def exercise_stl_set_unsigned():
a = shared.stl_set_unsigned()
assert a.size() == 0
a = shared.stl_set_unsigned([(2,1)])
assert a.size() == 1
assert tuple(a[0]) == (1, 2)
a = shared.stl_set_unsigned([(2,1),(3,5,2)])
assert native(a) == [(1, 2), (2, 3, 5)]
#
from scitbx.array_family import flex
b = shared.stl_vector_unsigned()
s = flex.size_t()
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert a.size() == 3
assert a[2].size() == 0
b.append([2,1])
b.append([])
b.append([4,3,2])
s.append(2)
s.append(1)
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert tuple(a[3]) == (2,3,4)
s[1] = 0
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert tuple(a[4]) == (1,2,3,4)
assert native(a) == [(1, 2), (2, 3, 5), (), (2, 3, 4), (1, 2, 3, 4)]
#
s = pickle.dumps(a, 1)
l = pickle.loads(s)
assert len(l) == len(a)
for ae,le in zip(a,l):
assert list(ae) == list(le)
def extract_trace (pdb_hierarchy, selection_cache=None) :
from scitbx.array_family import shared
if selection_cache is None :
selection_cache = pdb_hierarchy.atom_selection_cache()
last_atom = None
vertices = selection_cache.selection(
"(name ' CA ' or name ' P ') and (altloc 'A' or altloc ' ')")
last_i_seq = None
last_labels = None
atoms = pdb_hierarchy.atoms()
bonds = shared.stl_set_unsigned(atoms.size())
for i_seq, atom in enumerate(atoms) :
labels = atom.fetch_labels()
if vertices[i_seq] :
if last_i_seq is not None :
if (labels.chain_id == last_labels.chain_id and
labels.model_id == last_labels.model_id and
labels.resseq_as_int() == (last_labels.resseq_as_int() + 1) and
((labels.altloc == last_labels.altloc) or
(labels.altloc == "A" and last_labels.altloc == "") or
(labels.altloc == "" and last_labels.altloc == "A"))) :
bonds[last_i_seq].append(i_seq)
bonds[i_seq].append(last_i_seq)
last_i_seq = i_seq
last_labels = labels
return bonds
def set_noncovalent_bonds(self, model_id, bonded_atoms, auto_show=False):
if isinstance(bonded_atoms, list):
from scitbx.array_family import shared
bonded_atoms = shared.stl_set_unsigned(bonded_atoms)
model = self.get_model(model_id)
if model is not None:
model.set_noncovalent_bonds(bonded_atoms)
if auto_show:
model.flag_show_noncovalent_bonds = True
self.update_scene = True
def set_noncovalent_bonds (self, model_id, bonded_atoms, auto_show=False) :
if isinstance(bonded_atoms, list) :
from scitbx.array_family import shared
bonded_atoms = shared.stl_set_unsigned(bonded_atoms)
model = self.get_model(model_id)
if model is not None :
model.set_noncovalent_bonds(bonded_atoms)
if auto_show :
model.flag_show_noncovalent_bonds = True
self.update_scene = True
def exercise():
bonds = shared.stl_set_unsigned([[1, 2, 3, 5], [0, 4], [0], [0], [1],
[0, 6, 7, 8], [5], [5], [5], []])
atoms_drawable = flex.bool([True for i in xrange(0, 10)])
atoms_drawable_non_h = flex.bool(
[True, True, False, False, False, True, False, False, False, True])
# all atoms drawable
visibility = gltbx.viewer_utils.atom_visibility(
bonds=bonds, atoms_drawable=atoms_drawable, flag_show_points=True)
assert (list(visibility.bonds_visible) == [
True, True, True, True, True, True, True, True, True, False
])
assert (list(visibility.points_visible) == [
False, False, False, False, False, False, False, False, False, True
])
# hydrogens off, points on
visibility = gltbx.viewer_utils.atom_visibility(
bonds=bonds,
atoms_drawable=atoms_drawable_non_h,
flag_show_points=True)
assert (list(visibility.bonds_visible) == [
True, True, False, False, False, True, False, False, False, False
])
assert (list(visibility.points_visible) == [
False, False, False, False, False, False, False, False, False, True
])
# equivalent to "not element H"
atoms_selected_non_h = flex.bool(
[True, True, False, False, False, True, False, False, False, True])
visibility.get_selection_visibility(bonds=bonds,
atoms_selected=atoms_selected_non_h)
assert (list(visibility.selected_points_visible) == [
False, False, False, False, False, False, False, False, False, True
])
