Source code for pkpd.protocols.protocol_pkpd_nca_niv

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# * Authors:     Carlos Oscar Sorzano (
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# * Kinestat Pharma
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import pyworkflow.protocol.params as params
from .protocol_pkpd_sa_base import ProtPKPDSABase
from pkpd.models.sa_models import NCAEVModel
from pkpd.pkpd_units import PKPDUnit, strUnit
from pyworkflow.protocol.constants import LEVEL_ADVANCED


[docs]class ProtPKPDNCAEV(ProtPKPDSABase): """ Non-compartmental analysis of a non-intravenous bolus.\n Protocol created by\n""" _label = 'nca ev' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('protAbsorption', params.PointerParam, label="Non-IV Input experiment", pointerClass='ProtPKPDAbsorptionRate', important=True, help='Select an execution of a protocol estimating the absorption rate.') form.addParam('areaCalc', params.EnumParam, choices=["Trapezoidal","Mixed"], label="Method for AUC, AUMC calculation", default=1, expertLevel=LEVEL_ADVANCED, help='The mixed integration uses the trapezoidal is used in the raising side and the log-trapezoidal in the decay side.\n' 'See explanation at\n') form.addParam('protNCAIV', params.PointerParam, label="IV Input experiment (optional)", allowsNull=True, pointerClass='ProtPKPDNCAIVExp,ProtPKPDNCAIVObs', help='A companion experiment with intraveneous bolus is used to estimate the bioavailability and the Mean Absorption Time. ' 'The sample names in both experiments must be exactly the same.')
[docs] def getListOfFormDependencies(self): return [self.protAbsorption.get().getObjId()]
#--------------------------- STEPS functions --------------------------------------------
[docs] def getInputExperiment(self): return self.protAbsorption.get().outputExperiment
[docs] def setupFromFormParameters(self): self.experimentIV = None if self.protNCAIV.get() != None: self.experimentIV=self.readExperiment(self.protNCAIV.get().outputExperiment.fnPKPD)
[docs] def getXYvars(self): self.varNameX = self.protAbsorption.get().protElimination.get().predictor.get() self.varNameY = self.protAbsorption.get().protElimination.get().predicted.get()
[docs] def createAnalysis(self): self.analysis = NCAEVModel() self.analysis.setExperiment(self.experiment) self.analysis.setXVar(self.varNameX) self.analysis.setYVar(self.varNameY) self.analysis.F = self.protAbsorption.get().absorptionF.get() if self.areaCalc == 0: self.analysis.areaCalc = "Trapezoidal" elif self.areaCalc == 1: self.analysis.areaCalc = "Mixed"
[docs] def prepareForSampleAnalysis(self, sampleName): sample = self.experiment.samples[sampleName] sample.interpretDose() self.analysis.D = sample.getDoseAt(0.0) self.analysis.Ke = float(sample.descriptors["Ke"]) return True
[docs] def postAnalysis(self, sampleName): if self.experimentIV!=None: if sampleName in self.experimentIV.samples: sampleNIV = self.experiment.samples[sampleName] DNIV= self.analysis.D sampleIV = self.experimentIV.samples[sampleName] sampleIV.interpretDose() DIV = sampleIV.getDoseAt(0.0) F = float(sampleNIV.descriptors['AUC_0inf'])/float(sampleNIV.descriptors['AUC_0inf'])*DIV/DNIV MAT = float(sampleNIV.descriptors['MRT']) - float(sampleIV.descriptors['MRT']) self.experiment.addParameterToSample(sampleName, "F", PKPDUnit.UNIT_NONE, "Estimated bioavailability", F) self.experiment.addParameterToSample(sampleName, "MAT", self.analysis.parameterUnits[-1], "Estimated Mean Absorption Time", MAT) print("F = %f"%F) print("MAT = %f [%s]"%(MAT,strUnit(self.analysis.parameterUnits[-1])))
#--------------------------- INFO functions -------------------------------------------- def _summary(self): msg=[] msg.append("Non-compartmental analysis for the observations of the variable %s"%self.protAbsorption.get().protElimination.get().predicted.get()) return msg def _warnings(self): experiment = self.readExperiment(self.getInputExperiment().fnPKPD,show=False) incorrectList = experiment.getNonBolusDoses() if len(incorrectList)==0: return [] else: return ["This protocol is meant only for intravenous bolus regimens. Check the doses for %s"%(','.join(incorrectList))]