# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'info@kinestat.com'
# *
# **************************************************************************
import numpy as np
import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.pkpd_units import PKPDUnit
# TESTED in test_workflow_gabrielsson_pk06.py
[docs]class ProtPKPDNCAEstimateBioavailability(ProtPKPD):
""" Estimate bioavailability as F=(AUCpo/Dpo) / (AUCiv/Div) [Gabrielsson 2010, p. 546], i.e., the ratio \n
between the oral and intravenous AUC normalized by their respective doses.
Protocol created by http://www.kinestatpharma.com\n"""
_label = 'bioavailability nca'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection('Input')
form.addParam('protNCAEV', params.PointerParam, label="Extra-vascular NCA",
pointerClass='ProtPKPDNCAEV',
help='Non-compartmental analysis of the Extra-Vascular route, the dose must be a bolus\n'
'The sample names in both (EV and IV) analysis must be exactly the same.')
form.addParam('protNCAIV', params.PointerParam, label="IV NCA",
pointerClass='ProtPKPDNCAIVExp,ProtPKPDNCAIVObs',
help='Non-compartmental analysis of the Extra-Vascular route, the dose must be a bolus\n'
'The sample names in both (EV and IV) analysis must be exactly the same.')
#--------------------------- STEPS functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('runEstimateF')
self._insertFunctionStep('createOutput')
[docs] def runEstimateF(self):
self.experimentEV=self.readExperiment(self.protNCAEV.get().outputExperiment.fnPKPD)
self.experimentIV=self.readExperiment(self.protNCAIV.get().outputExperiment.fnPKPD)
Flist = []
for sampleEVname, sampleEV in self.experimentEV.samples.items():
if sampleEVname in self.experimentIV.samples:
sampleEV.interpretDose()
DEV=sampleEV.getDoseAt(0)
sampleIV=self.experimentIV.samples[sampleEVname]
sampleIV.interpretDose()
DIV=sampleIV.getDoseAt(0)
AUCev=sampleEV.descriptors['AUC_0inf']
AUCiv=sampleIV.descriptors['AUC_0inf']
if AUCev!="NA" and AUCiv!="NA":
F=(float(AUCev)/DEV)/(float(AUCiv)/DIV)
Flist.append(F)
self.experimentEV.addParameterToSample(sampleEV.sampleName,"bioavailability",PKPDUnit.UNIT_NONE,
"bioavailability",F)
else:
self.experimentEV.addParameterToSample(sampleEV.sampleName,"bioavailability",PKPDUnit.UNIT_NONE,
"bioavailability","NA")
else:
self.experimentEV.addParameterToSample(sampleEV.sampleName,"bioavailability",PKPDUnit.UNIT_NONE,
"bioavailability","NA")
self.experimentEV.write(self._getPath("experiment.pkpd"))
fhSummary=open(self._getPath("summary.txt"),"w")
if len(Flist)>0:
Fmean = np.mean(Flist)
fhSummary.write("Average bioavailability (normalized between 0 and 1)=%f\n"%Fmean)
if Fmean>1:
fhSummary.write("Bioavailability larger than 1 is caused by PK non-linearities and dependences of AUC on the dose\n")
fhSummary.close()
[docs] def createOutput(self):
self._defineOutputs(outputExperiment=self.experimentEV)
self._defineSourceRelation(self.protNCAEV, self.experimentEV)
self._defineSourceRelation(self.protNCAIV, self.experimentEV)
#--------------------------- INFO functions --------------------------------------------
def _summary(self):
msg=[]
self.addFileContentToMessage(msg,self._getPath("summary.txt"))
return msg
def _citations(self):
return ['Gabrielsson2010']