def test_data_types(self):
"""Test that import works"""
# Make sure that interface is 8-bit clean
buf = b"test string \x82\x00\xb8 with 8-bit data and embedded null"
RMF.set_log_level("trace")
bh = RMF.BufferConstHandle(buf)
name = RMF._get_temporary_file_path("buffer")
print(name)
self.assertEqual(bh.get_buffer(), buf)
RMF.write_buffer(bh, name)
bbh = RMF.read_buffer(name)
self.assertEqual(bbh.get_buffer(), bh.get_buffer())
#!/usr/bin/env python from IMP.npctransport import * import IMP.rmf import RMF import sys f=open(sys.argv[1], "rb") o= Output() #config.SetTotalBytesLimit(50000000) o.ParseFromString(f.read()) bch= RMF.BufferConstHandle(o.rmf_conformation); RMF.write_buffer(bch, sys.argv[2] )
def test_init_from_rmf(self):
""" Testing whether initialize_positions_from_rmf indeed
restores the beads coordinates correctly """
IMP.set_log_level(IMP.SILENT)
test_util.test_protobuf_installed(self)
# First simulation with one seed:
output_pb1 = self.get_tmp_file_name("output1.pb")
output_rmf1 = IMP.create_temporary_file_name("output", ".rmf")
print("Starting first simulation with RMF file " + output_rmf1)
sd = self._make_and_run_simulation(output_pb1, output_rmf1, seed=1)
e1 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After first simulation")
print("Energy %.2f" % e1)
coordsI = self._get_beads_coords(sd)
sd = None
# Second simulation with another seed:
output_pb2 = self.get_tmp_file_name("output2.pb")
output_rmf2 = IMP.create_temporary_file_name("output2", ".rmf")
print("*** Starting second simulation with RMF file " + output_rmf2)
print("YYY")
sd = self._make_and_run_simulation(output_pb2, output_rmf2, seed=2)
print("XXX")
e2 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After second simulation")
print("Energy %.2f" % e2)
coordsII = self._get_beads_coords(sd)
# Restoration from first simulation through rmf file:
print("*** Initializing positions from RMF file " + output_rmf1)
fl = RMF.open_rmf_file_read_only(output_rmf1)
sd.initialize_positions_from_rmf(fl)
e3 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e3)
self.assertAlmostEqual(e1, e3, delta=0.0001)
self.assertNotAlmostEqual(e1, e2, delta=0.0001)
coordsIII = self._get_beads_coords(sd)
# make sure that all coordinates were restored and as sanity
# check control, also that the second simulation is different than
# the first one:
for i in range(len(coordsI)):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j],
coordsIII[i][j],
delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j],
coordsII[i][j],
delta=0.00001)
# Simulate more to scramble stuff
sd.get_bd().optimize(1000)
e4 = sd.get_bd().get_scoring_function().evaluate(False)
print("Energy %.2f" % e4)
coordsIV = self._get_beads_coords(sd)
# Restoration from first simulation through output protobuf file:
print("*** Initializing positions from ProtoBuf file " + output_pb1)
f = open(output_pb1, "rb")
config = IMP.npctransport.Output()
config.ParseFromString(f.read())
bch = RMF.BufferConstHandle(config.rmf_conformation)
fch = RMF.open_rmf_buffer_read_only(bch)
sd.initialize_positions_from_rmf(fch)
e5 = sd.get_bd().get_scoring_function().evaluate(False)
print("*** After initializing positions from RMF file " + output_rmf1)
print("Energy %.2f" % e5)
self.assertAlmostEqual(e1, e5, delta=0.00001)
self.assertNotAlmostEqual(e1, e4, delta=0.00001)
coordsV = self._get_beads_coords(sd)
for i in range(len(coordsI)):
for j in range(3):
self.assertAlmostEqual(coordsI[i][j],
coordsV[i][j],
delta=0.00001)
self.assertNotAlmostEqual(coordsI[i][j],
coordsIV[i][j],
delta=0.00001)