# no hydrogens, no points
visibility = gltbx.viewer_utils.atom_visibility(
bonds=bonds,
atoms_drawable=atoms_drawable_non_h,
flag_show_points=False)
assert (list(visibility.bonds_visible) == [
True, True, False, False, False, True, False, False, False, False
])
assert (not True in list(visibility.points_visible))
visibility.get_selection_visibility(bonds=bonds,
atoms_selected=atoms_selected_non_h)
assert (not True in list(visibility.selected_points_visible))
def build_simple_two_way_bond_sets(sites_cart,
elements,
conformer_indices=None,
search_max_distance=None,
tolerance_factor_expected_bond_length=1.3,
fallback_expected_bond_length=2.0,
fallback_search_max_distance=3.0):
assert sites_cart.size() == elements.size()
assert (isinstance(tolerance_factor_expected_bond_length, float)
or isinstance(tolerance_factor_expected_bond_length, int))
assert (isinstance(fallback_expected_bond_length, float)
or isinstance(fallback_expected_bond_length, int))
assert (isinstance(fallback_search_max_distance, float)
or isinstance(fallback_search_max_distance, int))
if (conformer_indices is None):
conformer_indices = flex.size_t(sites_cart.size(), 0)
stripped_elements = elements.strip().upper()
if (search_max_distance is None):
search_max_distance = 2 * max(
[vdw_radii.get(e, 0.0) for e in stripped_elements])
if (search_max_distance == 0.0):
search_max_distance = fallback_search_max_distance
else:
search_max_distance *= tolerance_factor_expected_bond_length
else:
assert isinstance(search_max_distance, float)
box_symmetry = cctbx.crystal.symmetry(
unit_cell=cctbx.uctbx.non_crystallographic_unit_cell(
sites_cart=sites_cart,
buffer_layer=search_max_distance *
(1 + 1.e-4)), # uncritical tolerance
space_group_symbol="P1").special_position_settings()
asu_mappings = box_symmetry.asu_mappings(
buffer_thickness=search_max_distance, sites_cart=sites_cart)
pair_generator = cctbx.crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=search_max_distance,
minimal=True)
result = shared.stl_set_unsigned(sites_cart.size())
return pair_generator.distance_based_simple_two_way_bond_sets(
elements=stripped_elements,
conformer_indices=conformer_indices,
expected_bond_lengths=expected_bond_lengths,
vdw_radii=vdw_radii,
fallback_expected_bond_length=fallback_expected_bond_length,
tolerance_factor_expected_bond_length=
tolerance_factor_expected_bond_length)
def build_simple_two_way_bond_sets(
sites_cart,
elements,
conformer_indices=None,
search_max_distance=None,
tolerance_factor_expected_bond_length=1.3,
fallback_expected_bond_length=2.0,
fallback_search_max_distance=3.0,
):
assert sites_cart.size() == elements.size()
assert isinstance(tolerance_factor_expected_bond_length, float) or isinstance(
tolerance_factor_expected_bond_length, int
)
assert isinstance(fallback_expected_bond_length, float) or isinstance(fallback_expected_bond_length, int)
assert isinstance(fallback_search_max_distance, float) or isinstance(fallback_search_max_distance, int)
if conformer_indices is None:
conformer_indices = flex.size_t(sites_cart.size(), 0)
stripped_elements = elements.strip().upper()
if search_max_distance is None:
search_max_distance = 2 * max([vdw_radii.get(e, 0.0) for e in stripped_elements])
if search_max_distance == 0.0:
search_max_distance = fallback_search_max_distance
else:
search_max_distance *= tolerance_factor_expected_bond_length
else:
assert isinstance(search_max_distance, float)
box_symmetry = cctbx.crystal.symmetry(
unit_cell=cctbx.uctbx.non_crystallographic_unit_cell(
sites_cart=sites_cart, buffer_layer=search_max_distance * (1 + 1.0e-4)
), # uncritical tolerance
space_group_symbol="P1",
).special_position_settings()
asu_mappings = box_symmetry.asu_mappings(buffer_thickness=search_max_distance, sites_cart=sites_cart)
pair_generator = cctbx.crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=search_max_distance, minimal=True
)
result = shared.stl_set_unsigned(sites_cart.size())
return pair_generator.distance_based_simple_two_way_bond_sets(
