def exercise_zeolite_atlas(distance_cutoff=3.5):
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print("Skipping exercise_zeolite_atlas(): input file not available")
return
with open(atlas_file) as f:
all_entries = strudat.read_all_entries(f)
for i, entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if ("--full" in sys.argv[1:] or i % 20 == 0):
tst_direct_space_asu.exercise_neighbors_pair_generators(
structure=structure, verbose="--Verbose" in sys.argv[1:])
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
bond_counts = flex.size_t(structure.scatterers().size(), 0)
for pair in pair_generator:
bond_counts[pair.i_seq] += 1
if (pair.j_sym == 0):
bond_counts[pair.j_seq] += 1
for atom, bond_count in zip(entry.atoms, bond_counts):
assert atom.connectivity is not None
assert atom.connectivity == bond_count
def check_distances(sites_cart, point_distance, verbose):
asu_mappings = non_crystallographic_asu_mappings(sites_cart=sites_cart)
distance_cutoff = point_distance * math.sqrt(2) * 0.99
simple_pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
assert simple_pair_generator.count_pairs() == pair_generator.count_pairs()
pair_generator.restart()
neighbors = {}
for pair in pair_generator:
assert pair.j_seq != pair.i_seq
assert pair.j_sym == 0
assert approx_equal(pair.dist_sq, point_distance**2)
neighbors[pair.i_seq] = neighbors.get(pair.i_seq, 0) + 1
neighbors[pair.j_seq] = neighbors.get(pair.j_seq, 0) + 1
n_dict = {}
for n in neighbors.values():
n_dict[n] = n_dict.get(n, 0) + 1
if (verbose):
print n_dict
if (len(neighbors) > 0):
assert max(neighbors.values()) <= 12
def get_crystal_contact_operators(hierarchy, crystal_symmetry,
distance_cutoff):
"""Use an alternate method to identify the symmetry operations required to generate crystal contacts"""
# Extract the xray structure from the reference hierarchy
struc = hierarchy.extract_xray_structure(crystal_symmetry=crystal_symmetry)
atoms = hierarchy.atoms()
# Extract the mappings that will tell us the adjacent symmetry copies
asu_mappings = struc.asu_mappings(buffer_thickness=distance_cutoff)
uc = asu_mappings.unit_cell()
# Symmetry operations for each atom
mappings = asu_mappings.mappings()
# There should be one mappings list per atom
assert len(struc.scatterers()) == len(mappings)
# Get all atom pairs within distance_cutoff distance
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings, distance_cutoff=distance_cutoff)
sym_operations = []
for pair in pair_generator:
# obtain rt_mx_ji - symmetry operator that should be applied to j-th atom
# to transfer it to i-th atom
rt_mx_i = asu_mappings.get_rt_mx_i(pair)
rt_mx_j = asu_mappings.get_rt_mx_j(pair)
rt_mx_ji = rt_mx_i.inverse().multiply(rt_mx_j)
# if it is not a unit matrix, that is symmetry related pair of atoms
if not rt_mx_ji.is_unit_mx():
if rt_mx_ji not in sym_operations:
sym_operations.append(rt_mx_ji)
return sym_operations
def exercise_zeolite_atlas(distance_cutoff=3.5):
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print "Skipping exercise_zeolite_atlas(): input file not available"
return
all_entries = strudat.read_all_entries(open(atlas_file))
for i,entry in enumerate(all_entries.entries):
structure = entry.as_xray_structure()
if ("--full" in sys.argv[1:] or i % 20 == 0):
tst_direct_space_asu.exercise_neighbors_pair_generators(
structure=structure,
verbose="--Verbose" in sys.argv[1:])
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
bond_counts = flex.size_t(structure.scatterers().size(), 0)
for pair in pair_generator:
bond_counts[pair.i_seq] += 1
if (pair.j_sym == 0):
bond_counts[pair.j_seq] += 1
for atom,bond_count in zip(entry.atoms, bond_counts):
assert atom.connectivity is not None
assert atom.connectivity == bond_count
def sel_within(self, radius, primary_selection):
assert radius > 0
assert self.special_position_settings is not None
return crystal.neighbors_fast_pair_generator(
asu_mappings=self.special_position_settings.asu_mappings(
buffer_thickness=radius,
sites_cart=self.root.atoms().extract_xyz()),
distance_cutoff=radius).neighbors_of(
primary_selection=primary_selection)
def sel_within(self, radius, primary_selection):
assert radius > 0
assert self.special_position_settings is not None
return crystal.neighbors_fast_pair_generator(
asu_mappings=self.special_position_settings.asu_mappings(
buffer_thickness=radius,
sites_cart=self.root.atoms().extract_xyz()),
distance_cutoff=radius).neighbors_of(
primary_selection=primary_selection)
def get_pair_generator(crystal_symmetry, buffer_thickness, sites_cart):
sst = crystal_symmetry.special_position_settings().site_symmetry_table(
sites_cart=sites_cart)
from cctbx import crystal
conn_asu_mappings = crystal_symmetry.special_position_settings().\
asu_mappings(buffer_thickness = buffer_thickness)
conn_asu_mappings.process_sites_cart(original_sites=sites_cart,
site_symmetry_table=sst)
conn_pair_asu_table = crystal.pair_asu_table(
asu_mappings=conn_asu_mappings)
conn_pair_asu_table.add_all_pairs(distance_cutoff=buffer_thickness)
pair_generator = crystal.neighbors_fast_pair_generator(
conn_asu_mappings, distance_cutoff=buffer_thickness)
return group_args(pair_generator=pair_generator,
conn_asu_mappings=conn_asu_mappings)
def exercise_icosahedron(max_level=2, verbose=0):
for level in range(0, max_level + 1):
if (0 or verbose):
print("level:", level)
icosahedron = scitbx.math.icosahedron(level=level)
try:
distance_cutoff = icosahedron.next_neighbors_distance() * (1 +
1.e-3)
estimated_distance_cutoff = False
except RuntimeError as e:
assert str(e) == "next_neighbors_distance not known."
