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dmsaylor commited on Nov 8, 2022

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be39ed5

1 Parent(s): d095768

Initialized the "extraction efficiency" module

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Files changed (6) hide show

CHRIS.py +4 -1
efficiency_module/__init__.py +5 -0
efficiency_module/efficiency.py +15 -0
efficiency_module/templates/efficiency_index.html +26 -0
efficiency_module/templates/efficiency_report.html +171 -0
templates/main.html +6 -0

CHRIS.py CHANGED Viewed

@@ -1,7 +1,7 @@
 from flask import Flask, render_template
 app = Flask(__name__)
-app.debug = False
 from color_module import blueprint
 app.register_blueprint(blueprint)
@@ -9,6 +9,9 @@ app.register_blueprint(blueprint)
 from exposure_module import blueprint
 app.register_blueprint(blueprint)
 @app.route('/', methods=['GET'])
 def app_init():
     return render_template('main.html')

 from flask import Flask, render_template
 app = Flask(__name__)
+app.debug = True
 from color_module import blueprint
 app.register_blueprint(blueprint)
 from exposure_module import blueprint
 app.register_blueprint(blueprint)
+from efficiency_module import blueprint
+app.register_blueprint(blueprint)
 @app.route('/', methods=['GET'])
 def app_init():
     return render_template('main.html')

efficiency_module/__init__.py ADDED Viewed

	@@ -0,0 +1,5 @@

+from flask import Blueprint
+blueprint = Blueprint('efficiency_module', __name__, template_folder='templates', static_folder='static', static_url_path='/efficiency_module')
+from . import efficiency

efficiency_module/efficiency.py ADDED Viewed

	@@ -0,0 +1,15 @@

+import numpy as np
+from flask import render_template, request
+from . import blueprint
+# load the index page for the exposure module
+@blueprint.route('/efficiency', methods=['GET'])
+def efficiency():
+    return render_template('efficiency_index.html')
+# build the report page for the exposure module
+@blueprint.route('/efficiency', methods=['POST'])
+def eff_post():
+    return render_template('efficiency_report.html')

efficiency_module/templates/efficiency_index.html ADDED Viewed

	@@ -0,0 +1,26 @@

+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <title>CHRIS</title>
+  <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.slim.min.js" integrity="sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js" integrity="sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN" crossorigin="anonymous"></script>
+  <script src="https://cdn.jsdelivr.net/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" integrity="sha384-VHvPCCyXqtD5DqJeNxl2dtTyhF78xXNXdkwX1CZeRusQfRKp+tA7hAShOK/B/fQ2" crossorigin="anonymous"></script>
+  <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" />
+<header>
+  <h1 style="text-align:center"><font color="#0070C0">CH</font>emical <font color="#0070C0">RIS</font>k calculator (CHRIS) - Extraction efficiency RST</h1>
+</header>
+<body>
+<form method="POST">
+</body>
+</html>

efficiency_module/templates/efficiency_report.html ADDED Viewed

	@@ -0,0 +1,171 @@

+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>CHRIS Report</title>
+<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
+<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>
+<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" />
+<header>
+   <h1 style="text-align:center"><font color="#0070C0">CH</font>emical <font color="#0070C0">RIS</font>k calculator (CHRIS) Report - Bulk chemicals </h1>
+</header>
+<body>
+<p> The following report was generated using CHRIS v.2.0 beta on
+<script> document.write(new Date().toLocaleDateString()); </script>.
+</p>
+<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 the worst case single day exposure = {{release}} mg. </u>
+<p>
+<p>
+This estimate was derived using solutions to the conservative plane sheet model for mass release, \( M \):
+\[
+M(\tau)= \left\{
+  \begin{array}{cr}
+      2 M_0 \sqrt{\tau/\pi} & \tau \leq 0.2 \\
+      M_0\left(1-8 \exp\left[-\tau \pi^2/4 \right]/\pi^2\right) & \tau > 0.2
+      \end{array} \right.
+\]
+where \( \tau= D t A^2 / V^2 \) and \( A \) and \( V \) are the surface area and volume of the polymer matrix, respectively, \( M_0 \) is total mass initially contained in the polymer, \( D \) is a conservative estimate of the diffusion coefficient of the leachable within the polymer matrix, and \( t \) is time.  Based on the input provided, the calculation was based on the following values:
+</p>
+<p>
+\( A \) = {{area}} cm<sup>2</sup> <br>
+\( V \) = {{vol}} cm<sup>3</sup> <br>
+\( M_0 \) = {{amount}} mg <br>
+\( D \) = {{diff}} cm<sup>2</sup>/h <br>
+\( t \) = {{time}} h <br>
+</p>
+<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] %}
+<p>
+<font color="green"> You have confirmed your system complies with the model assumptions and no further data are needed to support using the exposure estimation provided by CHRIS in a submission to CDRH. </font>
+</p>
+{% else %}
+<p>
+<font color="red"> You have not confirmed compliance with one or more of the underlying assumptions upon which the exposure calculation is based.  Therefore, it may be necessary to provide a justification and supporting data for why the results obtained for a system that may not comply with unchecked assumptions below are still valid if the assessment is used to support a submission to CDRH: </font> <br>
+</p>
+{% if not assume[0] %}
+<font color="red"> &bull; The polymer matrix does not swell or degrade in the clinical use environment. <br> </font>
+{% endif %}
+{% if not assume[1] %}
+<font color="red"> &bull; Any particles/aggregates of the chemical are much smaller than the smallest component dimension (&le; 50x). <br> </font>
+{% endif %}
+{% if not assume[2] %}
+<font color="red"> &bull; The chemical is homogeneously distributed throughout the polymer. <br> </font>
+{% endif %}
+{% if not assume[3] %}
+<font color="red"> &bull; The total amount of the chemical is present in dilute concentrations (&le; 2 %).  <br> </font>
+{% endif %}
+{% if not assume[4] %}
+<font color="red"> &bull; Manufacturing processes do not impact the integrity of the polymer.  <br> </font>
+{% endif %}
+{% endif %}
+<h2> Screening level toxicological risk assessment </h2>
+<p>
+The threshold for toxicological concern (TTC) for {{exposure}} contact is {{TTC}} mg.  Based on the exposure estimation this results in a margin of safety (MOS) of {{MOS}}.
+</p>
+{% if MOS >= 1 %}
+<p>
+<font color="green"> The MOS based on the mutagenic TTC is greater than one; therefore, no further analysis is needed for systemic biocompatibility endpoints.  </font>
+</p>
+<p>
+<font color="red"> *Note*: This assessment assumes that the chemical is not in the cohort of concern. </font>
+</p>
+{% else %}
+<p>
+<font color="red"> The MOS based on the mutagenic TTC is less than one; therefore, further analysis is needed to address systemic biocompatibility endpoints.  For example, a compound specific tolerable intake value could be independently derived and compared to the exposure estimate provided above.  </font>
+</p>
+{% endif %}
+<button type="button" onclick="javascript:history.back()">Back</button>
+</body>
+</html>

templates/main.html CHANGED Viewed

@@ -56,4 +56,10 @@ This module can be used similarly to the color additive tool, but can be applied
     the total amount of the chemical is known, e.g. from a certificate of analysis.
 </p>
 </body>

     the total amount of the chemical is known, e.g. from a certificate of analysis.
 </p>
+3. <a href="/efficiency"> Extraction efficiency RST</a>
+<p>
+This module can be used to estimate the fraction of the total pool of a bulk chemical that will be extracted under different conditions.
+</p>
 </body>