elements=stripped_elements,
conformer_indices=conformer_indices,
expected_bond_lengths=expected_bond_lengths,
vdw_radii=vdw_radii,
fallback_expected_bond_length=fallback_expected_bond_length,
tolerance_factor_expected_bond_length=tolerance_factor_expected_bond_length,
)
def get_simple_bonds(self, selection_phil=None):
# assert 0 # used in GUI to draw bonds
# this function wants
# shared.stl_set_unsigned([(i_seq, j_seq),(i_seq, j_seq)])
desired_annotation = None
if (selection_phil is not None):
if isinstance(selection_phil, str):
selection_phil = iotbx.phil.parse(selection_phil)
params = sec_str_master_phil.fetch(source=selection_phil).extract()
desired_annotation = iotbx.pdb.secondary_structure.annotation.from_phil(
phil_helices=params.secondary_structure.protein.helix,
phil_sheets=params.secondary_structure.protein.sheet,
pdb_hierarchy=self.pdb_hierarchy)
else:
desired_annotation = self.actual_sec_str
hb_proxies, hb_angles = self.create_protein_hbond_proxies(
annotation=desired_annotation, log=sys.stdout)
from scitbx.array_family import shared
simple_bonds = []
for p in hb_proxies:
simple_bonds.append(p.i_seqs)
return shared.stl_set_unsigned(simple_bonds)
def get_simple_bonds (self, selection_phil=None) :
# assert 0 # used in GUI to draw bonds
# this function wants
# shared.stl_set_unsigned([(i_seq, j_seq),(i_seq, j_seq)])
desired_annotation = None
if (selection_phil is not None) :
if isinstance(selection_phil, str) :
selection_phil = iotbx.phil.parse(selection_phil)
params = sec_str_master_phil.fetch(source=selection_phil).extract()
desired_annotation = iotbx.pdb.secondary_structure.annotation.from_phil(
phil_helices=params.secondary_structure.protein.helix,
phil_sheets=params.secondary_structure.protein.sheet,
pdb_hierarchy=self.pdb_hierarchy)
else :
desired_annotation = self.actual_sec_str
hb_proxies = self.create_protein_hbond_proxies(
annotation=desired_annotation,
log=sys.stdout)
from scitbx.array_family import shared
simple_bonds = []
for p in hb_proxies:
simple_bonds.append(p.i_seqs)
return shared.stl_set_unsigned(simple_bonds)
def exercise () :
bonds = shared.stl_set_unsigned([
[1, 2, 3, 5],
[0, 4],
[0],
[0],
[1],
[0, 6, 7, 8],
[5],
[5],
[5],
[]
])
atoms_drawable = flex.bool([True for i in xrange(0, 10) ])
atoms_drawable_non_h = flex.bool(
[True, True, False, False, False, True, False, False, False, True]
)
# all atoms drawable
visibility = gltbx.viewer_utils.atom_visibility(
bonds = bonds,
atoms_drawable = atoms_drawable,
flag_show_points = True
)
assert (list(visibility.bonds_visible) ==
[True, True, True, True, True, True, True, True, True, False]
)
assert (list(visibility.points_visible) ==
[False, False, False, False, False, False, False, False, False, True]
)
# hydrogens off, points on
visibility = gltbx.viewer_utils.atom_visibility(
bonds = bonds,
atoms_drawable = atoms_drawable_non_h,
flag_show_points = True
)
assert (list(visibility.bonds_visible) ==
[True, True, False, False, False, True, False, False, False, False]
)
assert (list(visibility.points_visible) ==
[False, False, False, False, False, False, False, False, False, True]
)
# equivalent to "not element H"
atoms_selected_non_h = flex.bool(
[True, True, False, False, False, True, False, False, False, True]
)
visibility.get_selection_visibility(
bonds = bonds,
atoms_selected = atoms_selected_non_h
)
assert (list(visibility.selected_points_visible) ==
[False, False, False, False, False, False, False, False, False, True]
)
# no hydrogens, no points
visibility = gltbx.viewer_utils.atom_visibility(
bonds = bonds,
atoms_drawable = atoms_drawable_non_h,
flag_show_points = False
)
assert (list(visibility.bonds_visible) ==
[True, True, False, False, False, True, False, False, False, False]
)
assert (not True in list(visibility.points_visible))
visibility.get_selection_visibility(
bonds = bonds,
atoms_selected = atoms_selected_non_h
)
assert (not True in list(visibility.selected_points_visible))