def process_nonbonded_for_links(self,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
link_metals = True,
link_residues = True,
link_carbohydrates = True,
link_amino_acid_rna_dna = False,
link_ligands = False,
max_bonded_cutoff = None,
metal_coordination_cutoff = 3.,
amino_acid_bond_cutoff = 2.,
inter_residue_bond_cutoff = 2.,
second_row_buffer = 0.5,
carbohydrate_bond_cutoff = 2.,
ligand_bond_cutoff = 2.,
log = None,
verbose = False,
):
assert hasattr(self, "cif")
if max_bonded_cutoff is None:
max_bonded_cutoff = max(metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
ligand_bond_cutoff,
inter_residue_bond_cutoff+second_row_buffer,
)
# check that linking required
## has_checks = []
## for i, link_boolean in enumerate([link_carbohydrates,
## ]
## ):
## if i==0: ct = "common_saccharide"
## rc = False
## if link_boolean:
## rc = check_all_classes(self.pdb_hierarchy, ct)
## has_checks.append(rc)
## has_checks.append(link_amino_acid_rna_dna)
## if not filter(None, has_checks): return
#
if max_bonded_cutoff > 15:
raise Sorry("One of the following parameters: \nmetal_coordination_"+
"cutoff, amino_acid_bond_cutoff,"+
"inter_residue_bond_cutoff, \ncarbohydrate_bond_cutoff,"
"bonds.bond_distance_cutoff \nis greater than 15A. Please check and"+
" correct these parameters.")
if verbose and log is not None:
print >> log,"""
metal_coordination_cutoff %s
amino_acid_bond_cutoff %s
carbohydrate_bond_cutoff %s
inter_residue_bond_cutoff %s
second_row_buffer %s
""" % ( metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
inter_residue_bond_cutoff,
second_row_buffer,
)
from cctbx import crystal
from cctbx.array_family import flex
#
def _nonbonded_pair_objects(max_bonded_cutoff=3.,
i_seqs=None,
):
if i_seqs is None:
atoms = self.pdb_hierarchy.atoms()
i_seqs = flex.size_t()
for atom in atoms:
i_seqs.append(atom.i_seq)
if (self.model_indices is not None):
model_indices = self.model_indices.select(i_seqs)
conformer_indices = self.conformer_indices.select(i_seqs)
sym_excl_indices = self.sym_excl_indices.select(i_seqs)
donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(i_seqs)
asu_mappings = self.special_position_settings.asu_mappings(
buffer_thickness=max_bonded_cutoff)
sites_cart = self.sites_cart.select(i_seqs)
asu_mappings.process_sites_cart(
original_sites=sites_cart,
site_symmetry_table=self.site_symmetry_table().select(i_seqs))
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
model_indices=model_indices,
conformer_indices=conformer_indices,
sym_excl_indices=sym_excl_indices,
donor_acceptor_excl_groups=donor_acceptor_excl_groups,
nonbonded_params=geometry_restraints.nonbonded_params(
default_distance=1),
nonbonded_types=flex.std_string(conformer_indices.size()),
nonbonded_charges=flex.int(conformer_indices.size(), 0),
nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff,
min_cubicle_edge=5,
shell_asu_tables=[pair_asu_table])
return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
#
def _nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies,
max_bonded_cutoff=3.):
rc = nonbonded_proxies.get_sorted(by_value="delta",
sites_cart=sites_cart,
include_proxy=True,
)
if rc is None: return
rc, junk = rc
for item in rc:
yield item
#
if(log is not None):
print >> log, """
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : %-5s - %0.2f
Amimo acid : %-5s - %0.2f
Carbohydrate : %-5s - %0.2f
Ligands : %-5s - %0.2f
Amino acid - RNA/DNA : %-5s
""" % (link_metals,
metal_coordination_cutoff,
link_residues,
amino_acid_bond_cutoff,
link_carbohydrates,
carbohydrate_bond_cutoff,
link_ligands,
ligand_bond_cutoff,
link_amino_acid_rna_dna,
)
t0=time.time()
atoms = self.pdb_hierarchy.atoms()
bond_data = []
bond_data_i_seqs = {}
simple_bonds = 0
sym_bonds = 0
link_data = []
simple_links = 0
sym_links = 0
done = ResidueLinkClass()
links = {}
custom_links = {}
# main loop
nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, nonbonded_i_seqs = \
_nonbonded_pair_objects(max_bonded_cutoff=max_bonded_cutoff,
)
initial_pair_asu_table_table = bond_asu_table.table().deep_copy()
for ii, item in enumerate(
_nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies=nonbonded_proxies,
max_bonded_cutoff=max_bonded_cutoff,
)
):
labels, i_seq, j_seq, distance, vdw_distance, sym_op, rt_mx_ji, proxy = item
# XXX this is a poor job!!!
if bond_asu_table.contains(i_seq, j_seq, 0): continue
if bond_asu_table.contains(i_seq, j_seq, 1): continue
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
if verbose:
