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CHRIS / exposure2_module /exposure.py

3v324v23

extending new template to all tools

570b086 about 1 month ago

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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
# MP is looked up lazily only when it can affect ceramic classification.
get_properties = []
# 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.get("/exposure2_module/COU")
def COU():
    return render_template(
        "exposure2_COU.html",
        tool_title="CHRIS - Bulk Chemicals (v2)",
        nav_links=[
            ("Tool", "/exposure2"),
            ("CoU", "/exposure2_module/COU"),
            ("About", "/exposure2_module/RST"),
        ],
        footer_text="Office of Science and Engineering Laboratories · ",
        contact_email="david.saylor@fda.hhs.gov",
    )
@blueprint.get("/exposure2_module/RST")
def RST():
    return render_template("exposure2_RST.html",
        tool_title="CHRIS - Bulk Chemicals (v2)",
        nav_links=[
            ("Tool", "/exposure2"),
            ("CoU", "/exposure2_module/COU"),
            ("About", "/exposure2_module/RST"),
        ],
        footer_text="Office of Science and Engineering Laboratories · ",
        contact_email="david.saylor@fda.hhs.gov",
    )

@blueprint.route('/exposure2', methods=['GET'])
def exposure():
    return render_template('exposure2_index.html', polymers=polymers,
        tool_title="CHRIS - Bulk Chemicals (v2)",
        nav_links=[
            ("Tool", "/exposure2"),
            ("CoU", "/exposure2_module/COU"),
            ("About", "/exposure2_module/RST"),
        ],
        footer_text="Office of Science and Engineering Laboratories · ",
        contact_email="david.saylor@fda.hhs.gov",
    )


# 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'])
    else:
        LogP_origin, rho_origin = '',''
        iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)

    if error > 0:
        return render_template('chemError.html', chemName=chemName, IDtype=IDtype, error=error,
                               error_message=ERROR_CODES.get(error, 'Unknown chemical identification error')
                               ,
                               tool_title="CHRIS - Bulk Chemicals (v2)",
                               nav_links=[
                                   ("Tool", "/exposure2"),
                                   ("CoU", "/exposure2_module/COU"),
                                   ("About", "/exposure2_module/RST"),
                               ],
                               footer_text="Office of Science and Engineering Laboratories · ",
                               contact_email="david.saylor@fda.hhs.gov",
                               )

    # metals/ceramics logic; only look up MP if the structural checks need it
    is_metal, is_ceramic, mp, material_mp_origin, mp_searched = ClassifyMaterial(cas, iupac, smiles)
    if debug:
        LogP_origin = f' ({LogP_origin})'
        rho_origin = f' ({rho_origin})'
        mp_origin = f' ({material_mp_origin})' if mp_searched else ''
    else:
        mp_origin = ''

    #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 not mp_searched:
        mp = 'Not searched'
    elif mp is np.nan or mp is None:
        mp = 'Not found'

    #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('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
                               ,
                               tool_title="CHRIS - Bulk Chemicals (v2)",
                               nav_links=[
                                   ("Tool", "/exposure2"),
                                   ("CoU", "/exposure2_module/COU"),
                                   ("About", "/exposure2_module/RST"),
                               ],
                               footer_text="Office of Science and Engineering Laboratories · ",
                               contact_email="david.saylor@fda.hhs.gov",
                               )
    #else:
    if is_ceramic:
        MW = 1100.

    if MW < 100. and not use_new:
        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"])
    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
                           ,
                           tool_title="CHRIS - Bulk Chemicals (v2)",
                           nav_links=[
                               ("Tool", "/exposure2"),
                               ("CoU", "/exposure2_module/COU"),
                               ("About", "/exposure2_module/RST"),
                           ],
                           footer_text="Office of Science and Engineering Laboratories · ",
                           contact_email="david.saylor@fda.hhs.gov",
                           )

	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
	# MP is looked up lazily only when it can affect ceramic classification.
	get_properties = []
	# 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.get("/exposure2_module/COU")
	def COU():
	return render_template(
	"exposure2_COU.html",
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)
	@blueprint.get("/exposure2_module/RST")
	def RST():
	return render_template("exposure2_RST.html",
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)

	@blueprint.route('/exposure2', methods=['GET'])
	def exposure():
	return render_template('exposure2_index.html', polymers=polymers,
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)


	# 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'])
	else:
	LogP_origin, rho_origin = '',''
	iupac, cas, smiles, MW, LogP, rho, mp, molImage, error = ResolveChemical(chemName, IDtype, get_properties=get_properties)

	if error > 0:
	return render_template('chemError.html', chemName=chemName, IDtype=IDtype, error=error,
	error_message=ERROR_CODES.get(error, 'Unknown chemical identification error')
	,
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)

	# metals/ceramics logic; only look up MP if the structural checks need it
	is_metal, is_ceramic, mp, material_mp_origin, mp_searched = ClassifyMaterial(cas, iupac, smiles)
	if debug:
	LogP_origin = f' ({LogP_origin})'
	rho_origin = f' ({rho_origin})'
	mp_origin = f' ({material_mp_origin})' if mp_searched else ''
	else:
	mp_origin = ''

	#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 not mp_searched:
	mp = 'Not searched'
	elif mp is np.nan or mp is None:
	mp = 'Not found'

	#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('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
	,
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)
	#else:
	if is_ceramic:
	MW = 1100.

	if MW < 100. and not use_new:
	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"])
	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
	,
	tool_title="CHRIS - Bulk Chemicals (v2)",
	nav_links=[
	("Tool", "/exposure2"),
	("CoU", "/exposure2_module/COU"),
	("About", "/exposure2_module/RST"),
	],
	footer_text="Office of Science and Engineering Laboratories · ",
	contact_email="david.saylor@fda.hhs.gov",
	)