)
+    pngImageB64String = RatePlot(tarray, rates)
+
+    return render_template('color2_report.html', caIndex=caIndex, TI=TI, isCA=isCA, 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,
+                           ceramic=ceramic, impurity=impurity, iMOS=iMOS)
 

color2_module/templates/chemError.html

@@ -0,0 +1,24 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>CHRIS-ChemError</title>
+    <link rel= "stylesheet" type= "text/css" href= "{{ url_for('static',filename='styles.css') }}">
+
+</head>
+
+<img src="{{ url_for('static',filename='images/FDAlogo.png') }}" style="float: left;" height="100"/>
+<img src="{{ url_for('static',filename='images/FDAgraphic.png') }}" style="float: right;"  height="100"/>
+<br clear="all" />
+
+<body>
+
+<div style="font-size:5rem;text-align:center"> &#129318; </div>
+
+<p style="font-size:2rem;text-align:center">
+    Uh-oh! Something went wrong. We were unable to match your chemical.  Please return to the previous page and try a
+    different identifier.
+</p>
+
+
+</body>

color2_module/templates/color2_index.html

@@ -16,7 +16,7 @@
 </header>
 
 <p> For details on how to use the CHRIS color additive module, please read the <a href="{{url_for('.static', filename='README.html')}}"> instructions</a> and
-  <a href="https://www.fda.gov/media/163472/download"> Summary of Evidence and Basis of Qualification (SEBQ)</a>, which includes limitations of use. Answers to frequently asked questions can be
+  <a href="{{url_for('.static', filename='COU.html')}}"> Context of Use (CoU)</a>, which includes limitations of use. Answers to frequently asked questions can be
   found <a href="{{url_for('.static', filename='FAQ.html')}}"> here</a>. For a history of updates, please see the <a href="{{url_for('.static', filename='Changelog.html')}}"> changelog</a>. </p>
 
 <body>
@@ -34,11 +34,14 @@ Identity: <select name="CA" id="CA" onchange="javascript:caCheck();">
   {% endfor %}
 </select> 
 <span id="otherID" style="display:none">
-    &nbsp; &rArr; Chemical name: <input name="chemName" id="chemName" type="text" value="ENTER CHEMICAL NAME" required>
+    &nbsp; &rArr; Identifier type: <select name="IDtype">
+    <option value="CAS" selected>CAS</option>
+    <option value="SMILES" >SMILES</option>
+    <option value="common" >Common name</option>
+  </select>
+  Identifier: <input name="chemName" id="chemName" type="text" value="">
   </span> <br>
 
-Molecular weight (g/mol): <input name="MW" id="MW" step="any" value="1100" min="0.0" max="1100.0" type="number" disabled required><br>
-
 Amount (mg): <input name="amount" id="amount" value="1.0" step="any" min="0.000001" type="number" required> <br>
 
 Total impurity concentration (%): <input name="impurity" id="impurity" value="0.1" step="any" min="0.000001" max='100.0' type="number" required> <br>
@@ -48,25 +51,17 @@ Total impurity concentration (%): <input name="impurity" id="impurity" value="0.
 <script type="text/javascript">
 
 function caCheck() {
-    var caMW = ['{{caMW[0]}}','{{caMW[1]}}','{{caMW[2]}}','{{caMW[3]}}','{{caMW[4]}}','{{caMW[5]}}','{{caMW[6]}}','{{caMW[7]}}','{{caMW[8]}}','{{caMW[9]}}','{{caMW[10]}}','{{caMW[11]}}','{{caMW[12]}}','{{caMW[13]}}'];
     var iCA = parseInt(document.getElementById("CA").selectedIndex);
 
-
-    document.getElementById('MW').disabled = true;
     document.getElementById('impurity').disabled = false;
 
-    if (iCA >= 13) {
-    //    document.getElementById('impurity').disabled = true;
-    } 
-    if (iCA >= 12) {
-        document.getElementById('MW').disabled = false;
-    } 
     if (iCA >= 11) {
       document.getElementById('otherID').style.display = "inline";
-      document.getElementById('chemName').value = "ENTER CHEMICAL NAME";
+      document.getElementById('chemName').value = "";
+      document.getElementById('chemName').required = true;
     } else {
-      document.getElementById("MW").value = parseFloat(caMW[iCA]);
       document.getElementById('otherID').style.display = "none";
+      document.getElementById('chemName').required = false;
     }
 }
 