print i_seq, j_seq, atom1.quote(),
print atom2.quote(),
print "Distance: %0.2f" % distance, rt_mx_ji, sym_op
# don't link atoms not in the same conformer (works for models also)...
if not atom1.is_in_same_conformer_as(atom2):
assert 0
continue
# don't link atoms in same residue group
if atom1.parent().parent()==atom2.parent().parent(): continue
atom_group1 = atom1.parent()
atom_group2 = atom2.parent()
# dont't like atom groups in different altloc expect " "
if atom_group1.altloc.strip()==atom_group2.altloc.strip(): pass
elif atom_group1.altloc.strip()=="": pass
elif atom_group2.altloc.strip()=="": pass
else: continue
# don't link some classes
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
use_only_bond_cutoff = False
if verbose:
print """
Residue classes
%s
%s """ % (classes1, classes2)
#if not link_ligands and (classes1.other or classes2.other):
# continue
# is_proxy_set between any of the atoms ????????
if classes1.common_amino_acid and classes2.common_amino_acid:
if not link_residues:
continue
# special amino acid linking
# - cyclic
# - beta, delta ???
if possible_cyclic_peptide(atom1, atom2): # first & last peptide
use_only_bond_cutoff = True
if sym_op:
if classes1.common_amino_acid and classes2.common_saccharide: continue
if classes2.common_amino_acid and classes1.common_saccharide: continue
#
# bonded atoms can't link to same atom, eg MG-PG and MG-O1P
#
if bond_data:
bonded = False
if i_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[i_seq]:
if bond_asu_table.contains(j_seq, t_i, 0): bonded = True
if j_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[j_seq]:
if bond_asu_table.contains(i_seq, t_i, 0): bonded = True
if bonded: continue
#
key = [
atom1.id_str()[9:-1],
atom2.id_str()[9:-1],
]
key.sort()
if sym_op:
key.append(str(rt_mx_ji))
key = tuple(key)
# hydrogens
if atom1.element.strip() in hydrogens:
done[atom2.id_str()] = atom1.id_str()
if atom2.element.strip() in hydrogens:
done[atom1.id_str()] = atom2.id_str()
# bond length cutoff & some logic
if not linking_utils.is_atom_pair_linked(
atom1,
atom2,
distance=distance,
max_bonded_cutoff=max_bonded_cutoff,
amino_acid_bond_cutoff=amino_acid_bond_cutoff,
inter_residue_bond_cutoff=inter_residue_bond_cutoff,
second_row_buffer=second_row_buffer,
saccharide_bond_cutoff=carbohydrate_bond_cutoff,
metal_coordination_cutoff=metal_coordination_cutoff,
use_only_bond_cutoff=use_only_bond_cutoff,
link_metals=link_metals,
verbose=verbose,
):
if verbose:
print "is not linked", atom1.quote(),atom2.quote(),key
print 'link_metals',link_metals
if ( atom1.element.strip().upper() in hydrogens or
atom2.element.strip().upper() in hydrogens):
pass
else:
done.setdefault(key, [])
done[key].append([atom1.name, atom2.name])
continue
# check some valences...
if not (classes1.common_element or classes2.common_element):
if not linking_utils.check_valence(self.pdb_hierarchy, atom1):
print >> log, " Atom %s rejected from bonding due to valence issues." % atom1.quote()
continue
if not linking_utils.check_valence(self.pdb_hierarchy, atom2):
print >> log, " Atom %s rejected from bonding due to valence issues." % atom2.quote()
continue
# got a link....
class1 = linking_utils.get_classes(atom1, #_group1.resname,
important_only=True,
)
class2 = linking_utils.get_classes(atom2, #_group2.resname,
important_only=True,
)
class_key = [class1, class2]
class_key.sort()
class_key = tuple(class_key)
if verbose: print 'class_key',class_key
#
if not link_metals and "metal" in class_key: continue
#atoms_must_be = {}
if not link_residues:
if class_key in [
("common_amino_acid", "common_amino_acid"),
("common_amino_acid", "other"),
]: continue
#else:
# atoms_must_be.setdefault(("common_amino_acid",
# "common_amino_acid"),["C", "N"])
# atoms_must_be.setdefault(("common_amino_acid", "other"),["C", "N"])
if not link_carbohydrates and "common_saccharide" in class_key: continue
if not link_amino_acid_rna_dna:
if "common_amino_acid" in class_key and "common_rna_dna" in class_key:
continue
#
names = [atom1.name, atom2.name]
if verbose: print 'names',names
names.sort()
atom1_key = None
atom2_key = None
if class1 in linking_setup.maximum_per_atom_links: # is one
atom1_key = atom1.id_str()
if class2 in linking_setup.maximum_per_atom_links: # is one
atom2_key = atom2.id_str()
if verbose:
print '-'*80
print 'class_key',class_key
print 'done'
for k, item in done.items():
print "> %s : %s" % (k, item)
