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_01():
pdb_inp = iotbx.pdb.input(source_info=None, lines=m5_str)
ph = pdb_inp.construct_hierarchy()
xrs_answer = pdb_inp.xray_structure_simple()
xrs_answer.switch_to_neutron_scattering_dictionary()
ph.write_pdb_file(file_name="answer.pdb")
f_calc = xrs_answer.structure_factors(d_min=1).f_calc()
fft_map = f_calc.fft_map(resolution_factor=0.1)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
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(m5_str_HD_rotated.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)
xrs = ppf.all_chain_proxies.pdb_inp.xray_structure_simple()
ph = ppf.all_chain_proxies.pdb_hierarchy
ph.write_pdb_file(file_name="poor.pdb")
xrs.switch_to_neutron_scattering_dictionary()
f_calc_poor = f_calc.structure_factors_from_scatterers(
xray_structure=xrs).f_calc()
#
rotatable_h_selection = hydrogens.rotatable(
pdb_hierarchy=ph,
mon_lib_srv=mon_lib_srv,
restraints_manager=restraints_manager,
log=None)
hydrogens.fit_rotatable(pdb_hierarchy=ph,
xray_structure=xrs,
map_data=map_data,
rotatable_h_selection=rotatable_h_selection)
ph.write_pdb_file(file_name="result.pdb")
#
f_calc_fixed = f_calc.structure_factors_from_scatterers(
xray_structure=xrs).f_calc()
def r_factor(x, y):
n = flex.sum(flex.abs(abs(x).data() - abs(y).data()))
d = flex.sum(flex.abs(abs(x).data() + abs(y).data())) / 2
return n / d
assert r_factor(f_calc, f_calc_poor) > 0.2
assert r_factor(f_calc, f_calc_fixed) < 0.015
def exercise_01():
pdb_inp = iotbx.pdb.input(source_info=None, lines=m5_str)
ph = pdb_inp.construct_hierarchy()
xrs_answer = pdb_inp.xray_structure_simple()
xrs_answer.switch_to_neutron_scattering_dictionary()
ph.write_pdb_file(file_name = "answer.pdb")
f_calc = xrs_answer.structure_factors(d_min=1).f_calc()
fft_map = f_calc.fft_map(resolution_factor=0.1)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
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(m5_str_HD_rotated.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)
xrs = ppf.all_chain_proxies.pdb_inp.xray_structure_simple()
ph = ppf.all_chain_proxies.pdb_hierarchy
ph.write_pdb_file(file_name = "poor.pdb")
xrs.switch_to_neutron_scattering_dictionary()
f_calc_poor = f_calc.structure_factors_from_scatterers(
xray_structure = xrs).f_calc()
#
rotatable_h_selection = hydrogens.rotatable(
pdb_hierarchy = ph,
mon_lib_srv = mon_lib_srv,
restraints_manager = restraints_manager,
log = None)
hydrogens.fit_rotatable(pdb_hierarchy=ph, xray_structure=xrs,
map_data=map_data,rotatable_h_selection=rotatable_h_selection)
ph.write_pdb_file(file_name = "result.pdb")
#
f_calc_fixed = f_calc.structure_factors_from_scatterers(
xray_structure = xrs).f_calc()
def r_factor(x,y):
n = flex.sum( flex.abs( abs(x).data() - abs(y).data() ) )
d = flex.sum( flex.abs( abs(x).data() + abs(y).data() ) )/2
return n/d
assert r_factor(f_calc, f_calc_poor) > 0.2
assert r_factor(f_calc, f_calc_fixed) < 0.015
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