def angles(O):
return graph_utils.extract_edge_list(
graph_utils.bond_bending_edge_sets(
edge_sets=graph_utils.construct_edge_sets(
n_vertices=len(O.sites),
edge_list=O.bonds),
omit_bonds=True))
def angles(O):
return graph_utils.extract_edge_list(
graph_utils.bond_bending_edge_sets(
edge_sets=graph_utils.construct_edge_sets(n_vertices=len(
O.sites),
edge_list=O.bonds),
omit_bonds=True))
def process(file_name, clash_threshold=2.0):
time_start = time.time()
pdb_inp = iotbx.pdb.input(file_name=file_name)
pdb_atoms = pdb_inp.atoms()
print "Time reading pdb file: %.2f" % (time.time() - time_start)
print "Number of atoms:", pdb_atoms.size()
pdb_atoms.set_chemical_element_simple_if_necessary()
sites_cart = pdb_atoms.extract_xyz()
#
time_start = time.time()
bond_list = extract_edge_list(edge_sets=build_simple_two_way_bond_sets(
sites_cart=sites_cart,
elements=pdb_atoms.extract_element()))
print "Time building bond list: %.2f" % (time.time() - time_start)
print "Number of bonds:", len(bond_list)
#
time_start = time.time()
tardy_tree = scitbx.graph.tardy_tree.construct(
sites=sites_cart,
edge_list=bond_list)
print "Time building tardy tree: %.2f" % (time.time() - time_start)
#
time_start = time.time()
tardy_model = scitbx.rigid_body.tardy_model(
labels=[atom.id_str() for atom in pdb_atoms],
sites=sites_cart,
masses=[1]*sites_cart.size(),
tardy_tree=tardy_tree,
potential_obj=None)
q_size_each_joint = tardy_model.q_size_each_joint()
q_fixed = tardy_model.pack_q()[:q_size_each_joint[0]]
assert q_size_each_joint[1:].all_eq(1) # must all be revolute joints
q_size_moving = q_size_each_joint.size() - 1
print "Time building tardy model: %.2f" % (time.time() - time_start)
print "Degrees of freedom:", q_size_moving
#
mt = flex.mersenne_twister()
two_pi = 2 * math.pi
clash_detector = build_clash_detector(
n_sites=sites_cart.size(),
bond_list=bond_list,
threshold=clash_threshold)
time_start = time.time()
n_conf = 10000
n_clash_conf = 0
for i_conf in xrange(n_conf):
q = q_fixed.deep_copy()
q.extend(mt.random_double(size=q_size_moving)*two_pi)
tardy_model.unpack_q(q_packed=q)
conf_sites_cart = tardy_model.sites_moved()
if (clash_detector.has_clash(sites_cart=conf_sites_cart)):
n_clash_conf += 1
time_diff = time.time() - time_start
print "time / %d conf: %.2f seconds" % (n_conf, time_diff)
print "time / conf: %.3f milli seconds" % (time_diff / n_conf * 1000)
if (time_diff != 0):
print "conf / second: %.2f" % (n_conf / time_diff)
print "Fraction of conformations with clashes: %d / %d = %.2f %%" % (
n_clash_conf, n_conf, 100. * n_clash_conf / n_conf)
def arch_dof(n_vertices, edge_list):
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=edge_list)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
dofs = [rigidity.determine_degrees_of_freedom(
n_dim=3, n_vertices=n_vertices, edge_list=bbel, method=method)
for method in ["float", "integer"]]
assert dofs[0] == dofs[1]
return es, dofs[0]
def arch_dof(n_vertices, edge_list):
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=edge_list)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
dofs = [rigidity.determine_degrees_of_freedom(
n_dim=3, n_vertices=n_vertices, edge_list=bbel, method=method)
for method in ["float", "integer"]]
assert dofs[0] == dofs[1]
return es, dofs[0]
def find_cluster_loops(O):
assert O.find_cluster_loop_repeats is None
if (O.edge_sets is None):
O.find_cluster_loop_repeats = 0
return
O.find_cluster_loop_repeats = -1
cm = O.cluster_manager
while True:
O.find_cluster_loop_repeats += 1
cm.merge_clusters_with_multiple_connections(edge_sets=O.edge_sets)
ces = cm.cluster_edge_sets(edge_list=O.edge_list)
cel = extract_edge_list(edge_sets=ces)
ctt = construct(n_vertices=len(cm.clusters), edge_list=cel)
ccm = ctt.cluster_manager
ccm.merge_clusters_with_multiple_connections(edge_sets=ctt.edge_sets)
if (len(ccm.clusters) == len(cm.clusters)):
break
for cc in ccm.clusters:
cii = cc[0]
for cij in cc[1:]:
cii = cm.connect_clusters(cii=cii, cij=cij, optimize=True)
cm.tidy()
return O
def find_cluster_loops(O):
assert O.find_cluster_loop_repeats is None
if (O.edge_sets is None):
O.find_cluster_loop_repeats = 0
return
O.find_cluster_loop_repeats = -1
cm = O.cluster_manager
while True:
O.find_cluster_loop_repeats += 1
cm.merge_clusters_with_multiple_connections(edge_sets=O.edge_sets)
ces = cm.cluster_edge_sets(edge_list=O.edge_list)
cel = extract_edge_list(edge_sets=ces)
ctt = construct(n_vertices=len(cm.clusters), edge_list=cel)
ccm = ctt.cluster_manager
ccm.merge_clusters_with_multiple_connections(
edge_sets=ctt.edge_sets)
if (len(ccm.clusters) == len(cm.clusters)):
break
for cc in ccm.clusters:
cii = cc[0]
for cij in cc[1:]:
cii = cm.connect_clusters(cii=cii, cij=cij, optimize=True)
cm.tidy()
return O
def extract_edge_list(O):
return extract_edge_list(edge_sets=O.edge_sets)
def run(args):
assert len(args) == 0
#
el = []
n_vertices = 0
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == 0
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == 0
bbel = utils.extract_edge_list(edge_sets=bbes)
assert len(bbel) == 0
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert len(piel) == 0
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == 0
