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)