def build_angle_start_by_tor_id(
mon_lib_atom_names,
sites_cart,
rotamer_tor_atom_ids_by_tor_id,
i_q_packed_by_tor_id):
result = {}
atom_indices = sequence_index_dict(seq=mon_lib_atom_names)
for tor_id in i_q_packed_by_tor_id.keys():
d_sites = []
atom_ids = []
for atom_id in rotamer_tor_atom_ids_by_tor_id[tor_id]:
i = atom_indices.get(atom_id)
if (i is None):
return (atom_id, tor_id)
d_sites.append(sites_cart[i])
atom_ids.append(str(atom_id))
dihe = scitbx.math.dihedral_angle(sites=d_sites, deg=True)
if (dihe is None) :
raise RuntimeError(("scitbx.math.dihedral_angle returned None!\n"+
"Atom IDs: %s\nSites: %s\n") % (", ".join(atom_ids),
", ".join([ str(xyz) for xyz in d_sites ])))
assert dihe is not None
assert tor_id not in result
result[tor_id] = dihe
return result
def run(args):
assert len(args) == 0
if '--exercise-retrieve-unless-exists' in args:
exercise_retrieve_unless_exists()
else:
print('Skipping exercise_retrieve_unless_exists')
exercise_misc()
assert utils.sequence_index_dict(["a", "b"]) == {"a": 0, "b": 1}
assert utils.flat_list(0) == [0]
assert utils.flat_list([1,2,3]) == [1,2,3]
assert utils.flat_list([1,[2,3,4],3]) == [1,2,3,4,3]
assert utils.flat_list([1,[2,3,4],[[3,4],[5,6]]]) == [1,2,3,4,3,4,5,6]
try:
raise RuntimeError("Trial")
except KeyboardInterrupt: raise
except Exception:
assert utils.format_exception() == "RuntimeError: Trial"
else: raise Exception_expected
try:
assert 1 == 2
except KeyboardInterrupt: raise
except Exception:
s = utils.format_exception()
assert s.startswith("AssertionError: ")
assert s.find("tst_utils.py line ") >= 0
else: raise Exception_expected
exercise_indented_display()
exercise_approx_equal()
exercise_file_utils()
exercise_dir_utils()
exercise_group_args()
exercise_round2()
print(utils.format_cpu_times())
def build_angle_start_by_tor_id(mon_lib_atom_names, sites_cart,
rotamer_tor_atom_ids_by_tor_id,
i_q_packed_by_tor_id):
result = {}
atom_indices = sequence_index_dict(seq=mon_lib_atom_names)
for tor_id in i_q_packed_by_tor_id.keys():
d_sites = []
atom_ids = []
for atom_id in rotamer_tor_atom_ids_by_tor_id[tor_id]:
i = atom_indices.get(atom_id)
if (i is None):
return (atom_id, tor_id)
d_sites.append(sites_cart[i])
atom_ids.append(str(atom_id))
dihe = scitbx.math.dihedral_angle(sites=d_sites, deg=True)
if (dihe is None):
raise Sorry(
("scitbx.math.dihedral_angle returned None!\n" +
"Atom IDs: %s\nSites: %s\n") %
(", ".join(atom_ids), ", ".join([str(xyz)
for xyz in d_sites])))
assert dihe is not None
assert tor_id not in result
result[tor_id] = dihe
return result
def report_tors(
mon_lib_atom_names,
sites_cart,
tor_atom_ids_by_tor_id,
target_angles,
verbose):
n_mismatches = 0
i_seq_by_atom_name = sequence_index_dict(seq=mon_lib_atom_names)
for tor_id,atom_ids in tor_atom_ids_by_tor_id.items():
js = [i_seq_by_atom_name.get(ai) for ai in atom_ids]
if (js.count(None) != 0):
angle_model = None
else:
d_sites = [sites_cart[j] for j in js]
angle_model = scitbx.math.dihedral_angle(sites=d_sites, deg=True)
target_angle = target_angles.get(tor_id)
if (angle_model is not None and target_angle is not None):
if (cctbx.geometry_restraints.angle_delta_deg(
angle_1=angle_model,
angle_2=target_angle) > 1.e-5):
annotation = "MISMATCH"