distance_cutoff = 0.4 / (2**(level - 1))
estimated_distance_cutoff = True
asu_mappings = crystal.direct_space_asu.non_crystallographic_asu_mappings(
sites_cart=icosahedron.sites)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
if (0 or verbose):
ps = pair_asu_table.show_distances(sites_cart=icosahedron.sites) \
.distances_info
print("level", level, "min", flex.min(ps.distances))
print(" ", " ", "max", flex.max(ps.distances))
assert ps.pair_counts.all_eq(pair_asu_table.pair_counts())
if (level == 0):
for d in ps.distances:
assert approx_equal(d, 1.0514622242382672)
elif (level < 2):
s = StringIO()
ps = pair_asu_table.show_distances(sites_cart=icosahedron.sites, out=s) \
.distances_info
assert ps.pair_counts.all_eq(pair_asu_table.pair_counts())
assert len(s.getvalue().splitlines()) == [72, 320][level]
del s
if (level == 0):
assert pair_asu_table.pair_counts().all_eq(5)
else:
assert pair_asu_table.pair_counts().all_eq(3)
del pair_asu_table
max_distance = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff).max_distance_sq()**.5
if (0 or verbose):
print("max_distance:", max_distance)
if (not estimated_distance_cutoff):
assert approx_equal(max_distance,
icosahedron.next_neighbors_distance())
assert approx_equal(
max_distance / icosahedron.next_neighbors_distance(), 1)
def exercise_icosahedron(max_level=2, verbose=0):
for level in xrange(0,max_level+1):
if (0 or verbose):
print "level:", level
icosahedron = scitbx.math.icosahedron(level=level)
try:
distance_cutoff = icosahedron.next_neighbors_distance()*(1+1.e-3)
estimated_distance_cutoff = False
except RuntimeError, e:
assert str(e) == "next_neighbors_distance not known."
distance_cutoff = 0.4/(2**(level-1))
estimated_distance_cutoff = True
asu_mappings = crystal.direct_space_asu.non_crystallographic_asu_mappings(
sites_cart=icosahedron.sites)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
if (0 or verbose):
ps = pair_asu_table.show_distances(sites_cart=icosahedron.sites) \
.distances_info
print "level", level, "min", flex.min(ps.distances)
print " ", " ", "max", flex.max(ps.distances)
assert ps.pair_counts.all_eq(pair_asu_table.pair_counts())
if (level == 0):
for d in ps.distances:
assert approx_equal(d, 1.0514622242382672)
elif (level < 2):
s = StringIO()
ps = pair_asu_table.show_distances(sites_cart=icosahedron.sites, out=s) \
.distances_info
assert ps.pair_counts.all_eq(pair_asu_table.pair_counts())
assert len(s.getvalue().splitlines()) == [72,320][level]
del s
if (level == 0):
assert pair_asu_table.pair_counts().all_eq(5)
else:
assert pair_asu_table.pair_counts().all_eq(3)
del pair_asu_table
max_distance = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff).max_distance_sq()**.5
if (0 or verbose):
print "max_distance:", max_distance
if (not estimated_distance_cutoff):
assert approx_equal(max_distance, icosahedron.next_neighbors_distance())
assert approx_equal(max_distance/icosahedron.next_neighbors_distance(),1)
def contacts_to_all(self, pdb_hier, symmetry, cutoff=6.0):
#finds all contacts within cutoff in an entire pdb_hier
xrs = pdb_hier.extract_xray_structure(crystal_symmetry=symmetry)
asu_mappings = xrs.asu_mappings(buffer_thickness=cutoff + 1.0)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings, distance_cutoff=cutoff)
natoms = pdb_hier.atoms().size()
#distance matrix impractical as we may have multiple contacts to the same atom by symmetry
#all of which need to be preserved
all_cont = {}
for i in range(natoms):
all_cont[i] = []
for pair in pair_generator:
pi = pair.i_seq
pj = pair.j_seq
ps = pair.j_sym
pd = int(np.sqrt(pair.dist_sq) *