print 'key',key
print 'atom keys',atom1_key, atom2_key
# exclude duplicate symmetry op.
if key in done:
if names in done[key]: continue
if atom1.parent().altloc==atom2.parent().altloc:
if atom1_key:
if atom1_key in done: continue
done[atom1_key] = key
if atom2_key:
if atom2_key in done: continue
done[atom2_key] = key
#
current_number_of_links = len(done.setdefault(key, []))
if(current_number_of_links >=
linking_setup.maximum_inter_residue_links.get(class_key, 1)
):
if verbose:
print "too many links:",current_number_of_links,linking_setup.maximum_inter_residue_links.get(class_key, 1), class_key
continue
#
done[key].append(names)
done_key = key
# get all possible links
i_seqs = []
for atom in atom_group1.atoms():
i_seqs.append(atom.i_seq)
j_seqs = []
for atom in atom_group2.atoms():
j_seqs.append(atom.i_seq)
ij_seqs = []
for i in i_seqs:
for j in j_seqs:
tmp = [i,j]
tmp.sort()
ij_seqs.append(tuple(tmp))
# check that a link not already made
link_found = False
if verbose:
print 'len simple bond proxies',len(geometry_proxy_registries.bond_simple.proxies)
# Consistency check - debugging only
# for bsp in geometry_proxy_registries.bond_simple.proxies:
# if bsp.i_seqs[1] not in initial_pair_asu_table_table[bsp.i_seqs[0]].keys():
# print "ERROR!!!", bsp.i_seqs
# STOP()
# Proposed fast loop: Time building additional restraints for
# ribosome went from 5272 to 204 seconds.
for p in ij_seqs:
if p[1] in initial_pair_asu_table_table[p[0]].keys():
link_found = True
break
# VERY SLOW !!! - original loop
# for bond_simple_proxy in geometry_proxy_registries.bond_simple.proxies:
# if bond_simple_proxy.i_seqs in ij_seqs:
# link_found = True
# break
if link_found: continue
# check for any link between atom groups based on residue name, eg ASN-NAG
# get predefined link
link, swap, key = linking_utils.is_atom_group_pair_linked(
atom_group1,
atom_group2,
self.mon_lib_srv,
)
if verbose:
print 'link',link
print 'swap',swap
print 'key',key
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
space_group = self.special_position_settings.space_group()
#
if len(done_key)==2:
link_rt_mx_ji = sgtbx.rt_mx(symbol="x,y,z", t_den=space_group.t_den())
else:
link_rt_mx_ji = sgtbx.rt_mx(symbol=done_key[2], t_den=space_group.t_den())
#
if link:
# apply a standard link
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
if len(bond_i_seqs)==0:
if verbose:
print 'failed to link using %s' % key
continue
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1]+=bond_i_seqs[0] # odd?
if verbose: print "predefined residue named link",key
self.cif["link_%s" % key] = link.cif_object
continue
#
#if atoms_must_be:
# # this could be fancier...
# # link_residues is peptide and SG links
# atoms_must_be_key = [atom1.element.strip(), atom2.element.strip()]
# #atoms_must_be_key = [atom1.name.strip(), atom2.name.strip()]
# atoms_must_be_key.sort()
# if class_key in atoms_must_be and "S" not in atoms_must_be_key:
# if atoms_must_be[class_key]!=atoms_must_be_key:
# continue
rc = linking_utils.process_atom_groups_for_linking_single_link(
self.pdb_hierarchy,
atom1,
atom2,
verbose=verbose,
)
if not rc:
done.remove_link(done_key, names)
continue
pdbres, link_key, link_atoms = rc
assert len(link_key)==1
key = link_key[0]
link = self.mon_lib_srv.link_link_id_dict.get(key, None)
if verbose:
print 'pdbres',pdbres
print 'link',link
print 'link_key',link_key
print 'link_atoms',link_atoms
if key.find("ALPHA1")>-1 or key.find("BETA1")>-1: # is handled in elif
key, cif, bond_i_seqs = \
glyco_utils.apply_glyco_link_using_proxies_and_atoms(
atom_group2,
atom_group1,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
link_carbon_dist=carbohydrate_bond_cutoff,
)
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1]+=bond_i_seqs
self.cif["link_%s" % key] = cif
continue
elif link:
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1]+=bond_i_seqs[0]
continue
else:
# possible peptide or rna/dna link
rc = check_for_peptide_links(atom1, atom2)
# no peptide links across symmetry
if len(done_key)==3:
rc = None
if rc:
key, swap = rc
link = self.mon_lib_srv.link_link_id_dict.get(key)
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
rc = _apply_link_using_proxies(link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
if not rc:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
rc = _apply_link_using_proxies(link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
# not added to links so not LINK record
if sym_op:
sym_links += 1
link_data.append( (atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
key,
)
)
else:
simple_links += 1
link_data.append( (atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx_ji,
key,
)
)
continue
#
custom_links.setdefault(ii, [])
custom_links[ii].append([atom_group1, atom_group2, atom1, atom2])
# simple
bond_name = "bond"
if ((classes1.common_rna_dna or
classes1.ccp4_mon_lib_rna_dna) and
(classes2.common_rna_dna or classes2.ccp4_mon_lib_rna_dna)):
bond_name = "h-dna"
elif (linking_utils.get_classes(atom1, important_only=True)=="metal" or
linking_utils.get_classes(atom2, important_only=True)=="metal"):
bond_name = "metal-coordination"
if sym_op:
sym_bonds += 1
bond_data.append( (atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
bond_name,
)
)
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy)
else:
simple_bonds += 1
bond_data.append( (atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx,
bond_name,
)
)
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy.i_seqs)
