def get_rmsd_from_start(self):
if self.rmsd_from_start is not None:
return self.rmsd_from_start
# calculate rmsd
self.rmsd_from_start = ssb.calculate_rmsd_smart(
self.original_boxed_hierarchy,
self.model.get_hierarchy(),
backbone_only=True)
return self.rmsd_from_start
def get_rmsd_from_start(self):
if self.rmsd_from_start is not None:
return self.rmsd_from_start
# calculate rmsd
self.rmsd_from_start = ssb.calculate_rmsd_smart(
self.original_boxed_hierarchy,
self.whole_pdb_h,
backbone_only=True)
return self.rmsd_from_start
def exercise_00(prefix="exercise_00"):
"Build poly-ALA alpha helix"
ph = ssb.secondary_structure_from_sequence(
alpha_helix_template, "".join(["A"]*12))
ph.atoms().reset_i_seq()
#ph.write_pdb_file(file_name="%s_result.pdb"%prefix)
sites_1 = ph.atoms().extract_xyz()
sites_2 = iotbx.pdb.input(source_info=None,
lines=alpha_helix_answer).construct_hierarchy().atoms().extract_xyz()
#of = open("1.pdb","w")
#print >> of, alpha_helix_answer
#of.close()
assert sites_1.size()==sites_2.size(), [sites_1.size(),sites_2.size()]
d1 = flex.sqrt((sites_1 - sites_2).dot())
rmsd = ssb.calculate_rmsd_smart(ph, iotbx.pdb.input(source_info=None,
lines=alpha_helix_answer).construct_hierarchy())
assert rmsd < 0.1, rmsd
def get_rmsd_from_start2(self):
return ssb.calculate_rmsd_smart(self.original_boxed_hierarchy,
self.model.get_hierarchy(),
backbone_only=False)
def get_rmsd_from_start2(self):
return ssb.calculate_rmsd_smart(
self.original_boxed_hierarchy,
self.whole_pdb_h,
backbone_only=False)
