def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
# necessary for comparison
xray_structure = processed_pdb_file.xray_structure()
restraints_manager = mmtbx.restraints.manager(geometry=geometry_restraints,
normalization=False)
angle_proxies = restraints_manager.geometry.get_all_angle_proxies()
riding_h_manager = riding.manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = riding_h_manager.h_connectivity
# get bonds stored in connectivity
bond_list = {}
angle_list = {}
for neighbors in h_connectivity:
if (neighbors is None): continue
ih = neighbors.ih
a0 = neighbors.a0
i_a0 = a0['iseq']
a1 = neighbors.a1
i_a1 = a1['iseq']
bond_list[ih] = [i_a0, a0['dist_ideal']]
selected_atoms = tuple(sorted([ih, i_a0, i_a1]))
angle_list[selected_atoms] = a1['angle_ideal']
if neighbors.a2:
a2 = neighbors.a2
selected_atoms2 = tuple(sorted([ih, i_a0, a2['iseq']]))
angle_list[selected_atoms2] = a2['angle_ideal']
if neighbors.a3:
a3 = neighbors.a3
selected_atoms3 = tuple(sorted([ih, i_a0, a3['iseq']]))
angle_list[selected_atoms3] = a3['angle_ideal']
if neighbors.h1:
h1 = neighbors.h1
selected_atoms4 = tuple(sorted([ih, i_a0, h1['iseq']]))
angle_list[selected_atoms4] = h1['angle_ideal']
if neighbors.b1:
i_b1 = neighbors.b1['iseq']
third_nb_dict = {ih: i_b1}
# determine bonds from pdb_str
model = mmtbx.model.manager(restraints_manager=restraints_manager,
xray_structure=xray_structure,
pdb_hierarchy=pdb_hierarchy)
bond_ctrl = {}
for i in model.xh_connectivity_table():
bond_ctrl[i[1]] = [i[0], i[3]]
# List of angle restraints
angles = [(4, 1, 12), (0, 1, 12), (2, 1, 12), (13, 4, 14), (5, 4, 14),
(5, 4, 13), (1, 4, 13), (1, 4, 14), (8, 6, 15), (5, 6, 15),
(9, 7, 16), (5, 7, 16), (10, 8, 17), (6, 8, 17), (10, 11, 19),
(7, 9, 18), (10, 9, 18)]
angle_ctrl = {}
for ap in angle_proxies:
if (ap.i_seqs in angles):
angle_ctrl[tuple(sorted(list(ap.i_seqs)))] = ap.angle_ideal
# HH needs also third neighbors:
third_nb_ctrl = {19: 8}
assert (
bond_list == bond_ctrl), '1-2 neighbors and distance_ideal are wrong'
assert (
angle_list == angle_ctrl), '1-3 neighbors and angle_ideal are wrong'
assert (third_nb_dict == third_nb_ctrl), '1-4 neighbors are wrong'
def exercise():
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
restraints_manager = model.get_restraints_manager()
angle_proxies = restraints_manager.geometry.get_all_angle_proxies()
connectivity_manager = connectivity.determine_connectivity(
pdb_hierarchy=model.get_hierarchy(),
geometry_restraints=restraints_manager.geometry)
h_connectivity = connectivity_manager.h_connectivity
# get bonds stored in connectivity
bond_list = {}
angle_list = {}
for neighbors in h_connectivity:
if (neighbors is None): continue
ih = neighbors.ih
a0 = neighbors.a0
i_a0 = a0['iseq']
a1 = neighbors.a1
i_a1 = a1['iseq']
bond_list[ih] = [i_a0, a0['dist_ideal']]
selected_atoms = tuple(sorted([ih, i_a0, i_a1]))
angle_list[selected_atoms] = a1['angle_ideal']
if neighbors.a2:
a2 = neighbors.a2
selected_atoms2 = tuple(sorted([ih, i_a0, a2['iseq']]))
angle_list[selected_atoms2] = a2['angle_ideal']
if neighbors.a3:
a3 = neighbors.a3
selected_atoms3 = tuple(sorted([ih, i_a0, a3['iseq']]))
angle_list[selected_atoms3] = a3['angle_ideal']
