def test_averEff(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "standard.conf"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_profiling(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "high.prb"
options.configfilename = "standard.conf"
options.prffile = "profile.log"
runMCFRET(options)
self.assertTrue(os.path.exists("profile.log"))
def test_stepFunctionBelowReject(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "step.prb"
options.configfilename = "stepreject.conf"
options.expbfile = "expbursts.bst"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_expBurstCorrected(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "aver.prb"
options.configfilename = "expbstcorr.conf"
options.expbfile = "expbursts.bst"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
def test_output(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.binaryofile = "binary.pkl"
options.burstcompofile = "burstcomp.txt"
options.burstsizeofile = "burstsizes.txt"
options.decaytimeofile = "decaytimes.txt"
options.endtimeofile = "endtimes.txt"
options.pbfile = "high.prb"
options.configfilename = "standard.conf"
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 1., delta = 0.05)
def test_cextensionPhotongenerator(self):
options = FakeOptions()
options.efficiencyofile = "effs.txt"
options.pbfile = "step.prb"
options.configfilename = "cextension.conf"
options.expbfile = "expbursts.bst"
try:
# from FRETUtils.PhotonGenerator import tryGetCPhoton #@UnusedImport
runMCFRET(options)
self.assertAlmostEqual(numpy.loadtxt("effs.txt").mean(), 0.5, delta = 0.05)
except ImportError:
pass
def main():
(options, args) = getCmdlineOptions()
runMCFRET(options)
print """
# %s - %s
# (C) 2012 Martin Hoefling and Helmut Grubmueller
#
# Please cite the usage as:
#
# Hoefling M, Lima N, Haenni D, Seidel CAM, Schuler B, Grubmueller H,
# Structural Heterogeneity and Quantitative FRET Efficiency Distributions
# of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo
# Approach. (2011) PLoS ONE 6(5): e19791. doi:10.1371/journal.pone.0019791
#
# and
#
# Hoefling M, Grubmueller H,
# In silico FRET from simulated dye dynamics. (2012), Computer Physics
# Communications 184(3):814-852
#
""" % (os.path.basename(sys.argv[0]), program_version)
def main():
(options, args) = getCmdlineOptions()
runMCFRET(options)
print """
# %s - %s
# (C) 2012 Martin Hoefling and Helmut Grubmueller
#
# Please cite the usage as:
#
# Hoefling M, Lima N, Haenni D, Seidel CAM, Schuler B, Grubmueller H,
# Structural Heterogeneity and Quantitative FRET Efficiency Distributions
# of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo
# Approach. (2011) PLoS ONE 6(5): e19791. doi:10.1371/journal.pone.0019791
#
# and
#
# Hoefling M, Grubmueller H,
# In silico FRET from simulated dye dynamics. (2012), Computer Physics
# Communications 184(3):814-852
#
""" % (os.path.basename(sys.argv[0]), program_version)