1000) / 1000.0 #avoid base2 float issues for uniquifying
all_cont[pi].append(
(pj, pd, ps)) #need both from and to (across asu)
all_cont[pj].append((pi, pd, ps))
ncont = 0
awl_db = {} # refs to awl objects to pass
for awl in pdb_hier.atoms_with_labels():
awl_db[awl.i_seq] = awl
all_cont_db = {}
for iseq, clist in all_cont.iteritems():
#print "PROTO",iseq,clist
ncont = ncont + len(clist)
source_at = iseq
source_awl = awl_db[source_at]
uni_c = set(clist)
# for each source awl, generate list of unique tuples (cont awl,distance,sym)
cpairs = list(
(awl_db[c_at[0]], c_at[1], c_at[2]) for c_at in uni_c)
contacts, s_unique_id = self.get_contacts(source_awl,
cpairs,
cutoff=cutoff)
all_cont_db[s_unique_id] = contacts
print " Found %d contact pairs" % ncont
return all_cont_db
def check_distances(sites_cart, point_distance, verbose):
asu_mappings = non_crystallographic_asu_mappings(sites_cart=sites_cart)
distance_cutoff = point_distance * math.sqrt(2) * 0.99
simple_pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
assert simple_pair_generator.count_pairs() == pair_generator.count_pairs()
pair_generator.restart()
neighbors = {}
for pair in pair_generator:
assert pair.j_seq != pair.i_seq
assert pair.j_sym == 0
assert approx_equal(pair.dist_sq, point_distance**2)
neighbors[pair.i_seq] = neighbors.get(pair.i_seq, 0) + 1
neighbors[pair.j_seq] = neighbors.get(pair.j_seq, 0) + 1
n_dict = {}
for n in neighbors.values():
n_dict[n] = n_dict.get(n, 0) + 1
if (verbose):
print(n_dict)
if (len(neighbors) > 0):
assert max(neighbors.values()) <= 12
def create_super_sphere(pdb_hierarchy,
crystal_symmetry,
select_within_radius,
link_min=1.0,
link_max=2.0,
r=None):
if (r is None):
# This is equivalent to (but much faster):
#
#r = grm.geometry.pair_proxies().nonbonded_proxies.\
# get_symmetry_interacting_indices_unique(
# sites_cart = pdb_hierarchy.atoms().extract_xyz())
#
sites_cart = pdb_hierarchy.atoms().extract_xyz()
sst = crystal_symmetry.special_position_settings().site_symmetry_table(
sites_cart=sites_cart)
r = {}
from cctbx import crystal
cutoff = select_within_radius + 1 # +1 is nonbonded buffer
conn_asu_mappings = crystal_symmetry.special_position_settings().\
asu_mappings(buffer_thickness=cutoff)
conn_asu_mappings.process_sites_cart(original_sites=sites_cart,
site_symmetry_table=sst)
conn_pair_asu_table = crystal.pair_asu_table(
asu_mappings=conn_asu_mappings)
conn_pair_asu_table.add_all_pairs(distance_cutoff=cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
conn_asu_mappings, distance_cutoff=cutoff)
for pair in pair_generator:
rt_mx_i = conn_asu_mappings.get_rt_mx_i(pair)
rt_mx_j = conn_asu_mappings.get_rt_mx_j(pair)
rt_mx_ji = rt_mx_i.inverse().multiply(rt_mx_j)
if str(rt_mx_ji) == "x,y,z": continue
r.setdefault(pair.j_seq, []).append(rt_mx_ji)
for k, v in zip(r.keys(), r.values()): # remove duplicates!
r[k] = list(set(v))
c = iotbx.pdb.hierarchy.chain(
id="SS") # all symmetry related full residues
fm = crystal_symmetry.unit_cell().fractionalization_matrix()
om = crystal_symmetry.unit_cell().orthogonalization_matrix()
selection = r.keys()
for rg in pdb_hierarchy.residue_groups():
keep = False
for i in rg.atoms().extract_i_seq():
if (i in selection):
keep = True
break
if (keep):
ops = r[i]
for op in ops:
rg_ = rg.detached_copy()
xyz = rg_.atoms().extract_xyz()
new_xyz = flex.vec3_double()
for xyz_ in xyz:
t1 = fm * flex.vec3_double([xyz_])
t2 = op * t1[0]
t3 = om * flex.vec3_double([t2])
new_xyz.append(t3[0])
rg_.atoms().set_xyz(new_xyz)
rg_.link_to_previous = True
c.append_residue_group(rg_)
resseq = 0
for rg in c.residue_groups():