# END MAIN LOOP for ii, item in enumerate(nonbonded?)
#
#
if verbose:
for key in sorted(custom_links):
print '-'*80
print key
for pair in custom_links[key]:
for atom in pair:
try: print atom.quote()
except Exception: print atom
pair_sym_table = pair_asu_table.extract_pair_sym_table()
#for sym_pair in pair_sym_table.iterator():
# print sym_pair.i_seq, sym_pair.j_seq,
# print atoms[sym_pair.i_seq].quote(), atoms[sym_pair.j_seq].quote()
n_simple, n_symmetry = 0, 0
self.pdb_link_records.setdefault("LINK", [])
for ijk, sym_pair in enumerate(pair_sym_table.iterator()):
i_seq, j_seq = sym_pair.i_seqs()
origin_id=0
if bond_data[ijk][-1]=="metal-coordination": origin_id=2
# adding link to PDB
#assert len(bond_i_seqs)==1
self.pdb_link_records["LINK"].append([self.pdb_atoms[i_seq],
self.pdb_atoms[j_seq],
link_rt_mx_ji,
])
assert i_seq == nonbonded_i_seqs[i_seq]
assert j_seq == nonbonded_i_seqs[j_seq]
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
if (sym_pair.rt_mx_ji.is_unit_mx()): n_simple += 1
else: n_symmetry += 1
# check for NA linkage
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
ans = bondlength_defaults.run(atom1, atom2)
equil = 2.3
weight = 0.02
slack = 0.
if len(ans) >0:
equil = ans[0]
if len(ans) > 1:
weight = ans[1]
if len(ans) > 2:
slack = ans[2]
if equil is None:
equil = 2.3
bond_params_table.update(
i_seq=i_seq,
j_seq=j_seq,
params=geometry_restraints.bond_params(
distance_ideal=equil,
weight=1.0/weight**2,
slack=slack,
origin_id=origin_id,
))
bond_asu_table.add_pair(
i_seq=i_seq,
j_seq=j_seq,
rt_mx_ji=sym_pair.rt_mx_ji)
# output
if link_data:
print >> log, " Number of additional links: simple=%d, symmetry=%d" % (
simple_links,
sym_bonds,
)
for label1, label2, sym_op, link_name in sorted(link_data):
if sym_op is None:
print >> log, " Simple link: %s - %s" % (label1, label2)
for label1, label2, sym_op, bond_type in sorted(bond_data):
if sym_op:
print >> log, " Symmetry link: %s - %s sym. op: %s" % (label1,
label2,
sym_op,
)
if(log is not None):
print >> log," Number of custom bonds: simple=%d, symmetry=%d" % (
n_simple, n_symmetry)
if (n_symmetry == 0):
blanks = ""
else:
blanks = " "
#
def _sort_on_id(ag1, ag2):
ag1=ag1[0]
ag2=ag2[0]
if ag1.id_str()[4:]==ag2.id_str()[4:]:
if ag1.altloc<ag2.altloc:
return -1
return 1
elif ag1.id_str()[4:]<ag2.id_str()[4:]:
return -1
return 1
#
if links:
explained = []
print >> log, " Links applied"
for key in sorted(links):
print >> log, " %s" % key
links[key].sort(_sort_on_id)
for ag1, ag2, i_seq, j_seq in links[key]:
self.pdb_link_records["LINK"].append([self.pdb_atoms[i_seq],
self.pdb_atoms[j_seq],
"x,y,z", #link_rt_mx_ji,
])
if ag1.altloc or ag2.altloc:
print >> log, ' "%s" - "%s" : altloc "%s" - "%s"' % (
ag1.id_str(),
ag2.id_str(),
ag1.altloc,
ag2.altloc,
)
else:
print >> log, ' "%s" - "%s"' % (ag1.id_str(),
ag2.id_str(),
)
explain=""
if key.find("ALPHA")==0 or key.find("BETA")==0:
true_alpha_beta = glyco_utils.get_alpha_beta(ag2.resname,
fake=False,
)
if true_alpha_beta and key.find(true_alpha_beta.upper())==-1:
one = "a beta"
two = "an alpha"
if true_alpha_beta=="alpha":
one = "an alpha"
two = "a beta"
explain = "%s~> Even though %s is %s isomer," % (' '*7,
ag2.resname,
one)
explain += " %s linkage is required..." % (two)
if explain not in explained:
print >> log, explain
explained.append(explain)
if bond_data:
print >> log, " Number of additional bonds: simple=%d, symmetry=%d" % (
simple_bonds,
sym_bonds,
)
for caption, bond_type in [
("Coordination",'metal-coordination'),
("Other bonds",'bond'),
]:
print >> log, " %s:" % caption
for label1, label2, sym_op, bt in sorted(bond_data):
if sym_op is None and bt == bond_type:
print >> log, " Simple bond: %s - %s" % (label1, label2)
for label1, label2, sym_op, bt in sorted(bond_data):
if sym_op and bt == bond_type:
print >> log, " Symmetry bond: %s - %s sym. op: %s" % (label1,
label2,
sym_op,
)
if(log is not None):
print >> log, ' Time building additional restraints: %0.2f' % (
time.time()-t0)
def process_nonbonded_for_links(
self,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
link_metals=True,
link_residues=True,
link_carbohydrates=True,
link_amino_acid_rna_dna=False,
link_ligands=False,
link_small_molecules=False,
max_bonded_cutoff=None,
metal_coordination_cutoff=3.,
amino_acid_bond_cutoff=2.,
inter_residue_bond_cutoff=2.,
second_row_buffer=0.5,
carbohydrate_bond_cutoff=2.,