n_mismatches += 1
else:
annotation = "OK_target"
else:
annotation = "no_target"
if (verbose): print tor_id, atom_ids, angle_model, annotation
assert n_mismatches == 0, n_mismatches
def run(args):
assert len(args) == 0
exercise_forward_compatibility()
exercise_misc()
assert utils.sequence_index_dict(["a", "b"]) == {"a": 0, "b": 1}
assert utils.flat_list(0) == [0]
assert utils.flat_list([1, 2, 3]) == [1, 2, 3]
assert utils.flat_list([1, [2, 3, 4], 3]) == [1, 2, 3, 4, 3]
assert utils.flat_list([1, [2, 3, 4],
[[3, 4], [5, 6]]]) == [1, 2, 3, 4, 3, 4, 5, 6]
try:
raise RuntimeError("Trial")
except KeyboardInterrupt:
raise
except Exception:
assert utils.format_exception() == "RuntimeError: Trial"
else:
raise Exception_expected
try:
assert 1 == 2
except KeyboardInterrupt:
raise
except Exception:
s = utils.format_exception()
assert s.startswith("AssertionError: ")
assert s.find("tst_utils.py line ") >= 0
else:
raise Exception_expected
exercise_indented_display()
exercise_approx_equal()
exercise_file_utils()
exercise_dir_utils()
print utils.format_cpu_times()
def run(args):
assert len(args) == 0
if '--exercise-retrieve-unless-exists' in args:
exercise_retrieve_unless_exists()
else:
print 'Skipping exercise_retrieve_unless_exists'
exercise_forward_compatibility()
exercise_misc()
assert utils.sequence_index_dict(["a", "b"]) == {"a": 0, "b": 1}
assert utils.flat_list(0) == [0]
assert utils.flat_list([1,2,3]) == [1,2,3]
assert utils.flat_list([1,[2,3,4],3]) == [1,2,3,4,3]
assert utils.flat_list([1,[2,3,4],[[3,4],[5,6]]]) == [1,2,3,4,3,4,5,6]
try:
raise RuntimeError("Trial")
except KeyboardInterrupt: raise
except Exception:
assert utils.format_exception() == "RuntimeError: Trial"
else: raise Exception_expected
try:
assert 1 == 2
except KeyboardInterrupt: raise
except Exception:
s = utils.format_exception()
assert s.startswith("AssertionError: ")
assert s.find("tst_utils.py line ") >= 0
else: raise Exception_expected
exercise_indented_display()
exercise_approx_equal()
exercise_file_utils()
exercise_dir_utils()
print utils.format_cpu_times()
def report_tors(
mon_lib_atom_names,
sites_cart,
tor_atom_ids_by_tor_id,
target_angles,
verbose):
n_mismatches = 0
i_seq_by_atom_name = sequence_index_dict(seq=mon_lib_atom_names)
for tor_id,atom_ids in tor_atom_ids_by_tor_id.items():
js = [i_seq_by_atom_name.get(ai) for ai in atom_ids]
if (js.count(None) != 0):
angle_model = None
else:
d_sites = [sites_cart[j] for j in js]
angle_model = scitbx.math.dihedral_angle(sites=d_sites, deg=True)
target_angle = target_angles.get(tor_id)
if (angle_model is not None and target_angle is not None):
if (cctbx.geometry_restraints.angle_delta_deg(
angle_1=angle_model,
angle_2=target_angle) > 1.e-5):
annotation = "MISMATCH"
n_mismatches += 1
else:
annotation = "OK_target"
else:
annotation = "no_target"
if (verbose): print tor_id, atom_ids, angle_model, annotation
assert n_mismatches == 0, n_mismatches
def tardy_model(comp_comp_id,
input_atom_names,
mon_lib_atom_names,
sites_cart,
bonds_to_omit,
constrain_dihedrals_with_sigma_less_than_or_equal_to,
external_edge_list=None,
external_clusters=None,
return_none_if_unexpected_degrees_of_freedom=False,
tree_root_atom_names=set(["N", "CA", "C", "O"]),
terminal_backbone_atom_names=set(