rg.resseq = "%4d" % resseq
resseq += 1
# Now we need to re-order residues and group by chains so that they can be
# linked by pdb interpretation.
super_sphere_hierarchy = pdb_hierarchy.deep_copy()
#
all_chains = iotbx.pdb.utils.all_chain_ids()
all_chains = [chid.strip() for chid in all_chains]
for cid in list(set([i.id for i in pdb_hierarchy.chains()])):
all_chains.remove(cid)
all_chains = iter(all_chains)
#
def get_atom(atoms, name):
for a in atoms:
if (a.name.strip().lower() == name.strip().lower()):
return a.xyz
residue_groups_i = list(c.residue_groups())
residue_groups_j = list(c.residue_groups())
residue_groups_k = list() # standard aa residues only
#
def dist(r1, r2):
return math.sqrt((r1[0] - r2[0])**2 + (r1[1] - r2[1])**2 +
(r1[2] - r2[2])**2)
#
def grow_chain(residue_groups_j, chunk, ci):
n_linked = 0
for rgj in residue_groups_j:
nj = get_atom(atoms=rgj.atoms(), name="N")
if (nj is None): continue
d_ci_nj = dist(ci, nj)
if (d_ci_nj < link_max and d_ci_nj > link_min):
n_linked += 1
chunk.append(rgj)
residue_groups_j.remove(rgj)
break
return n_linked, rgj
# Find all isolated single residues, and also save starters
starters = []
for rgi in residue_groups_i:
ci = get_atom(atoms=rgi.atoms(), name="C")
ni = get_atom(atoms=rgi.atoms(), name="N")
if (ci is None or ni is None): # collect non-proteins
c = iotbx.pdb.hierarchy.chain(id=all_chains.next())
c.append_residue_group(rgi)
super_sphere_hierarchy.models()[0].append_chain(c)
continue
residue_groups_k.append(rgi)
c_linked = 0
n_linked = 0
for rgj in residue_groups_j:
cj = get_atom(atoms=rgj.atoms(), name="C")
nj = get_atom(atoms=rgj.atoms(), name="N")
if (cj is None or nj is None): continue
d_ci_nj = dist(ci, nj)
d_ni_cj = dist(ni, cj)
if (d_ci_nj < link_max and d_ci_nj > link_min):
n_linked += 1
if (d_ni_cj < link_max and d_ni_cj > link_min):
c_linked += 1
assert c_linked in [1, 0], c_linked # Either linked or not!
assert n_linked in [1, 0], n_linked # Either linked or not!
if (c_linked == 0 and n_linked == 0): # isolated single residue
c = iotbx.pdb.hierarchy.chain(id=all_chains.next())
rgi.link_to_previous = True
c.append_residue_group(rgi)
super_sphere_hierarchy.models()[0].append_chain(c)
elif (c_linked == 0): # collect c-terminal residues
starters.append(rgi)
# Grow continuous chains from remaining residues starting from c-terminals
for rgi in starters:
ci = get_atom(atoms=rgi.atoms(), name="C")
chunk = [rgi]
n_linked = 1
while n_linked == 1:
n_linked, rgj = grow_chain(residue_groups_k, chunk, ci)
if (n_linked == 1):
ci = get_atom(atoms=rgj.atoms(), name="C")
c = iotbx.pdb.hierarchy.chain(id=all_chains.next())
for i, rg in enumerate(chunk):
rg.resseq = "%4d" % i
c.append_residue_group(rg)
super_sphere_hierarchy.models()[0].append_chain(c)
#
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=super_sphere_hierarchy.atoms().extract_xyz(),
buffer_layer=10)
cs_super_sphere = box.crystal_symmetry()
return group_args(hierarchy=super_sphere_hierarchy,
crystal_symmetry=cs_super_sphere,
selection_r=r)
def compare_ions(hierarchy,
reference_hierarchy,
reference_xrs,
distance_cutoff=2.0,
log=None,
ignore_elements=(),
only_elements=(),
sel_str_base="segid ION"):
"""
Compares two pdb structures to determine the number of ions that appear in the
reference structure and are either matched or missing in the other structure.
Parameters
----------
hierarchy : iotbx.pdb.hierarchy.root
reference_hierarchy : iotbx.pdb.hierarchy.root
reference_xrs : ...
distance_cutoff : float, optional
log : file, optional
ignore_element : iterable, optional
only_elements : iterable, optional
sel_str_base : str, optional
Returns
-------
int
Number of ions in reference_hierarchy that were also found in hierarchy.
int
Number of ions in reference_hierarchy that were not found in hierarchy.