ligand_bond_cutoff=2.,
small_molecule_bond_cutoff=2.,
include_selections=None,
exclude_selections=None,
log=None,
verbose=False,
):
assert hasattr(self, "_cif")
if max_bonded_cutoff is None:
max_bonded_cutoff = max(
metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
ligand_bond_cutoff,
small_molecule_bond_cutoff,
inter_residue_bond_cutoff + second_row_buffer,
)
max_bonded_cutoff_standard = max_bonded_cutoff
if include_selections:
for selection_1, selection_2, cutoff in include_selections:
max_bonded_cutoff = max(max_bonded_cutoff, cutoff)
# check that linking required
## has_checks = []
## for i, link_boolean in enumerate([link_carbohydrates,
## ]
## ):
## if i==0: ct = "common_saccharide"
## rc = False
## if link_boolean:
## rc = check_all_classes(self.pdb_hierarchy, ct)
## has_checks.append(rc)
## has_checks.append(link_amino_acid_rna_dna)
## if not filter(None, has_checks): return
#
if max_bonded_cutoff > 15:
raise Sorry(
"One of the following parameters: \nmetal_coordination_" +
"cutoff, amino_acid_bond_cutoff," +
"inter_residue_bond_cutoff, \ncarbohydrate_bond_cutoff,"
"bonds.bond_distance_cutoff \nis greater than 15A. Please check and"
+ " correct these parameters.")
if verbose and log is not None:
print >> log, """
metal_coordination_cutoff %s
amino_acid_bond_cutoff %s
carbohydrate_bond_cutoff %s
inter_residue_bond_cutoff %s
second_row_buffer %s
""" % (
metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
inter_residue_bond_cutoff,
second_row_buffer,
)
from cctbx import crystal
from cctbx.array_family import flex
#
def _nonbonded_pair_objects(
max_bonded_cutoff=3.,
i_seqs=None,
):
if i_seqs is None:
atoms = self.pdb_hierarchy.atoms()
i_seqs = flex.size_t()
for atom in atoms:
i_seqs.append(atom.i_seq)
if (self.model_indices is not None):
model_indices = self.model_indices.select(i_seqs)
conformer_indices = self.conformer_indices.select(i_seqs)
sym_excl_indices = self.sym_excl_indices.select(i_seqs)
donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(
i_seqs)
asu_mappings = self.special_position_settings.asu_mappings(
buffer_thickness=max_bonded_cutoff)
sites_cart = self.sites_cart.select(i_seqs)
asu_mappings.process_sites_cart(
original_sites=sites_cart,
site_symmetry_table=self.site_symmetry_table().select(i_seqs))
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
model_indices=model_indices,
conformer_indices=conformer_indices,
sym_excl_indices=sym_excl_indices,
donor_acceptor_excl_groups=donor_acceptor_excl_groups,
nonbonded_params=geometry_restraints.nonbonded_params(
default_distance=1),
nonbonded_types=flex.std_string(conformer_indices.size()),
nonbonded_charges=flex.int(conformer_indices.size(), 0),
nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff,
min_cubicle_edge=5,
shell_asu_tables=[pair_asu_table])
return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
#
def _nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies, max_bonded_cutoff=3.):
rc = nonbonded_proxies.get_sorted(
by_value="delta",
sites_cart=sites_cart,
include_proxy=True,
)
if rc is None: return
rc, junk = rc
for item in rc:
yield item
#
if (log is not None):
print >> log, """
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : %-5s - %0.2f
Amimo acid : %-5s - %0.2f
Carbohydrate : %-5s - %0.2f
Ligands : %-5s - %0.2f
Small molecules : %-5s - %0.2f
Amino acid - RNA/DNA : %-5s
""" % (
link_metals,
metal_coordination_cutoff,
link_residues,
amino_acid_bond_cutoff,
link_carbohydrates,
carbohydrate_bond_cutoff,
link_ligands,
ligand_bond_cutoff,
link_small_molecules,
small_molecule_bond_cutoff,
link_amino_acid_rna_dna,
)
t0 = time.time()
atoms = self.pdb_hierarchy.atoms()
bond_data = []
bond_data_i_seqs = {}
simple_bonds = 0
sym_bonds = 0
link_data = []
simple_links = 0
sym_links = 0
done = ResidueLinkClass()
links = {}
custom_links = {}
exclude_out_lines = {}
# main loop
nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, nonbonded_i_seqs = \
_nonbonded_pair_objects(max_bonded_cutoff=max_bonded_cutoff,
)
initial_pair_asu_table_table = bond_asu_table.table().deep_copy()
for ii, item in enumerate(
_nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies=nonbonded_proxies,
max_bonded_cutoff=max_bonded_cutoff,
)):
labels, i_seq, j_seq, distance, vdw_distance, sym_op, rt_mx_ji, proxy = item
#
# include & exclude selection
#
if (include_selections and distance >= max_bonded_cutoff_standard):
