def exercise_00(debug=True):
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
for i, l in enumerate(loop):
if(debug): print "-"*70, i
ppf = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
raw_records = flex.std_string(l[0].splitlines()),
force_symmetry = True)
geometry = ppf.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5.0)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry, normalization = False)
ph = ppf.all_chain_proxies.pdb_hierarchy
sel = hydrogens.rotatable(pdb_hierarchy=ph, mon_lib_srv=mon_lib_srv,
restraints_manager = restraints_manager, log=None)
if(debug):
print
print sel
print l[2]
print l[0]
print "\n".join([a.format_atom_record() for a in ph.atoms()])
ppf.all_chain_proxies.pdb_inp.write_pdb_file(file_name = "m%s.pdb"%str(i))
if(debug): print "-"*80
assert sel == l[2], "%s != %s" % (sel, l[2])
assert hydrogens.count_rotatable(sel) == l[1]
def exercise_02(debug=False):
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
ppf = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
raw_records = flex.std_string(exercise_02_str.splitlines()),
force_symmetry = True)
geometry = ppf.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5.0)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry, normalization = False)
ph = ppf.all_chain_proxies.pdb_hierarchy
sel = hydrogens.rotatable(pdb_hierarchy=ph, mon_lib_srv=mon_lib_srv,
restraints_manager = restraints_manager, log = None)
n_rot_h = hydrogens.count_rotatable(sel)
assert n_rot_h == 43, n_rot_h