"""
if log is None:
log = null_out()
sel_cache = hierarchy.atom_selection_cache()
sel_str = sel_str_base
if len(only_elements) > 0:
sel_str += " and (%s)" % " or ".join(
["element %s" % e for e in only_elements])
elif len(ignore_elements) > 0:
sel_str += " and not (%s)" % " or ".join(
["element %s" % e for e in ignore_elements])
ion_isel = sel_cache.selection(sel_str).iselection()
if len(ion_isel) == 0:
return [], []
pdb_atoms = hierarchy.atoms()
pdb_atoms.reset_i_seq()
ions = pdb_atoms.select(ion_isel)
asu_mappings = reference_xrs.asu_mappings(
buffer_thickness=distance_cutoff + 0.1)
unit_cell = reference_xrs.unit_cell()
sites_cart = ions.extract_xyz()
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
asu_mappings.process_sites_frac(
sites_frac,
min_distance_sym_equiv=reference_xrs.min_distance_sym_equiv())
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
reference_atoms = reference_hierarchy.atoms()
n_xray = reference_xrs.scatterers().size()
ion_ref_i_seqs = []
for k in range(len(ions)):
ion_ref_i_seqs.append([])
for pair in pair_generator:
if ((pair.i_seq < n_xray and pair.j_seq < n_xray)
or (pair.i_seq >= n_xray and pair.j_seq >= n_xray)):
continue
if pair.i_seq < n_xray:
ion_seq, ref_seq = pair.j_seq, pair.i_seq
else:
ion_seq, ref_seq = pair.i_seq, pair.j_seq
site_frac = sites_frac[ion_seq - n_xray]
dxyz = sqrt(pair.dist_sq)
j_seq = ion_seq - n_xray
ion_ref_i_seqs[j_seq].append(ref_seq)
# FIXME better filtering needed - right now we risk double-counting ions in
# the reference model, although I haven't found a case of this yet
matched = []
missing = []
for i_seq, ref_i_seqs in enumerate(ion_ref_i_seqs):
ion = ions[i_seq]
if len(ref_i_seqs) == 0:
print("No match for %s" % ion.id_str(), file=log)
missing.append(ion.id_str())
else:
ref_ions = []
for i_seq in ref_i_seqs:
ref_atom = reference_atoms[i_seq]
if ion.element.upper() == ref_atom.element.upper():
ref_ions.append(ref_atom.id_str())
if len(ref_ions) >= 1:
matched.append(ion.id_str())
if len(ref_ions) > 1:
print("Multiple matches for %s:" % ion.id_str(), file=log)
for ref_ion in ref_ions:
print(" %s" % ref_ion, file=log)
else:
print("Ion %s matches %s" % (ion.id_str(), ref_ions[0]),
file=log)
else:
print("No match for %s" % ion.id_str(), file=log)
missing.append(ion.id_str())
return matched, missing
def exercise_with_zeolite(verbose):
if (not libtbx.env.has_module("iotbx")):
print("Skipping exercise_with_zeolite(): iotbx not available")
return
from iotbx.kriber import strudat
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print("Skipping exercise_with_zeolite(): input file not available")
return
strudat_contents = strudat.read_all_entries(open(atlas_file))
strudat_entry = strudat_contents.get("YUG")
si_structure = strudat_entry.as_xray_structure()
if (verbose):
out = sys.stdout
else:
out = StringIO()
drls = distance_and_repulsion_least_squares(
si_structure=si_structure,
distance_cutoff=3.5,
nonbonded_repulsion_function_type="prolsq",
n_macro_cycles=2,
out=out)
#
nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies
assert nbp.n_total() > 50
# expected is 60, but the exact number depends on the minimizer
#
site_labels = drls.minimized_structure.scatterers().extract_labels()
sites_cart = drls.start_structure.sites_cart()
pair_proxies = drls.geometry_restraints_manager.pair_proxies()
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out)
if (verbose):
sys.stdout.write(out.getvalue())
assert len(out.getvalue().splitlines()) == 48 * 4 + 2
assert out.getvalue().splitlines()[-1].find("remaining") < 0
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
0^Bond restraints: 48
0^Sorted by residual:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^bond SI1
0^ SI1
0^ ideal model delta sigma weight residual sym.op.
0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
0^... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
0^Bond restraints: 48
0^Sorted by delta:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^... (remaining 20 not shown)
""",
selections=[range(6), [-1]])
site_labels_long = ["abc" + label + "def" for label in site_labels]
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels_long,
f=out,
prefix="^0",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
^0Bond restraints: 48
^0Sorted by residual:
^0bond abcO3def
^0 abcO4def
^0 ideal model delta sigma weight residual
^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
^0bond abcSI1def
^0 abcSI1def
^0 ideal model delta sigma weight residual sym.op.