for selection_1, selection_2, bond_cutoff in include_selections:
if ((i_seq in selection_1 and j_seq in selection_2) or
(i_seq in selection_2 and j_seq in selection_1)):
metal_coordination_cutoff = bond_cutoff
amino_acid_bond_cutoff = bond_cutoff
carbohydrate_bond_cutoff = bond_cutoff
ligand_bond_cutoff = bond_cutoff
small_molecule_bond_cutoff = bond_cutoff
inter_residue_bond_cutoff = bond_cutoff
saccharide_bond_cutoff = bond_cutoff
link_residues = True
break
else:
continue # exclude this nonbond from consideration
exclude_this_nonbonded = False
if exclude_selections:
for selection_1, selection_2 in exclude_selections:
if selection_2: # check both
if ((i_seq in selection_1 and j_seq in selection_2) or
(i_seq in selection_2 and j_seq in selection_1)):
exclude_this_nonbonded = True
break
else:
if i_seq in selection_1 or j_seq in selection_1:
exclude_this_nonbonded = True
# XXX this is a poor job!!!
if bond_asu_table.contains(i_seq, j_seq, 0): continue
if bond_asu_table.contains(i_seq, j_seq, 1): continue
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
if exclude_this_nonbonded:
key = (selection_1, selection_2)
if key not in exclude_out_lines:
exclude_out_lines[key] = \
' bond %s\n%s%s\n%smodel %.2f' % (
atom1.id_str(),
' '*9,
atom2.id_str(),
' '*6,
distance)
continue
#
# moving sections of this to outside the loop
# - SF4
#
if link_metals:
moved = ['SF4', 'F3S']
if (atom1.parent().resname in moved
or atom2.parent().resname in moved):
continue
if verbose:
print i_seq, j_seq, atom1.quote(),
print atom2.quote(),
print "Distance: %0.2f" % distance, rt_mx_ji, sym_op
# don't link atoms not in the same conformer (works for models also)...
if not atom1.is_in_same_conformer_as(atom2):
assert 0
continue
# don't link atoms in same residue group
if atom1.parent().parent() == atom2.parent().parent(): continue
atom_group1 = atom1.parent()
atom_group2 = atom2.parent()
# dont't like atom groups in different altloc expect " "
if atom_group1.altloc.strip() == atom_group2.altloc.strip(): pass
elif atom_group1.altloc.strip() == "": pass
elif atom_group2.altloc.strip() == "": pass
else: continue
# don't link some classes
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
use_only_bond_cutoff = False
if verbose:
print """
Residue classes
%s
%s """ % (classes1, classes2)
# why was this commented out???
if not link_ligands and (classes1.other or classes2.other):
continue
if (not link_small_molecules
and (classes1.common_small_molecule
or classes2.common_small_molecule)):
continue
# is_proxy_set between any of the atoms ????????
if classes1.common_amino_acid and classes2.common_amino_acid:
if not link_residues:
continue
# special amino acid linking
# - cyclic
# - beta, delta ???
if possible_cyclic_peptide(atom1,
atom2): # first & last peptide
use_only_bond_cutoff = True
if sym_op:
if classes1.common_amino_acid and classes2.common_saccharide:
continue
if classes2.common_amino_acid and classes1.common_saccharide:
continue
#
# bonded atoms can't link to same atom, eg MG-PG and MG-O1P
#
if bond_data:
bonded = False
if i_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[i_seq]:
if bond_asu_table.contains(j_seq, t_i, 0):
bonded = True
if j_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[j_seq]:
if bond_asu_table.contains(i_seq, t_i, 0):
bonded = True
if bonded: continue
#
key = [
atom1.id_str()[9:-1],
atom2.id_str()[9:-1],
]
key.sort()
if sym_op:
key.append(str(rt_mx_ji))
key = tuple(key)
# hydrogens
if atom1.element.strip() in hydrogens:
done[atom2.id_str()] = atom1.id_str()
if atom2.element.strip() in hydrogens:
done[atom1.id_str()] = atom2.id_str()
# bond length cutoff & some logic
if not linking_utils.is_atom_pair_linked(
atom1,
atom2,
distance=distance,
max_bonded_cutoff=max_bonded_cutoff,
amino_acid_bond_cutoff=amino_acid_bond_cutoff,
inter_residue_bond_cutoff=inter_residue_bond_cutoff,
second_row_buffer=second_row_buffer,
saccharide_bond_cutoff=carbohydrate_bond_cutoff,
metal_coordination_cutoff=metal_coordination_cutoff,
use_only_bond_cutoff=use_only_bond_cutoff,
link_metals=link_metals,
verbose=verbose,
):
if verbose:
print "is not linked", atom1.quote(), atom2.quote(), key
print 'link_metals', link_metals
if (atom1.element.strip().upper() in hydrogens
or atom2.element.strip().upper() in hydrogens):
pass
else:
done.setdefault(key, [])
done[key].append([atom1.name, atom2.name])
