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)