^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
^0... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix=".=",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"),
"""\
.=Bond restraints: 48
.=Sorted by residual:
.=bond 4
.= 5
.= ideal model delta sigma weight residual
.= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
.=bond 0
.= 0
.= ideal model delta sigma weight residual sym.op.
.= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
.=... (remaining 20 not shown)
""",
selections=[range(6), range(-5, 0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="-+",
max_items=1)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue().replace("e-00", "e-0"), """\
-+Bond restraints: 48
-+Sorted by residual:
-+bond 4
-+ 5
-+ ideal model delta sigma weight residual
-+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
-+... (remaining 47 not shown)
""")
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="=+",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue(), """\
=+Bond restraints: 48
=+Sorted by residual:
=+... (remaining 48 not shown)
""")
#
sites_cart = si_structure.sites_cart()
site_labels = [sc.label for sc in si_structure.scatterers()]
asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5)
for min_cubicle_edge in [0, 5]:
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=asu_mappings.buffer_thickness(),
minimal=False,
min_cubicle_edge=min_cubicle_edge)
sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
asu_mappings=asu_mappings)
while (not pair_generator.at_end()):
p = geometry_restraints.nonbonded_asu_proxy(
pair=next(pair_generator), vdw_distance=3)
sorted_asu_proxies.process(p)
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="d%")
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(
out.getvalue(),
"""\
d%Nonbonded interactions: 7
d%Sorted by model distance:
...
d%nonbonded SI2
d% SI2
d% model vdw sym.op.
d% 3.092 3.000 -x+1,y,-z
...
d%nonbonded SI1
d% SI1
d% model vdw sym.op.
d% 3.216 3.000 -x+1/2,-y+1/2,-z+1
""",
selections=[range(2), range(10, 14),
range(26, 30)])
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="*j",
max_items=5)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(),
"""\
*jNonbonded interactions: 7
*jSorted by model distance:
...
*jnonbonded 0
*j 1
*j model vdw
*j 3.107 3.000
*jnonbonded 0
*j 0
*j model vdw sym.op.
*j 3.130 3.000 -x+1,y,-z+1
*j... (remaining 2 not shown)
""",
selections=[range(2), range(-9, 0)])
out = StringIO()
sorted_asu_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="@r",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
@rNonbonded interactions: 7
""")
def contacts_to_coord(self, coord, pdb_hier, symmetry, cutoff=6.0):
"""
Used to use extract map_model, but that caused problems
This function takes cartesian coordinate, pdb_hier, and symmetry and returns
sorted list of dictionaries, each a particular contact
very hacked together, jams pdb strings together
create a dummy pdb, put water at the peak site in the original coordinate system
then use fast pair generater to get all contacts to our peak atom
"""
dummy_atom = self.pput.write_atom(1, "O", "", "HOH", "ZZ", 9999, "",
coord[0], coord[1], coord[2], 1.0,
35.0, "O", "")
#hack to add an atom to a pdb
orig_str = pdb_hier.as_pdb_string(write_scale_records=False,
append_end=False,
interleaved_conf=0,
atoms_reset_serial_first_value=1,
atom_hetatm=True,
sigatm=False,
anisou=False,
siguij=False,
output_break_records=False)
nmodels = len(pdb_hier.models())
if nmodels == 1:
comb = orig_str + dummy_atom
else:
newmodel = nmodels + 1
comb = orig_str + "MODEL %s\n" % newmodel
comb = comb + dummy_atom
comb = comb + "ENDMDL\n"
dummy_pdb = iotbx.pdb.input(source_info=None,
lines=flex.split_lines(comb))
dummy_hier = dummy_pdb.construct_hierarchy()
atsel = "chain ZZ and resid 9999"
dummy_select = dummy_hier.atom_selection_cache().selection(
string=atsel)
atsel_index = np.argwhere(dummy_select.as_numpy_array())
dummy_xrs = dummy_pdb.xray_structure_simple(crystal_symmetry=symmetry)
#find neighbors with symmetry -- use pair_finding with asu_mappings
#doing this for each peak may be a bad idea, use all_contacts version instead if possible
asu_mappings = dummy_xrs.asu_mappings(buffer_thickness=cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings, distance_cutoff=cutoff)
peak_vector_list = []
#neighbor_mask = pair_generator.neighbors_of(atsel_arr)
#neighbors = pair_generator.select(neighbor_mask)
for pair in pair_generator:
if pair.i_seq == atsel_index:
#our peak is first atom, but we want pairs in both directions
#to provide exhaustive list of contacts
#store index number and difference vector and sym to make unique
#we don't care which symop, just how far away
rdist = int(
np.sqrt(pair.dist_sq) * 1000) / 1000.0 #avoid float error
peak_vector_list.append((pair.j_seq, rdist, pair.j_sym))
if pair.j_seq == atsel_index:
rdist = int(np.sqrt(pair.dist_sq) * 1000) / 1000.0
peak_vector_list.append((pair.i_seq, rdist, pair.j_sym))
unique = set(peak_vector_list)
dummy_atoms = dummy_hier.atoms()
#selection is boolean flex array, sizeof no atoms, can be indexed directly
#get awl for our dummy atom
s_awl = dummy_atoms.select(dummy_select)[0].fetch_labels()