continue
# check some valences...
if not (classes1.common_element or classes2.common_element):
if not linking_utils.check_valence(self.pdb_hierarchy, atom1):
print >> log, " Atom %s rejected from bonding due to valence issues." % atom1.quote(
)
continue
if not linking_utils.check_valence(self.pdb_hierarchy, atom2):
print >> log, " Atom %s rejected from bonding due to valence issues." % atom2.quote(
)
continue
# got a link....
class1 = linking_utils.get_classes(
atom1, #_group1.resname,
important_only=True,
)
class2 = linking_utils.get_classes(
atom2, #_group2.resname,
important_only=True,
)
class_key = [class1, class2]
class_key.sort()
class_key = tuple(class_key)
if verbose: print 'class_key', class_key
#
if not link_metals and "metal" in class_key: continue
#atoms_must_be = {}
if not link_residues:
if class_key in [
("common_amino_acid", "common_amino_acid"),
#("common_amino_acid", "other"),
]:
continue
#else:
# atoms_must_be.setdefault(("common_amino_acid",
# "common_amino_acid"),["C", "N"])
# atoms_must_be.setdefault(("common_amino_acid", "other"),["C", "N"])
if not link_carbohydrates and "common_saccharide" in class_key:
continue
if not link_amino_acid_rna_dna:
if "common_amino_acid" in class_key and "common_rna_dna" in class_key:
continue
#
names = [atom1.name, atom2.name]
if verbose: print 'names', names
names.sort()
atom1_key = None
atom2_key = None
if class1 in linking_setup.maximum_per_atom_links: # is one
atom1_key = atom1.id_str()
if class2 in linking_setup.maximum_per_atom_links: # is one
atom2_key = atom2.id_str()
if verbose:
print '-' * 80
print 'class_key', class_key
print 'done'
for k, item in done.items():
print "> %s : %s" % (k, item)
print 'key', key
print 'atom keys', atom1_key, atom2_key
# exclude duplicate symmetry op.
if key in done:
if names in done[key]: continue
if atom1.parent().altloc == atom2.parent().altloc:
if atom1_key:
if atom1_key in done: continue
done[atom1_key] = key
if atom2_key:
if atom2_key in done: continue
done[atom2_key] = key
#
current_number_of_links = len(done.setdefault(key, []))
if (current_number_of_links >=
linking_setup.maximum_inter_residue_links.get(
class_key, 1)):
if verbose:
print "too many links:", current_number_of_links, linking_setup.maximum_inter_residue_links.get(
class_key, 1), class_key
continue
#
done[key].append(names)
done_key = key
# get all possible links
i_seqs = []
for atom in atom_group1.atoms():
i_seqs.append(atom.i_seq)
j_seqs = []
for atom in atom_group2.atoms():
j_seqs.append(atom.i_seq)
ij_seqs = []
for i in i_seqs:
for j in j_seqs:
tmp = [i, j]
tmp.sort()
ij_seqs.append(tuple(tmp))
# check that a link not already made
link_found = False
if verbose:
print 'len simple bond proxies', len(
geometry_proxy_registries.bond_simple.proxies)
# Consistency check - debugging only
# for bsp in geometry_proxy_registries.bond_simple.proxies:
# if bsp.i_seqs[1] not in initial_pair_asu_table_table[bsp.i_seqs[0]].keys():
# print "ERROR!!!", bsp.i_seqs
# STOP()
# Proposed fast loop: Time building additional restraints for
# ribosome went from 5272 to 204 seconds.
for p in ij_seqs:
if p[1] in initial_pair_asu_table_table[p[0]].keys():
link_found = True
break
# VERY SLOW !!! - original loop
# for bond_simple_proxy in geometry_proxy_registries.bond_simple.proxies:
# if bond_simple_proxy.i_seqs in ij_seqs:
# link_found = True
# break
if link_found: continue
# check for any link between atom groups based on residue name, eg ASN-NAG
# get predefined link
link, swap, key = linking_utils.is_atom_group_pair_linked(
atom_group1,
atom_group2,
self.mon_lib_srv,
)
if verbose:
print 'link', link
print 'swap', swap
print 'key', key
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
space_group = self.special_position_settings.space_group()
#
if len(done_key) == 2:
link_rt_mx_ji = sgtbx.rt_mx(symbol="x,y,z",
t_den=space_group.t_den())
else:
link_rt_mx_ji = sgtbx.rt_mx(symbol=done_key[2],
t_den=space_group.t_den())
#
if link:
# apply a standard link
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
if len(bond_i_seqs) == 0:
if verbose:
print 'failed to link using %s' % key
continue
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs[0] # odd?
