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")
def create_from_pdb(file):
sls = IMP.SetLogState(IMP.NONE)
#datadir = '/home/elina/IMP/kernel/examples/CL/'
#datadir = '/Users/apolitis/imp-projects/imp-work/'
#datadir = '/u/cvr/apolitis/docs-imp/package-python/'
#file =sys.argv[0]
datadir = os.getcwd()
print datadir
t = IMP.atom.read_pdb(datadir + '/' + file, m,
IMP.atom.ATOMPDBSelector())
del sls
#IMP.atom.show_molecular_hierarchy(t)
c = IMP.atom.Chain(IMP.atom.get_by_type(t, IMP.atom.CHAIN_TYPE)[0])
if c.get_number_of_children() == 0:
IMP.atom.show_molecular_hierarchy(t)
# there is no reason to use all atoms, just approximate the pdb shape instead
s = IMP.atom.create_simplified_along_backbone(
c, resolution / 300.0)
IMP.atom.destroy(t)
# make the simplified structure rigid
rb = IMP.atom.create_rigid_body(s)
# rb=IMP.atom.create_rigid_body(c)
rb.set_coordinates_are_optimized(True)
return s