["OXT", "HXT", "H1", "H2", "H3"])):
assert len(mon_lib_atom_names) == len(input_atom_names)
assert len(sites_cart) == len(input_atom_names)
atom_indices = sequence_index_dict(seq=mon_lib_atom_names)
fixed_vertices = []
for i, atom_name in enumerate(mon_lib_atom_names):
if (atom_name in tree_root_atom_names):
fixed_vertices.append(i)
if (not (len(fixed_vertices) == len(tree_root_atom_names))):
return None
# check that terminal atoms are bonded correctly
# needed for nonstandard
terminal_bonds = {
"OXT": ["C", "HXT"],
"HXT": ["OXT"],
"H1": ["N"],
"H2": ["N"],
"H3": ["N"],
}
for bond in comp_comp_id.bond_list:
name1, name2 = bond.atom_ids()
if (name1 in terminal_backbone_atom_names
or name2 in terminal_backbone_atom_names):
if name1 in terminal_backbone_atom_names:
term = name1
other = name2
else:
term = name2
other = name1
if other not in terminal_bonds.get(term, []):
terminal_backbone_atom_names.remove(term)
for i, atom_name in enumerate(mon_lib_atom_names):
if (atom_name in terminal_backbone_atom_names):
fixed_vertices.append(i)
bonds_omitted = set()
edge_list = []
for bond in comp_comp_id.bond_list:
bond_atom_ids = bond.atom_ids()
if (bond_atom_ids in bonds_to_omit):
bonds_omitted.add(bond_atom_ids)
else:
ai = [atom_indices.get(atom_id) for atom_id in bond_atom_ids]
if (ai.count(None) == 0):
edge_list.append(tuple(sorted(ai)))
if (external_edge_list is not None):
for eed in external_edge_list:
edge_list.append(tuple(sorted(eed)))
unused = bonds_to_omit.difference(bonds_omitted)
if (len(unused) != 0):
raise Sorry(
"tree_generation_without_bond does not match any bonds: %s" %
str(unused))
if (constrain_dihedrals_with_sigma_less_than_or_equal_to is not None):
if (external_clusters is None):
external_clusters = []
else:
external_clusters = list(external_clusters)
for tor in comp_comp_id.tor_list:
if (tor.value_angle_esd <=
constrain_dihedrals_with_sigma_less_than_or_equal_to):
ai = [atom_indices.get(atom_id) for atom_id in tor.atom_ids()]
if (ai.count(None) == 0):
external_clusters.append(sorted(ai))
for plane in comp_comp_id.get_planes():
ai = []
for atom_id in plane.plane_atoms:
i = atom_indices.get(atom_id)
if (i is not None):
ai.append(i)
external_clusters.append(sorted(ai))
tardy_tree = scitbx.graph.tardy_tree.construct(
n_vertices=len(mon_lib_atom_names),
edge_list=edge_list,
external_clusters=external_clusters,
fixed_vertex_lists=[fixed_vertices]).build_tree()
assert len(tardy_tree.cluster_manager.loop_edges) == 0
tardy_model = scitbx.rigid_body.tardy_model(labels=input_atom_names,
sites=sites_cart,
masses=flex.double(
len(input_atom_names), 1),
tardy_tree=tardy_tree,
potential_obj=None)
joint_dofs = tardy_model.degrees_of_freedom_each_joint()
if (joint_dofs[0] != 0 or not joint_dofs[1:].all_eq(1)):
if (return_none_if_unexpected_degrees_of_freedom):
return None
msg = ["Unexpected degrees of freedom:"]
for dof, cluster in zip(joint_dofs,
tardy_tree.cluster_manager.clusters):
msg.append(" %s: %s" %
(dof, [input_atom_names[i] for i in cluster]))
raise Sorry("\n".join(msg))
return tardy_model
def tardy_model(
comp_comp_id,
input_atom_names,
mon_lib_atom_names,
sites_cart,
bonds_to_omit,
constrain_dihedrals_with_sigma_less_than_or_equal_to,
external_edge_list=None,
