def run(args):
assert len(args) == 0
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
from scitbx.array_family import flex
sites_cart = flex.vec3_double([
(25.655, 43.266, 42.630),
(24.038, 43.853, 43.337),
(23.048, 44.525, 43.290),
(21.223, 44.207, 41.475),
(24.951, 47.170, 37.585),
(19.298, 46.942, 51.808)])
elements = flex.std_string(["S", "C", "N", "CU", "ZN", "CA"])
bond_list = build_simple_two_way_bond_sets(
sites_cart=sites_cart, elements=elements)
assert [sorted(b) for b in bond_list] == [[1], [0,2], [1,3], [2], [], []]
#
# caffeine
sites_cart = flex.vec3_double([
(-2.986, 0.015, 1.643),
(-1.545, 0.015, 1.643),
(-0.733, 0.015, 2.801),
(0.592, 0.015, 2.395),
(0.618, 0.015, 1.034),
(1.758, 0.015, 0.102),
(3.092, -0.06, 0.694),
(1.525, 0.015, -1.360),
(2.489, -0.024, -2.139),
(0.158, 0.015, -1.888),
(-0.025, 0.024, -3.330),
(-0.986, 0.015, -0.959),
(-2.155, 0.008, -1.408),
(-0.733, 0.015, 0.565),
(-3.346, 0.016, 2.662),
(-3.347, 0.896, 1.133),
(-3.347, -0.868, 1.136),
(-1.083, 0.02, 3.822),
(3.184, -0.975, 1.26),
(3.245, 0.785, 1.348),
(3.835, -0.047, -0.09),
(0.508, 0.861, -3.756),
(-1.076, 0.113, -3.560),
(0.358, -0.896, -3.748)
])
elements = flex.std_string([
' C', ' N', ' C', ' N', ' C', ' N', ' C', ' C', ' O', ' N', ' C', ' C',
' O', ' C', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H'])
bonds = build_simple_two_way_bond_sets(
sites_cart=sites_cart, elements=elements)
assert bonds.size() == sites_cart.size()
assert list(bonds[0]) == [1, 14, 15, 16]
#
print "OK"
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 set_points_and_lines(O, app, minimum_covering_sphere_view_scale=1.3):
pdb_atoms = app.pdb_atoms
pdb_atoms.set_chemical_element_simple_if_necessary()
atom_tmp_sentinel = pdb_atoms.reset_tmp(first_value=0, increment=0)
for i, rg in enumerate(app.pdb_hierarchy.residue_groups()):
for atom in rg.atoms():
atom.tmp = i
O.points = pdb_atoms.extract_xyz()
if (app.co.serial_labels):
m = ""
need_m = (app.pdb_hierarchy.models_size() != 1)
for mdl in app.pdb_hierarchy.models():
if (need_m): m = mdl.id.strip() + ":"
for i in range(mdl.atoms_size()):
O.labels.append(m + str(i))
assert len(O.labels) == O.points.size()
else:
rg_done = set()
for atom in pdb_atoms:
i = atom.tmp
if (i not in rg_done):
rg_done.add(i)
l = atom.id_str()
else:
l = atom.name
O.labels.append(l)
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
bond_sets = build_simple_two_way_bond_sets(
sites_cart=O.points, elements=pdb_atoms.extract_element())
for i, bond_set in enumerate(bond_sets):
for j in bond_set:
if (i < j):
line = (i, j)
ai, aj = [pdb_atoms[_] for _ in line]
if (ai.is_in_same_conformer_as(aj)):
O.line_i_seqs.append(line)
if (ai.tmp == aj.tmp):
if (ai.tmp % 2 == 0):
color = (0, 0, 1)
else:
color = (0, 1, 0)
else:
color = (1, 0, 0)
O.line_colors[line] = color
del atom_tmp_sentinel
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius() * minimum_covering_sphere_view_scale)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
_ = app.co.labels_threshold
O.flag_show_labels = (_ == 0 or len(O.points) <= _)
O.labels_display_list = None
O.lines_display_list = None
O.points_display_list = None
def run(args):
assert len(args) == 0
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