@@ -83,8 +78,10 @@ $(window).on('pageshow', function() { caCheck(); });
         <h4 class="modal-title">Color additive</h4>
       </div>
       <div class="modal-body">
-        <p><em>Identity</em> - Select the color additive in the component being evaluated via the pull down list. If the color additive is not explicitly listed, please choose either "Other metal oxide color additive" or "Other non-metal oxide color additive" and enter the chemical name, including CAS # if known.  If "Other non-metal oxide color additive" is selected, please enter the molecular weight of the color additive in grams per mole. If you are evaluating an additive associated with a color additive please select "Other color additive associated compound" and enter the chemical name and molecular weight.  Note that CHRIS is limited to color additive associated substances with molecular weight up to 1100 g/mol.  For compounds with molecular weight > 1100 g/mol, this value can be used for a conservative exposure estimate.
-        <p><em>Molecular weight</em> - Enter the molecular weight of the substance in grams per mole.</p> 
+        <p><em>Identity</em> - Select the color additive in the component being evaluated via the pull down list.
+          If the color additive is not explicitly listed, please choose  "Other color additive" and ...
+          If you are evaluating an additive associated with a color additive please select "Other color additive associated compound" and
+          enter the chemical name and molecular weight ...
         <p><em>Amount</em> - Enter the total mass of the substance in the component being evaluated expressed in milligrams.</p>
         <p><em>Total impurity concentration</em> - If you have selected a color additive, please enter the combined concentration of all impurities associated with the color additive as a percentage (% mass/mass).</p>
       </div>

color2_module/templates/color2_report.html

@@ -8,6 +8,28 @@
     <script id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <link rel= "stylesheet" type= "text/css" href= "{{ url_for('static',filename='styles.css') }}">
 
+    <style>
+    * {
+      box-sizing: border-box;
+    }
+
+    /* Create two equal columns that floats next to each other */
+    .column {
+      float: left;
+      width: 50%;
+      padding: 10px;
+      vertical-align: top;
+      align: center;
+    }
+
+    /* Clear floats after the columns */
+    .row:after {
+      content: "";
+      display: table;
+      clear: both;
+    }
+    </style>
+
 </head>
 
 <header>
@@ -20,10 +42,34 @@
 <script> document.write(new Date().toLocaleDateString()); </script>.
 </p>
 
-<h3>Exposure </h3>
-
-<p>
-<u> Diffusion calculation for {{chemName}} leaching from {{polymers[pIndex]}} estimates a worst case single day
+<h2> Compound </h2>
+
+<div class="container">
+<div class="row">
+  <div class="column">
+      Input ::  {{chemName}} <br> <br>
+      IUPAC Name ::  {{iupac}} <br> <br>
+      CAS ::  {{cas}} <br> <br>
+      Molecular weight (g/mol) :: {{'%0.4f'%MW|float}}
+      {% if ceramic %} :: ceramic detected, assume maximum Mw {% endif %}
+      <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) :: {{mp}}{{mp_origin}}<br> <br>
+      {% endif %}
+      SMILES :: {{smiles}}
+  </div>
+  <div class="column">
+      <img src="{{molImage}}"/>
+  </div>
+</div>
+</div>
+
+<h2>Exposure </h2>
+
+<p>
+<u> Diffusion calculation for leaching from {{polymers[pIndex]}} estimates a worst case single day
     exposure = {{release}} mg. </u>
 <p>
 
@@ -52,7 +98,14 @@ where \( \tau= D t A^2 / V^2 \) and \( A \) and \( V \) are the surface area and
 \( t \) = {{time}} h <br>
 <p>
 
-<h3> Assumptions </h3>
+<p>
+In addition to the maximum daily (day 1) release rate, it can be helpful to examine the decay in release rate over time predicted by the model,
+    which is illustrated for the first 30 days of exposure in the plot below:
+</p>
+
+<img src="{{ image }}"/>
+
+<h2> Assumptions </h2>
 
 {% if assume[0] and assume[1] and assume[2] and assume[3] and assume[4] %}
 
@@ -93,7 +146,7 @@ where \( \tau= D t A^2 / V^2 \) and \( A \) and \( V \) are the surface area and
 
 {% endif %}
 
-<h3> Screening level toxicological risk assessment </h3>
+<h2> Screening level toxicological risk assessment </h2>
 
 {% if caIndex > 10 %}
 
@@ -164,7 +217,7 @@ of {{MOS}}.
 