#list((awl_db[c_at[0]],c_at[1],c_at[2]) for c_at in uni_c )
#next, get list of contacts (awl,dist)
selection = dummy_hier.atom_selection_cache().selection("not all")
if len(unique) == 0:
return []
cont_list = []
for conti in unique:
selection[conti[0]] = True
sel_awl = dummy_atoms.select(selection)[0].fetch_labels()
cont_list.append(
(sel_awl, conti[1],
conti[2])) #pass source awl, index for target, distance
selection[conti[0]] = False #unselect
contacts, s_unal = self.get_contacts(s_awl, cont_list, cutoff=cutoff)
return contacts
def exercise_with_zeolite(verbose):
if (not libtbx.env.has_module("iotbx")):
print "Skipping exercise_with_zeolite(): iotbx not available"
return
from iotbx.kriber import strudat
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
if (atlas_file is None):
print "Skipping exercise_with_zeolite(): input file not available"
return
strudat_contents = strudat.read_all_entries(open(atlas_file))
strudat_entry = strudat_contents.get("YUG")
si_structure = strudat_entry.as_xray_structure()
if (verbose):
out = sys.stdout
else:
out = StringIO()
drls = distance_and_repulsion_least_squares(
si_structure=si_structure,
distance_cutoff=3.5,
nonbonded_repulsion_function_type="prolsq",
n_macro_cycles=2,
out=out)
#
nbp = drls.geometry_restraints_manager.pair_proxies().nonbonded_proxies
assert nbp.n_total() > 50
# expected is 60, but the exact number depends on the minimizer
#
site_labels = drls.minimized_structure.scatterers().extract_labels()
sites_cart = drls.start_structure.sites_cart()
pair_proxies = drls.geometry_restraints_manager.pair_proxies()
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out)
if (verbose):
sys.stdout.write(out.getvalue())
assert len(out.getvalue().splitlines()) == 48*4+2
assert out.getvalue().splitlines()[-1].find("remaining") < 0
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
0^Bond restraints: 48
0^Sorted by residual:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^bond SI1
0^ SI1
0^ ideal model delta sigma weight residual sym.op.
0^ 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
0^... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="0^",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
0^Bond restraints: 48
0^Sorted by delta:
0^bond O3
0^ O4
0^ ideal model delta sigma weight residual
0^ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
0^... (remaining 20 not shown)
""",
selections=[range(6), [-1]])
site_labels_long = ["abc"+label+"def" for label in site_labels]
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels_long,
f=out,
prefix="^0",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
^0Bond restraints: 48
^0Sorted by residual:
^0bond abcO3def
^0 abcO4def
^0 ideal model delta sigma weight residual
^0 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
^0bond abcSI1def
^0 abcSI1def
^0 ideal model delta sigma weight residual sym.op.
^0 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
^0... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix=".=",
max_items=28)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
.=Bond restraints: 48
.=Sorted by residual:
.=bond 4
.= 5
.= ideal model delta sigma weight residual
.= 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
...
.=bond 0
.= 0
.= ideal model delta sigma weight residual sym.op.
.= 3.071 3.216 -0.145 2.08e+00 2.31e-01 4.83e-03 -x+1/2,-y+1/2,-z+1
.=... (remaining 20 not shown)
""",
selections=[range(6), range(-5,0)])
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="-+",
max_items=1)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue().replace("e-00", "e-0"), """\
-+Bond restraints: 48
-+Sorted by residual:
-+bond 4
-+ 5
-+ ideal model delta sigma weight residual
-+ 2.629 2.120 0.509 1.56e+00 4.10e-01 1.06e-01
-+... (remaining 47 not shown)
""")
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
f=out,
prefix="=+",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
=+Bond restraints: 48
=+Sorted by residual:
=+... (remaining 48 not shown)
""")
#
sites_cart = si_structure.sites_cart()
site_labels = [sc.label for sc in si_structure.scatterers()]
asu_mappings = si_structure.asu_mappings(buffer_thickness=3.5)
for min_cubicle_edge in [0, 5]:
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=asu_mappings.buffer_thickness(),
minimal=False,
min_cubicle_edge=min_cubicle_edge)
sorted_asu_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
asu_mappings=asu_mappings)
while (not pair_generator.at_end()):
p = geometry_restraints.nonbonded_asu_proxy(
pair=pair_generator.next(),
vdw_distance=3)
sorted_asu_proxies.process(p)
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="d%")
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
d%Nonbonded interactions: 7
d%Sorted by model distance:
...
d%nonbonded SI2
d% SI2
d% model vdw sym.op.
d% 3.092 3.000 -x+1,y,-z
...
d%nonbonded SI1
d% SI1
d% model vdw sym.op.
d% 3.216 3.000 -x+1/2,-y+1/2,-z+1
""",
selections=[range(2), range(10,14), range(26,30)])
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="*j",
max_items=5)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
*jNonbonded interactions: 7
*jSorted by model distance:
...