from scitbx.array_family import flex
sites_cart = flex.vec3_double([(25.655, 43.266, 42.630),
(24.038, 43.853, 43.337),
(23.048, 44.525, 43.290),
(21.223, 44.207, 41.475),
(24.951, 47.170, 37.585),
(19.298, 46.942, 51.808)])
elements = flex.std_string(["S", "C", "N", "CU", "ZN", "CA"])
bond_list = build_simple_two_way_bond_sets(sites_cart=sites_cart,
elements=elements)
assert [sorted(b) for b in bond_list] == [[1], [0, 2], [1, 3], [2], [], []]
#
# caffeine
sites_cart = flex.vec3_double([
(-2.986, 0.015, 1.643), (-1.545, 0.015, 1.643), (-0.733, 0.015, 2.801),
(0.592, 0.015, 2.395), (0.618, 0.015, 1.034), (1.758, 0.015, 0.102),
(3.092, -0.06, 0.694), (1.525, 0.015, -1.360), (2.489, -0.024, -2.139),
(0.158, 0.015, -1.888), (-0.025, 0.024, -3.330),
(-0.986, 0.015, -0.959), (-2.155, 0.008, -1.408),
(-0.733, 0.015, 0.565), (-3.346, 0.016, 2.662), (-3.347, 0.896, 1.133),
(-3.347, -0.868, 1.136), (-1.083, 0.02, 3.822), (3.184, -0.975, 1.26),
(3.245, 0.785, 1.348), (3.835, -0.047, -0.09), (0.508, 0.861, -3.756),
(-1.076, 0.113, -3.560), (0.358, -0.896, -3.748)
])
elements = flex.std_string([
' C', ' N', ' C', ' N', ' C', ' N', ' C', ' C', ' O', ' N', ' C', ' C',
' O', ' C', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H', ' H'
])
bonds = build_simple_two_way_bond_sets(sites_cart=sites_cart,
elements=elements)
assert bonds.size() == sites_cart.size()
assert list(bonds[0]) == [1, 14, 15, 16]
#
print "OK"
def set_points_and_lines(
O,
app,
minimum_covering_sphere_view_scale=1.3):
pdb_atoms = app.pdb_atoms
pdb_atoms.set_chemical_element_simple_if_necessary()
atom_tmp_sentinel = pdb_atoms.reset_tmp(first_value=0, increment=0)
for i,rg in enumerate(app.pdb_hierarchy.residue_groups()):
for atom in rg.atoms():
atom.tmp = i
O.points = pdb_atoms.extract_xyz()
if (app.co.serial_labels):
m = ""
need_m = (app.pdb_hierarchy.models_size() != 1)
for mdl in app.pdb_hierarchy.models():
if (need_m): m = mdl.id.strip() + ":"
for i in xrange(mdl.atoms_size()):
O.labels.append(m+str(i))
assert len(O.labels) == O.points.size()
else:
rg_done = set()
for atom in pdb_atoms:
i = atom.tmp
if (i not in rg_done):
rg_done.add(i)
l = atom.id_str()
else:
l = atom.name
O.labels.append(l)
from cctbx.crystal.distance_based_connectivity import \
build_simple_two_way_bond_sets
bond_sets = build_simple_two_way_bond_sets(
sites_cart=O.points,
elements=pdb_atoms.extract_element())
for i,bond_set in enumerate(bond_sets):
for j in bond_set:
if (i < j):
line = (i,j)
ai, aj = [pdb_atoms[_] for _ in line]
if (ai.is_in_same_conformer_as(aj)):
O.line_i_seqs.append(line)
if (ai.tmp == aj.tmp):
if (ai.tmp % 2 == 0):
color = (0,0,1)
else:
color = (0,1,0)
else:
color = (1,0,0)
O.line_colors[line] = color
del atom_tmp_sentinel
from scitbx.math import minimum_covering_sphere, sphere_3d
mcs = minimum_covering_sphere(O.points, epsilon=1.e-2)
O.minimum_covering_sphere = sphere_3d(
center=mcs.center(),
radius=mcs.radius()*minimum_covering_sphere_view_scale)
O.flag_show_minimum_covering_sphere = False
O.flag_show_rotation_center = False
_ = app.co.labels_threshold
O.flag_show_labels = (_ == 0 or len(O.points) <= _)
O.labels_display_list = None
O.lines_display_list = None
O.points_display_list = None