Exemplo n.º 1
0
def setGetNumberOfPoints(testId):
    print string.ljust("Check " + testId, rpadding),
    errorFlag = False
    value = random.randint(1, 100)
    rrPython.setNumPoints(value)
    if rrPython.getNumPoints() != value:
        errorFlag = True
    print passMsg(errorFlag)
Exemplo n.º 2
0
def setGetNumberOfPoints(testId):
    print string.ljust ("Check " + testId, rpadding),
    errorFlag = False
    value = random.randint (1, 100)
    rrPython.setNumPoints (value)
    if rrPython.getNumPoints () != value:
            errorFlag = True
    print passMsg (errorFlag)
import rrPython
import os

modelPath = ('C:\\roadRunner\\models\\feedback.xml')

sbml = rrPython.loadSBMLFromFile(modelPath)
rrPython.setTimeStart(0.0)
rrPython.setTimeEnd(3.0)
rrPython.setNumPoints(20)
rrPython.setSteadyStateSelectionList("time S1 S2 S3 S4")
results = rrPython.simulate()

print results
Exemplo n.º 4
0
import rrPython
import timeit
import cmd

modelPath = raw_input('Model location: (C:\\RoadRunner\\Models\\feedback.xml, etc.)')

rrPython.loadSBMLFromFile(modelPath)

simulations = raw_input('Number of simulations:')
start_Time = raw_input('Start time:')
start_Time = float(start_Time)
end_Time = raw_input('End time:')
end_Time = float(end_Time)
number_of_points = raw_input('Number of points:')
number_of_points = int(number_of_points)
simulations = int(simulations)

rrPython.setTimeStart(start_Time)
rrPython.setTimeEnd(end_Time)
rrPython.setNumPoints(number_of_points)

t = timeit.Timer('rrPython.simulate()','import rrPython')

totalTime = t.timeit(number = simulations)

meanTime = totalTime/simulations

print 'Average simulation time: ' + str(meanTime) + ' seconds'
Exemplo n.º 5
0
import rrPython
import os
import csv
os.chdir('C:\\RoadRunner\\bin')

function = 'setNumPoints'
rrPython.loadSBMLFromFile('C:\\RoadRunner\\Models\\feedback.xml')

try:
    points = rrPython.setNumPoints(10)
    if str(points) is not False:
        result = 'True'
    else:
        result = 'False'
except:
    result = 'False'


PythonTestResults = open('C:\\RoadRunner\\PythonTestResults.csv','a')
writer = csv.writer(PythonTestResults)
writevar = function + '=' + result
writer.writerow([writevar])
PythonTestResults.close()
import rrPython
import os

modelPath = ('C:\\roadRunner\\models\\feedback.xml')

sbml = rrPython.loadSBMLFromFile(modelPath)
rrPython.setTimeStart(0.0)
rrPython.setTimeEnd(3.0)
rrPython.setNumPoints(20)
rrPython.setSteadyStateSelectionList("time S1 S2 S3 S4")
results = rrPython.simulate()

print results
Exemplo n.º 7
0
import os
import rrPython

print 'RoadRunner Build Date: ' + rrPython.getCopyright()

startTime = 0
endTime = 5
numPoints = 50
selList="time,S1,S2"


result = rrPython.loadSBMLFromFile("..\\Models\\test_1.xml")

rrPython.setTimeStart(startTime)
rrPython.setTimeEnd(endTime)
rrPython.setNumPoints(numPoints)
rrPython.setTimeCourseSelectionList(selList)
k = rrPython.simulate()
print k

print "done"
Exemplo n.º 8
0
import rrPython
import timeit
import cmd

modelPath = raw_input(
    'Model location: (C:\\RoadRunner\\Models\\feedback.xml, etc.)')

rrPython.loadSBMLFromFile(modelPath)

simulations = raw_input('Number of simulations:')
start_Time = raw_input('Start time:')
start_Time = float(start_Time)
end_Time = raw_input('End time:')
end_Time = float(end_Time)
number_of_points = raw_input('Number of points:')
number_of_points = int(number_of_points)
simulations = int(simulations)

rrPython.setTimeStart(start_Time)
rrPython.setTimeEnd(end_Time)
rrPython.setNumPoints(number_of_points)

t = timeit.Timer('rrPython.simulate()', 'import rrPython')

totalTime = t.timeit(number=simulations)

meanTime = totalTime / simulations

print 'Average simulation time: ' + str(meanTime) + ' seconds'
Exemplo n.º 9
0
                                startTime = float(text[1])
                        if text[0] == 'duration:':
                                endTime = startTime + float(text[1])
                        if text[0] == 'steps:':
                                numberOfPoints = int(text[1])+1#add one to match online sbml validation
                        if text[0] == 'variables:':
                                varlist = text[1:]
                        if text[0] == 'amount:':
                                if len(text) >1:
                                    concheck = 1
                        if text[0] == 'concentration:':
                                if len(text) >1:
                                    amountcheck = 1
        rrPython.setTimeStart(startTime)
        rrPython.setTimeEnd(endTime)
        rrPython.setNumPoints(numberOfPoints)
        #if concheck == 1:
        #    compvalues = rrPython.getCompartmentByIndex()
        curtime = ['time']

        species = curtime + varlist
        #i=0
        #pattern = re.compile('[\W_]+')
        #for species[i] in species:
        #    species[i] = pattern.sub('',species[i])#removes non-alphanumeric characters from all variables names. Probably no longer needed.
        #    i+=1

        species = str(species).strip("[]")
        species = species.replace("'", "")
        species = species.replace(" ", "")
        rrPython.setSelectionList(species)
Exemplo n.º 10
0
                if text[0] == 'duration:':
                    endTime = startTime + float(text[1])
                if text[0] == 'steps:':
                    numberOfPoints = int(
                        text[1]) + 1  #add one to match online sbml validation
                if text[0] == 'variables:':
                    varlist = text[1:]
                if text[0] == 'amount:':
                    if len(text) > 1:
                        concheck = 1
                if text[0] == 'concentration:':
                    if len(text) > 1:
                        amountcheck = 1
        rrPython.setTimeStart(startTime)
        rrPython.setTimeEnd(endTime)
        rrPython.setNumPoints(numberOfPoints)
        #if concheck == 1:
        #    compvalues = rrPython.getCompartmentByIndex()
        curtime = ['time']

        species = curtime + varlist
        #i=0
        #pattern = re.compile('[\W_]+')
        #for species[i] in species:
        #    species[i] = pattern.sub('',species[i])#removes non-alphanumeric characters from all variables names. Probably no longer needed.
        #    i+=1

        species = str(species).strip("[]")
        species = species.replace("'", "")
        species = species.replace(" ", "")
        rrPython.setSelectionList(species)