 {% endif %}
 
-<h3> Impurities </h3>
+<h2> Impurities </h2>
 
 {% if iMOS >= 1 %}
 

color2_module/templates/metalError.html

@@ -0,0 +1,68 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>CHRIS-ChemError</title>
+    <link rel= "stylesheet" type= "text/css" href= "{{ url_for('static',filename='styles.css') }}">
+
+    <style>
+    * {
+      box-sizing: border-box;
+    }
+
+    /* Create two equal columns that floats next to each other */
+    .column {
+      float: left;
+      width: 50%;
+      padding: 10px;
+      vertical-align: top;
+      align: center;
+    }
+
+    /* Clear floats after the columns */
+    .row:after {
+      content: "";
+      display: table;
+      clear: both;
+    }
+    </style>
+
+</head>
+
+<img src="{{ url_for('static',filename='images/FDAlogo.png') }}" style="float: left;" height="100"/>
+<img src="{{ url_for('static',filename='images/FDAgraphic.png') }}" style="float: right;"  height="100"/>
+<br clear="all" />
+
+<body>
+
+<div style="font-size:5rem;text-align:center"> &#129318; </div>
+
+<h2> Compound </h2>
+
+<div class="container">
+<div class="row">
+  <div class="column">
+      Input ::  {{chemName}} <br> <br>
+      IUPAC Name ::  {{iupac}} <br> <br>
+      CAS ::  {{cas}} <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) :: {{mp}}{{mp_origin}} <br> <br>
+      {% endif %}
+      SMILES :: {{smiles}}
+  </div>
+  <div class="column">
+      <img src="{{molImage}}"/>
+  </div>
+</div>
+</div>
+
+<p style="font-size:2rem;text-align:center">
+    Unfortunately, CHRIS cannot be used for metals.  Please return to the previous page to evaluate
+    a different chemical.
+</p>
+
+
+</body>

efficiency_module/static/efficiency_COU.html

@@ -42,20 +42,20 @@ The salient limitations are enumerated below:</p>
 Therefore, the output is only applicable to compounds that are
 introduced either intentionally or unintentionally during synthesis
 (e.g., residual monomers and oligomers, catalysts, initiators) or
-compounding (e.g., stabilizers, antioxidants, plasticizers) are within
-scope. The model is not appropriate for surface residuals from
-processing, cleaning, and sterilization.</li>
+compounding (e.g., stabilizers, antioxidants, plasticizers). The model
+is not appropriate for surface residuals from processing, cleaning, and
+sterilization.</li>
 <li>The solvent is “perfectly mixed”. This should be a reasonable
-assumption provided the samples are adequately agitated in a static bath
-over the timeframe of the testing. However, this assumption may not be
-appropriate if sufficient agitation is not applied and a boundary layer
-develops that slows the release rate or if the extraction is conducted
-under flow conditions.</li>
+assumption provided the samples are adequately agitated over the
+timeframe of the testing. However, this assumption may not be
+appropriate if sufficient agitation is not applied and a signficant
+boundary layer develops that slows the release rate or if the extraction
+is conducted under flow conditions.</li>
 <li>Possible chemical reactions are not considered. Therefore, if the
 polymer matrix undergoes substantive degradation during the extraction
 test, the predictions may not be relevant. Further, the model does not
-consider the potential for individual extractable compounds to
-degrade.</li>
+consider the potential for individual extractable compounds to degrade
+over the selected timeframe.</li>
 <li>The test article is comprised of a single polymer matrix. In
 practice, complex devices may be comprised of multiple components and/or
 polymer matrices. In these scenarios, careful consideration of the

exposure2_module/exposure.py

@@ -71,7 +71,7 @@ def exp_post():
     # metals/ceramics logic
     mol = Chem.MolFromSmiles(smiles)
     mol = Chem.AddHs(mol)
-    natoms = mol.GetNumAtoms()
+    #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()):