def test_trajPhotonFlooding(self): options = FakeOptionsRK() options.pbfile = "mixed.prb" options.configfilename = "standardRKmulti.conf" runTrajPrbAdd(options) outdata = numpy.loadtxt(options.outtrajfile, comments = "#") self.assertAlmostEqual(outdata[:, 3].sum(), 16200. / 1000, delta = 100.0 / 1000)
def test_trajClippingPhotonFlooding(self): options = FakeOptionsRK() options.pbfile = "mixed.prb" options.configfilename = "standardRKclip.conf" runTrajPrbAdd(options) outdata = numpy.loadtxt(options.outtrajfile, comments = "#") self.assertEqual(len(outdata[:, 3]), 3760)
def test_trajClassAssignOnly(self): options = FakeOptionsRK() options.pbfile = "mixed.prb" runTrajPrbAdd(options) outdata = numpy.loadtxt(options.outtrajfile, comments = "#") self.assertAlmostEqual(outdata[0:1000, 3].sum(), 0.5, delta = 0.1) self.assertAlmostEqual(outdata[1000:2000, 3].sum(), 0.25, delta = 0.1) self.assertAlmostEqual(outdata[2000:3000, 3].sum(), 0.25, delta = 0.1) self.assertAlmostEqual(outdata[3000:4000, 3].sum(), 0.0, delta = 0.1)
def main(): (options, args) = getCmdlineOptions() runTrajPrbAdd(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)