if neighbors.h1:
h1 = neighbors.h1
selected_atoms4 = tuple(sorted([ih, i_a0, h1['iseq']]))
angle_list[selected_atoms4] = h1['angle_ideal']
if neighbors.b1:
i_b1 = neighbors.b1['iseq']
third_nb_dict = {ih: i_b1}
bond_ctrl = {}
for i in model.xh_connectivity_table():
bond_ctrl[i[1]] = [i[0], i[3]]
# List of angle restraints
angles = [(4, 1, 12), (0, 1, 12), (2, 1, 12), (13, 4, 14), (5, 4, 14),
(5, 4, 13), (1, 4, 13), (1, 4, 14), (8, 6, 15), (5, 6, 15),
(9, 7, 16), (5, 7, 16), (10, 8, 17), (6, 8, 17), (10, 11, 19),
(7, 9, 18), (10, 9, 18)]
angle_ctrl = {}
for ap in angle_proxies:
if (ap.i_seqs in angles):
angle_ctrl[tuple(sorted(list(ap.i_seqs)))] = ap.angle_ideal
# HH needs also third neighbors:
third_nb_ctrl = {19: 8}
assert (
bond_list == bond_ctrl), '1-2 neighbors and distance_ideal are wrong'
assert (
angle_list == angle_ctrl), '1-3 neighbors and angle_ideal are wrong'
assert (third_nb_dict == third_nb_ctrl), '1-4 neighbors are wrong'
def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = None,
raw_records = pdb_str,
force_symmetry = True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
xray_structure = processed_pdb_file.xray_structure()
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies = False)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry_restraints,
normalization = False)
sites_cart = xray_structure.sites_cart()
bond_proxies_simple, asu = restraints_manager.geometry.get_all_bond_proxies(
sites_cart = sites_cart)
angle_proxies = restraints_manager.geometry.get_all_angle_proxies()
hd_selection = xray_structure.hd_selection()
# determine values with code to be tested
connectivity = hydrogen_connectivity.determine_H_neighbors(
geometry_restraints = geometry_restraints,
bond_proxies = bond_proxies_simple,
angle_proxies = angle_proxies,
hd_selection = hd_selection,
sites_cart = sites_cart)
bond_list = {}
angle_list = {}
third_nb_list = {}
for ih in connectivity.keys():
a0 = (connectivity[ih][0])
bond_list[ih]=[a0.iseq, a0.dist_ideal]
for atom in connectivity[ih][1]:
helper = tuple(sorted([ih, a0.iseq, atom.iseq]))
angle_list[helper]=atom.angle_ideal
if(len(connectivity[ih])==3):
third_nb_list[ih]=[]
for atom in connectivity[ih][2]:
third_nb_list[ih].append(atom.iseq)
# print third_nb_list[ih]
#-----------------------------------------------------------------------------
# This is useful to keep for debugging: human readable output of connectivity
#-----------------------------------------------------------------------------
# for ih in connectivity.keys():
# if(len(connectivity[ih])==3):
# string = (" ".join([names[p.iseq] for p in connectivity[ih][2]]))
# else:
# string = 'n/a'
# print names[ih],': ', names[(connectivity[ih][0][0]).iseq], \
# ',', (" ".join([names[p.iseq] for p in connectivity[ih][1]])), \
# ',', string
#-----------------------------------------------------------------------------
# determine values directly from pdb_str
model = mmtbx.model.manager(
restraints_manager = restraints_manager,
xray_structure = xray_structure,
pdb_hierarchy = pdb_hierarchy)
bond_ctrl = {}
for i in model.xh_connectivity_table():
bond_ctrl[i[1]]=[i[0],i[3]]
# We know the angles beforehand
angles = [
(4, 1, 12),
(2, 1, 12),
