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a3c0189 90da2e9 a42874d a26b7e6 90da2e9 33ad9e8 90d06f0 90da2e9 a42874d 90da2e9 a3c0189 33ad9e8 90d06f0 90da2e9 33ad9e8 90da2e9 33ad9e8 90da2e9 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 | import numbers
import numpy as np
from flask import render_template, request
from functions import SigFigs, Piringer, WilkeChang, SheetRelease, SheetRates, RatePlot
from functions import Piecewise, PowerLaw
from polymers import Polymers, Polymers3
from ChemID import *
from . import blueprint
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()
else:
polymers, categories, params = Polymers3()
# load the index page for the exposure module
@blueprint.route('/exposure2', methods=['GET'])
def exposure():
return render_template('exposure2_index.html', polymers=polymers)
# build the report page for the exposure module
@blueprint.route('/exposure2', methods=['POST'])
def exp_post():
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'])
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, get_properties=get_properties)
if error > 0:
# TODO output more useful info
return render_template('exposure2_chemError.html')
#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, 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' not in get_properties:
mp = 'Not searched'
elif mp is np.nan or mp is None:
mp = 'Not found'
# metals/ceramics logic
if isinstance(mp, numbers.Number):
is_metal, is_ceramic = CeramicOrMetal(smiles,mp)
else:
is_metal, is_ceramic = CeramicOrMetal(smiles,100)
#ceramic = False
#mol = Chem.MolFromSmiles(smiles)
#atom_num_list = [a.GetAtomicNum() for a in mol.GetAtoms()]
#is_metal = set(atom_num_list) <= METAL_ATOM_SET
if is_metal:
# if all atoms are metals -> this is a metal
#if natoms == 1 and smiles != '[C]':
# only one atom, except for carbon -> assumed metal
# return render_template('chemError.html')
return render_template('exposure2_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 is_ceramic:
MW = 1100.
if MW < 100. and not use_new:
return render_template('exposure2_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"])
mass = float(request.form["mass"])
density = float(request.form["density"])
vol = mass / density
polymer = request.form["polymer"]
#pIndex = (np.where(polymers == polymer)[0])[0]
pIndex = np.argmax(polymers == polymer)
area = float(request.form["area"])
exposure = request.form["exposure"]
if exposure != "limited":
time = 24.
else:
time = float(request.form["exptime"])
if exposure != "long-term":
TTC = 0.12
else:
TTC = 0.0015
assume = np.array((request.form.get("assume1") is not None, request.form.get("assume2") is not None,
request.form.get("assume3") is not None, request.form.get("assume4") is not None,
request.form.get("assume5") is not None))
if use_new:
category = categories[pIndex]
diff = Piecewise(MW, params[category])
else:
if not np.isnan(Ap[pIndex]):
diff = Piringer(MW, Ap[pIndex])
else:
diff = WilkeChang(MW)
release = SheetRelease(amount, vol, area, time, diff)
MOS = TTC / release
release = SigFigs(release, 2)
MOS = SigFigs(MOS, 2)
diff = SigFigs(diff, 2)
# 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('exposure2_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=is_ceramic)
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