if verbose: print "predefined residue named link", key
self._cif.cif["link_%s" % key] = link.cif_object
continue
#
#if atoms_must_be:
# # this could be fancier...
# # link_residues is peptide and SG links
# atoms_must_be_key = [atom1.element.strip(), atom2.element.strip()]
# #atoms_must_be_key = [atom1.name.strip(), atom2.name.strip()]
# atoms_must_be_key.sort()
# if class_key in atoms_must_be and "S" not in atoms_must_be_key:
# if atoms_must_be[class_key]!=atoms_must_be_key:
# continue
rc = linking_utils.process_atom_groups_for_linking_single_link(
self.pdb_hierarchy,
atom1,
atom2,
verbose=verbose,
)
if not rc:
done.remove_link(done_key, names)
continue
pdbres, link_key, link_atoms = rc
assert len(link_key) == 1
key = link_key[0]
link = self.mon_lib_srv.link_link_id_dict.get(key, None)
if verbose:
print 'pdbres', pdbres
print 'link', link
print 'link_key', link_key
print 'link_atoms', link_atoms
if key.find("ALPHA1") > -1 or key.find(
"BETA1") > -1: # is handled in elif
key, cif, bond_i_seqs = \
glyco_utils.apply_glyco_link_using_proxies_and_atoms(
atom_group2,
atom_group1,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
link_carbon_dist=carbohydrate_bond_cutoff,
)
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs
self._cif.cif["link_%s" % key] = cif
continue
elif link:
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs[0]
continue
else:
# possible peptide or rna/dna link
rc = check_for_peptide_links(atom1, atom2)
# no peptide links across symmetry
if len(done_key) == 3:
rc = None
if rc:
key, swap = rc
link = self.mon_lib_srv.link_link_id_dict.get(key)
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
rc = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
if not rc:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
rc = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
)
# not added to links so not LINK record
if sym_op:
sym_links += 1
link_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
key,
))
else:
simple_links += 1
link_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx_ji,
key,
))
continue
#
custom_links.setdefault(ii, [])
custom_links[ii].append([atom_group1, atom_group2, atom1, atom2])
# simple
bond_name = "bond"
if ((classes1.common_rna_dna or classes1.ccp4_mon_lib_rna_dna) and
(classes2.common_rna_dna or classes2.ccp4_mon_lib_rna_dna)):
bond_name = "h-dna"
elif (linking_utils.get_classes(atom1, important_only=True)
== "metal" or linking_utils.get_classes(
atom2, important_only=True) == "metal"):
bond_name = "metal-coordination"
if sym_op:
sym_bonds += 1
bond_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
bond_name,
))
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy)
else:
simple_bonds += 1
bond_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx,
bond_name,
))
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy.i_seqs)
# END MAIN LOOP for ii, item in enumerate(nonbonded?)
#
#
if verbose:
for key in sorted(custom_links):
print '-' * 80
print key
for pair in custom_links[key]:
for atom in pair:
try:
print atom.quote()
except Exception:
print atom
pair_sym_table = pair_asu_table.extract_pair_sym_table()
n_simple, n_symmetry = 0, 0
self.pdb_link_records.setdefault("LINK", [])
retain = []
for ijk, sym_pair in enumerate(pair_sym_table.iterator()):
i_seq, j_seq = sym_pair.i_seqs()
origin_id = 0
if bond_data[ijk][-1] == "metal-coordination": origin_id = 2
#assert len(bond_i_seqs)==1
assert i_seq == nonbonded_i_seqs[i_seq]
assert j_seq == nonbonded_i_seqs[j_seq]
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
# check for NA linkage
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
ans = bondlength_defaults.run(atom1, atom2)
equil = 2.3
weight = 0.02
slack = 0.
if len(ans) > 0:
equil = ans[0]
if len(ans) > 1:
weight = ans[1]
if len(ans) > 2:
slack = ans[2]
if equil is None:
equil = 2.3
added_to_asu_table = False
try:
#bond_asu_table.add_pair([i_seq, j_seq])
bond_asu_table.add_pair(i_seq=i_seq,
j_seq=j_seq,
rt_mx_ji=sym_pair.rt_mx_ji)
added_to_asu_table = True
except RuntimeError, e:
error = """
Difficulties linking atoms
%s
%s
Suggestions include providing restraints for any unknown residues.
""" % (atom1.quote(), atom2.quote())
print >> log, error
if added_to_asu_table:
retain.append(ijk)
if (sym_pair.rt_mx_ji.is_unit_mx()): n_simple += 1
else: n_symmetry += 1
bond_params_table.update(
i_seq=i_seq,
j_seq=j_seq,
params=geometry_restraints.bond_params(
distance_ideal=equil,
weight=1.0 / weight**2,
slack=slack,
origin_id=origin_id,
))
# adding link to PDB
self.pdb_link_records["LINK"].append([
self.pdb_atoms[i_seq], self.pdb_atoms[j_seq],
sym_pair.rt_mx_ji
])