*jnonbonded 0
*j 1
*j model vdw
*j 3.107 3.000
*jnonbonded 0
*j 0
*j model vdw sym.op.
*j 3.130 3.000 -x+1,y,-z+1
*j... (remaining 2 not shown)
""",
selections=[range(2), range(-9,0)])
out = StringIO()
sorted_asu_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
f=out,
prefix="@r",
max_items=0)
if (verbose):
sys.stdout.write(out.getvalue())
assert not show_diff(out.getvalue(), """\
@rNonbonded interactions: 7
""")
def compare_ions(
hierarchy,
reference_hierarchy,
reference_xrs,
distance_cutoff=2.0,
log=None,
ignore_elements=(),
only_elements=(),
sel_str_base="segid ION",
):
"""
Compares two pdb structures to determine the number of ions that appear in the
reference structure and are either matched or missing in the other structure.
Parameters
----------
hierarchy : iotbx.pdb.hierarchy.root
reference_hierarchy : iotbx.pdb.hierarchy.root
reference_xrs : ...
distance_cutoff : float, optional
log : file, optional
ignore_element : iterable, optional
only_elements : iterable, optional
sel_str_base : str, optional
Returns
-------
int
Number of ions in reference_hierarchy that were also found in hierarchy.
int
Number of ions in reference_hierarchy that were not found in hierarchy.
"""
if log is None:
log = null_out()
sel_cache = hierarchy.atom_selection_cache()
sel_str = sel_str_base
if len(only_elements) > 0:
sel_str += " and (%s)" % " or ".join(["element %s" % e for e in only_elements])
elif len(ignore_elements) > 0:
sel_str += " and not (%s)" % " or ".join(["element %s" % e for e in ignore_elements])
ion_isel = sel_cache.selection(sel_str).iselection()
if len(ion_isel) == 0:
return [], []
pdb_atoms = hierarchy.atoms()
pdb_atoms.reset_i_seq()
ions = pdb_atoms.select(ion_isel)
asu_mappings = reference_xrs.asu_mappings(buffer_thickness=distance_cutoff + 0.1)
unit_cell = reference_xrs.unit_cell()
sites_cart = ions.extract_xyz()
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
asu_mappings.process_sites_frac(sites_frac, min_distance_sym_equiv=reference_xrs.min_distance_sym_equiv())
pair_generator = crystal.neighbors_fast_pair_generator(asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
reference_atoms = reference_hierarchy.atoms()
n_xray = reference_xrs.scatterers().size()
ion_ref_i_seqs = []
for k in range(len(ions)):
ion_ref_i_seqs.append([])
for pair in pair_generator:
if (pair.i_seq < n_xray and pair.j_seq < n_xray) or (pair.i_seq >= n_xray and pair.j_seq >= n_xray):
continue
if pair.i_seq < n_xray:
ion_seq, ref_seq = pair.j_seq, pair.i_seq
else:
ion_seq, ref_seq = pair.i_seq, pair.j_seq
site_frac = sites_frac[ion_seq - n_xray]
dxyz = sqrt(pair.dist_sq)
j_seq = ion_seq - n_xray
ion_ref_i_seqs[j_seq].append(ref_seq)
# FIXME better filtering needed - right now we risk double-counting ions in
# the reference model, although I haven't found a case of this yet
matched = []
missing = []
for i_seq, ref_i_seqs in enumerate(ion_ref_i_seqs):
ion = ions[i_seq]
if len(ref_i_seqs) == 0:
print >> log, "No match for %s" % ion.id_str()
missing.append(ion.id_str())
else:
ref_ions = []
for i_seq in ref_i_seqs:
ref_atom = reference_atoms[i_seq]
if ion.element.upper() == ref_atom.element.upper():
ref_ions.append(ref_atom.id_str())
if len(ref_ions) >= 1:
matched.append(ion.id_str())
if len(ref_ions) > 1:
print >> log, "Multiple matches for %s:" % ion.id_str()
for ref_ion in ref_ions:
print >> log, " %s" % ref_ion
else:
print >> log, "Ion %s matches %s" % (ion.id_str(), ref_ions[0])
else:
print >> log, "No match for %s" % ion.id_str()
missing.append(ion.id_str())
return matched, missing
