def add_log(self):
# Temporarily (for the duration of the 'with' block) set the
# log level and context.
# these are done by the IMP_OBJECT_LOG macro in C++
with IMP.SetLogState(self.get_log_level()):
with IMP.CreateLogContext(self.get_name() + "::add_log"):
self.set_was_used(True)
IMP.add_to_log(IMP.VERBOSE,
"A verbose message in the object\n")
class DummyObject(IMP.Object):
def __init__(self):
IMP.Object.__init__(self, "DummyObject%1%")
def add_log(self):
# Temporarily (for the duration of the 'with' block) set the
# log level and context.
# these are done by the IMP_OBJECT_LOG macro in C++
with IMP.SetLogState(self.get_log_level()):
with IMP.CreateLogContext(self.get_name() + "::add_log"):
self.set_was_used(True)
IMP.add_to_log(IMP.VERBOSE,
"A verbose message in the object\n")
# we can set the log level for all of IMP
IMP.set_log_level(IMP.TERSE)
# we can tell it to print the time each event occurs
IMP.set_log_timer(True)
# we can create a log context (valid for the duration of the 'with' block)
with IMP.CreateLogContext("my context"):
# we can print a message
IMP.add_to_log(IMP.TERSE, "This is my log message\n")
o = DummyObject()
o.set_log_level(IMP.VERBOSE)
o.add_log()
IMP.set_log_level(IMP.PROGRESS)
sd = IMP.npctransport.SimulationData(
flags.output,
flags.quick,
flags.rmf_file)
print "RMF file: ", sd.get_rmf_file_name()
print get_fgs_of_type(IMP.npctransport.get_type_of_fg(0), sd.get_root())
if(flags.cylinder_anchoring):
# set_fgs_in_cylinder(sd, 4)
set_fgs_three_types(sd)
color_fgs( sd )
ntrials = sd.get_number_of_trials()
print "Number of trials: ", ntrials
for i in range(ntrials):
clc = IMP.CreateLogContext("iteration")
if(not flags.quick): # TODO: why is that?
sd.reset_rmf()
print "Initializing..."
if(flags.initialization_rmf_file):
sd.initialize_positions_from_rmf(
flags.initialization_rmf_file )
else:
init_restraints = []
if(sd.get_has_slab()): # if has slab, exclude from channel initially
init_restraints.append( get_exclude_from_channel_restraint( sd ) )
IMP.npctransport.initialize_positions( sd, init_restraints )
nframes_running = math.ceil(sd.get_statistics_fraction()
* sd.get_number_of_frames())
nframes_equilib = sd.get_number_of_frames() - nframes_running
print "Equilibrating for frames...", nframes_equilib