#
el = [(0,1), (1,2), (2,3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == n_vertices
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == n_vertices
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0,1), (0,2), (1,2), (1,3), (2,3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == n_vertices
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0,2), (1,3)]
#
el = [(0,1), (1,2), (2,3), (3,4), (4,5), (5,6), (6,7)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0, 1), (0, 2),
(1, 2), (1, 3),
(2, 3), (2, 4),
(3, 4), (3, 5),
(4, 5), (4, 6),
(5, 6), (5, 7),
(6, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (1,4), (2,5), (3,6), (4,7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0, 2),
(1, 3),
(2, 4),
(3, 5),
(4, 6),
(5, 7)]
#
el = [(0,1), (1,2), (2,3), (0,3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0,1), (0,2), (0,3), (1,2), (1,3), (2,3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == []
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0,1), (1,2), (2,3), (3,4), (4,5), (0,5)]
n_vertices = 6
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0,1), (0,2), (0,4), (0,5),
(1,2), (1,3), (1,5),
(2,3), (2,4),
(3,4), (3,5),
(4,5)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (1,4), (2,5)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0,2), (0,4),
(1,3), (1,5),
(2,4),
(3,5)]
#
el = [(0,1), (1,2), (2,3), (2,6), (3,4), (3,7), (4,5), (0,5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0,1), (0,2), (0,4), (0,5),
(1,2), (1,3), (1,5), (1,6),
(2,3), (2,4), (2,6), (2,7),
(3,4), (3,5), (3,6), (3,7),
(4,5), (4,7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (0,6), (1,4), (1,7), (2,5), (4,6), (5,7), (6,7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0,2), (0,4),
(1,3), (1,5), (1,6),
(2,4), (2,7),
(3,5), (3,6),
(4,7)]
#
el = [(0,1), (1,2), (2,3), (2,6), (3,4), (3,7), (4,5), (0,5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 0
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 1
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1,3])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 2
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1,0])
assert sub.edge_list == [(0,1)]
assert len(sub.edge_sets()) == 2
assert sub.reindexing_dict == {0: 1, 1: 0}
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[6,7,3,2])
assert sub.edge_list == [(1,2), (2,3), (0,3)]
assert len(sub.edge_sets()) == 4
assert sub.reindexing_dict == {2: 3, 3: 2, 6: 0, 7: 1}
#
exercise_tree_marking()
#
print "OK"
def extract_edge_list(O): return extract_edge_list(edge_sets=O.edge_sets)
def run(args):
assert len(args) == 0
#
el = []
n_vertices = 0
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == 0
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == 0
bbel = utils.extract_edge_list(edge_sets=bbes)
assert len(bbel) == 0
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert len(piel) == 0
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == 0
#
el = [(0, 1), (1, 2), (2, 3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == n_vertices
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == n_vertices
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == n_vertices
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 7)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (1, 2), (1, 3), (2, 3), (2, 4), (3, 4),
(3, 5), (4, 5), (4, 6), (5, 6), (5, 7), (6, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (1, 4), (2, 5), (3, 6), (4, 7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3), (2, 4), (3, 5), (4, 6), (5, 7)]
#
el = [(0, 1), (1, 2), (2, 3), (0, 3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == []
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (0, 5)]
n_vertices = 6
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 4), (0, 5), (1, 2), (1, 3), (1, 5),
(2, 3), (2, 4), (3, 4), (3, 5), (4, 5)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (1, 4), (2, 5)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (0, 4), (1, 3), (1, 5), (2, 4), (3, 5)]
#
el = [(0, 1), (1, 2), (2, 3), (2, 6), (3, 4), (3, 7), (4, 5), (0, 5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 4), (0, 5), (1, 2), (1, 3), (1, 5),
(1, 6), (2, 3), (2, 4), (2, 6), (2, 7), (3, 4), (3, 5),
(3, 6), (3, 7), (4, 5), (4, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (0, 6), (1, 4), (1, 7), (2, 5), (4, 6), (5, 7),
(6, 7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (0, 4), (1, 3), (1, 5), (1, 6), (2, 4), (2, 7),
(3, 5), (3, 6), (4, 7)]
#
el = [(0, 1), (1, 2), (2, 3), (2, 6), (3, 4), (3, 7), (4, 5), (0, 5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 0
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 1
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1, 3])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 2
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1, 0])
assert sub.edge_list == [(0, 1)]
assert len(sub.edge_sets()) == 2
assert sub.reindexing_dict == {0: 1, 1: 0}
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[6, 7, 3, 2])
assert sub.edge_list == [(1, 2), (2, 3), (0, 3)]
assert len(sub.edge_sets()) == 4
assert sub.reindexing_dict == {2: 3, 3: 2, 6: 0, 7: 1}
#
exercise_tree_marking()
#
print("OK")