Source code for pkpd.protocols.protocol_pkpd

# **************************************************************************
# *
# * Authors:     Carlos Oscar Sorzano (
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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
# * 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 ''
# *
# **************************************************************************
In this module are protocol base classes related to PKPD

import sys
import os
from pwem.protocols import *
from pkpd.objects import PKPDExperiment, PKPDFitting
import pyworkflow.protocol.params as params

[docs]class ProtPKPD(EMProtocol):
[docs] def printSection(self, msg): print("**********************************************************************************************") print("Section: %s"%msg) print("**********************************************************************************************")
[docs] def readExperiment(self,fnIn, show=True, fullRead=True): experiment = PKPDExperiment() experiment.load(fnIn,fullRead=fullRead) if show: self.printSection("Reading %s"%fnIn) experiment._printToStream(sys.stdout) return experiment
[docs] def writeExperiment(self, experiment, fnOut): self.printSection("Writing %s"%fnOut) experiment._printToStream(sys.stdout) experiment.write(fnOut)
[docs] def readFitting(self, fnIn, show=True, cls=""): fitting = PKPDFitting(cls) fitting.load(fnIn) if show: self.printSection("Reading %s"%fnIn) fitting._printToStream(sys.stdout) return fitting
[docs] def doublePrint(self,fh,msg): fh.write(msg+"\n") print(msg)
[docs] def addFileContentToMessage(self,msg,fn): if os.path.exists(fn): fh = open(fn) for line in fh.readlines(): msg.append(line.strip()) fh.close()
[docs] def loadInputExperiment(self): """ If the protocol has an attribute 'inputExperiment', load that experiment from file. If not, return None. """ experiment = self.getAttributeValue('inputExperiment', None) if experiment: experiment.load() return experiment return None
[docs] def setInputExperiment(self): """ Set as self.experiment the experiment that is referenced in the attribute self.inputExperiment. """ self.setExperiment(self.loadInputExperiment())
[docs]def addDoseToForm(form): form.addParam('doses', params.TextParam, height=5, width=70, label="Doses", default="", help="Structure: [Dose Name] ; [via=ViaName] ; [doseType] ; [time description] ; [dose description]\n"\ "The dose name should have no space or special character\n"\ "The viaName must have been declared in the vias section" "Valid units are: h, mg, ug, ug/mL, ...\n"\ "The description is either a bolus or an infusion as shown in the examples\n"\ "For infusion the dose must be the amount per unit time, e.g., mg/min\n"\ "Examples:\n"\ "Infusion0 ; via=Intravenous; infusion; t=0.500000:0.750000 h; d=60*weight/1000 mg\n"\ "Bolus1 ; via=Oral; bolus; t=2.000000 h; d=100 mg\n"\ "Treatment ; via=Oral; repeated_bolus; t=0:8:48 h; d=100 mg")