(0, 1, 12),
(13, 4, 14),
(5, 4, 14),
(5, 4, 13),
(1, 4, 13),
(1, 4, 14),
(8, 6, 15),
(5, 6, 15),
(9, 7, 16),
(5, 7, 16),
(10, 8, 17),
(6, 8, 17),
(10, 11, 19),
(7, 9, 18),
(10, 9, 18)]
angle_ctrl = {}
for ap in angle_proxies:
if(ap.i_seqs in angles):
angle_ctrl[tuple(sorted(list(ap.i_seqs)))]=ap.angle_ideal
# HH needs also third neighbors:
third_nb_ctrl = {19: [8, 9]}
assert (bond_list == bond_ctrl), '1-2 neighbors and distance_ideal are wrong'
assert (angle_list == angle_ctrl), '1-3 neighbors and angle_ideal are wrong'
assert (third_nb_list == third_nb_ctrl), '1-4 neighbors are wrong'
def exercise():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
file_name=None,
raw_records=pdb_str,
force_symmetry=True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry_restraints = processed_pdb_file.geometry_restraints_manager(
show_energies=False)
# necessary for comparison
xray_structure = processed_pdb_file.xray_structure()
restraints_manager = mmtbx.restraints.manager(geometry=geometry_restraints,
normalization=False)
angle_proxies = restraints_manager.geometry.get_all_angle_proxies()
riding_h_manager = riding.manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints)
h_connectivity = riding_h_manager.h_connectivity
bond_list = {}
angle_list = {}
third_nb_list = {}
for ih in h_connectivity.keys():
a0 = (h_connectivity[ih][0])
bond_list[ih] = [a0.iseq, a0.dist_ideal]
for atom in h_connectivity[ih][1] + h_connectivity[ih][2]:
helper = tuple(sorted([ih, a0.iseq, atom.iseq]))
angle_list[helper] = atom.angle_ideal
if (len(h_connectivity[ih]) == 4):
third_nb_list[ih] = []
for third in h_connectivity[ih][3]:
third_nb_list[ih].append(third.iseq)
#-----------------------------------------------------------------------------
# This is useful to keep for debugging: human readable output of connectivity
#-----------------------------------------------------------------------------
# for ih in connectivity.keys():
# if(len(connectivity[ih])==3):
# string = (" ".join([names[p.iseq] for p in connectivity[ih][2]]))
# else:
# string = 'n/a'
# print names[ih],': ', names[(connectivity[ih][0][0]).iseq], \
# ',', (" ".join([names[p.iseq] for p in connectivity[ih][1]])), \
# ',', string
#-----------------------------------------------------------------------------
# determine bonds from pdb_str
model = mmtbx.model.manager(restraints_manager=restraints_manager,
xray_structure=xray_structure,
pdb_hierarchy=pdb_hierarchy)
bond_ctrl = {}
for i in model.xh_connectivity_table():
bond_ctrl[i[1]] = [i[0], i[3]]
# List of angle restraints
angles = [(4, 1, 12), (2, 1, 12), (0, 1, 12), (13, 4, 14), (5, 4, 14),
(5, 4, 13), (1, 4, 13), (1, 4, 14), (8, 6, 15), (5, 6, 15),
(9, 7, 16), (5, 7, 16), (10, 8, 17), (6, 8, 17), (10, 11, 19),
(7, 9, 18), (10, 9, 18)]
angle_ctrl = {}
for ap in angle_proxies:
if (ap.i_seqs in angles):
angle_ctrl[tuple(sorted(list(ap.i_seqs)))] = ap.angle_ideal
# HH needs also third neighbors:
third_nb_ctrl = {19: [8, 9]}
assert (
bond_list == bond_ctrl), '1-2 neighbors and distance_ideal are wrong'
assert (
angle_list == angle_ctrl), '1-3 neighbors and angle_ideal are wrong'
assert (third_nb_list == third_nb_ctrl), '1-4 neighbors are wrong'