external_clusters=None,
return_none_if_unexpected_degrees_of_freedom=False,
tree_root_atom_names=set(["N", "CA", "C", "O"]),
terminal_backbone_atom_names=set(["OXT", "HXT", "H1", "H2", "H3"])):
assert len(mon_lib_atom_names) == len(input_atom_names)
assert len(sites_cart) == len(input_atom_names)
atom_indices = sequence_index_dict(seq=mon_lib_atom_names)
fixed_vertices = []
for i,atom_name in enumerate(mon_lib_atom_names):
if (atom_name in tree_root_atom_names):
fixed_vertices.append(i)
if(not (len(fixed_vertices) == len(tree_root_atom_names))):
return None
# check that terminal atoms are bonded correctly
# needed for nonstandard
terminal_bonds = {
"OXT" : ["C", "HXT"],
"HXT" : ["OXT"],
"H1" : ["N"],
"H2" : ["N"],
"H3" : ["N"],
}
for bond in comp_comp_id.bond_list:
name1, name2 = bond.atom_ids()
if ( name1 in terminal_backbone_atom_names or
name2 in terminal_backbone_atom_names):
if name1 in terminal_backbone_atom_names:
term = name1
other = name2
else:
term = name2
other = name1
if other not in terminal_bonds.get(term, []):
terminal_backbone_atom_names.remove(term)
for i,atom_name in enumerate(mon_lib_atom_names):
if (atom_name in terminal_backbone_atom_names):
fixed_vertices.append(i)
bonds_omitted = set()
edge_list = []
for bond in comp_comp_id.bond_list:
bond_atom_ids = bond.atom_ids()
if (bond_atom_ids in bonds_to_omit):
bonds_omitted.add(bond_atom_ids)
else:
ai = [atom_indices.get(atom_id) for atom_id in bond_atom_ids]
if (ai.count(None) == 0):
edge_list.append(tuple(sorted(ai)))
if (external_edge_list is not None):
for eed in external_edge_list:
edge_list.append(tuple(sorted(eed)))
unused = bonds_to_omit.difference(bonds_omitted)
if (len(unused) != 0):
raise RuntimeError(
"tree_generation_without_bond does not match any bonds: %s"
% str(unused))
if (constrain_dihedrals_with_sigma_less_than_or_equal_to is not None):
if (external_clusters is None):
external_clusters = []
else:
external_clusters = list(external_clusters)
for tor in comp_comp_id.tor_list:
if ( tor.value_angle_esd
<= constrain_dihedrals_with_sigma_less_than_or_equal_to):
ai = [atom_indices.get(atom_id) for atom_id in tor.atom_ids()]
if (ai.count(None) == 0):
external_clusters.append(sorted(ai))
for plane in comp_comp_id.get_planes():
ai = []
for atom_id in plane.plane_atoms:
i = atom_indices.get(atom_id)
if (i is not None):
ai.append(i)
external_clusters.append(sorted(ai))
tardy_tree = scitbx.graph.tardy_tree.construct(
n_vertices=len(mon_lib_atom_names),
edge_list=edge_list,
external_clusters=external_clusters,
fixed_vertex_lists=[fixed_vertices]).build_tree()
assert len(tardy_tree.cluster_manager.loop_edges) == 0
tardy_model = scitbx.rigid_body.tardy_model(
labels=input_atom_names,
sites=sites_cart,
masses=flex.double(len(input_atom_names), 1),
tardy_tree=tardy_tree,
potential_obj=None)
joint_dofs = tardy_model.degrees_of_freedom_each_joint()
if (joint_dofs[0] != 0 or not joint_dofs[1:].all_eq(1)):
if (return_none_if_unexpected_degrees_of_freedom):
return None
msg = ["Unexpected degrees of freedom:"]
for dof,cluster in zip(joint_dofs,tardy_tree.cluster_manager.clusters):
msg.append(" %s: %s" % (dof, [input_atom_names[i] for i in cluster]))
raise RuntimeError("\n".join(msg))
return tardy_model