def is_atom_pair_linked(atom1,
atom2,
distance=None,
max_bonded_cutoff=3.,
amino_acid_bond_cutoff=1.9,
rna_dna_bond_cutoff=3.4,
rna_dna_angle_cutoff=35,
inter_residue_bond_cutoff=1.99,
second_row_buffer=.5,
metal_coordination_cutoff=3.,
saccharide_bond_cutoff=3.,
sulfur_bond_cutoff=2.5,
other_bond_cutoff=2., # this is the ligand distance
use_only_bond_cutoff=False,
link_metals=True,
verbose=False,
):
if atom1.element.strip().upper() in ad_hoc_non_linking_elements:
return False
if atom2.element.strip().upper() in ad_hoc_non_linking_elements:
return False
atom_pair = [atom1.element.strip().upper(), atom2.element.strip().upper()]
atom_pair.sort()
if atom_pair in ad_hoc_non_linking_pairs:
return False
skip_if_both = linking_setup.skip_if_both
skip_if_longer = linking_setup.update_skip_if_longer(amino_acid_bond_cutoff,
rna_dna_bond_cutoff,
inter_residue_bond_cutoff,
saccharide_bond_cutoff,
metal_coordination_cutoff,
sulfur_bond_cutoff,
other_bond_cutoff,
)
class1 = get_classes(atom1, important_only=True)
class2 = get_classes(atom2, important_only=True)
class1 = linking_setup.adjust_class(atom1, class1)
class2 = linking_setup.adjust_class(atom2, class2)
if ( linking_setup.sulfur_class(atom1, class1)=="sulfur" and
linking_setup.sulfur_class(atom2, class2)=="sulfur" ):
class1 = 'sulfur'
class2 = 'sulfur'
lookup = [class1, class2]
lookup.sort()
if verbose: print('lookup1',lookup,skip_if_both) #.get(lookup, None)
if lookup in skip_if_both: return False
lookup = tuple(lookup)
if verbose: print('lookup2',lookup)
limit = skip_if_longer.get(lookup, None)
if limit is not None:
if ( atom1.element not in ad_hoc_first_row or
atom2.element not in ad_hoc_first_row):
limit += second_row_buffer**2 # not completely accurate
if verbose: print('limit',limit)
if distance:
d2 = distance**2
else:
d2 = get_distance2(atom1, atom2)
if verbose: print("d2",d2)
if limit is not None and limit<d2:
if verbose: print('limit < d2',limit,d2)
return False
if use_only_bond_cutoff:
if verbose: print('use_only_bond_cutoff',use_only_bond_cutoff)
return True
#
if "common_rna_dna" in lookup and "common_amino_acid" in lookup:
return True
if "common_rna_dna" in lookup and "common_small_molecule" in lookup:
return True
if "common_amino_acid" in lookup and "common_small_molecule" in lookup:
return True
if "other" in lookup and "common_small_molecule" in lookup:
return True
#
# sulfur bridge
#
if verbose:
print(atom1.quote(),linking_setup.sulfur_class(atom1, class1))
print(atom2.quote(),linking_setup.sulfur_class(atom2, class2))
if ( linking_setup.sulfur_class(atom1, class1)=="sulfur" and
linking_setup.sulfur_class(atom2, class2)=="sulfur" ):
return True
#
# saccharides
#
if verbose: print('checking common_saccharide',lookup)
if "common_saccharide" in lookup:
limit = saccharide_bond_cutoff*saccharide_bond_cutoff
if "metal" in lookup:
limit = metal_coordination_cutoff*metal_coordination_cutoff
if verbose: print('d2,limit',d2,limit)
if d2>limit:
return False
return True
#
# metals
#
if "common_element" in lookup:
if(atom1.element.strip().upper() in ad_hoc_single_metal_residue_element_types or
atom2.element.strip().upper() in ad_hoc_single_metal_residue_element_types
):
return True
else:
print('lookup',lookup)
print(atom1.quote())
print(atom2.quote())
assert 0
if "metal" in lookup:
if not linking_setup.skip_if_non_linking(lookup, atom1, atom2):
return False
else:
if link_metals:
return is_atom_metal_coordinated(lookup, atom1, atom2)
return link_metals
#
# amino acids
#
if class1=="common_amino_acid" and class2=="common_amino_acid":
if verbose:
print("AMINO ACIDS",atom1.quote(), atom2.quote())
#
# other
#
if lookup==("other", "other"):
# non-standard residue to non-standard is too risky to do automatically ...
if verbose: print('other, other returns True')
return True
elif "other" in lookup:
if verbose: print('other returns True')
return True
if verbose: print('drop through '*5)
return False
def is_atom_pair_linked(atom1,
atom2,
distance=None,
max_bonded_cutoff=3.,
amino_acid_bond_cutoff=1.9,
rna_dna_bond_cutoff=3.4,
rna_dna_angle_cutoff=35,
inter_residue_bond_cutoff=1.99,
second_row_buffer=.5,
metal_coordination_cutoff=3.,
saccharide_bond_cutoff=3.,
sulfur_bond_cutoff=2.5,
other_bond_cutoff=2., # this is the ligand distance
use_only_bond_cutoff=False,
link_metals=True,
verbose=False,
):
if atom1.element.strip().upper() in ad_hoc_non_linking_elements:
return False
if atom2.element.strip().upper() in ad_hoc_non_linking_elements:
return False
atom_pair = [atom1.element.strip().upper(), atom2.element.strip().upper()]
atom_pair.sort()
if atom_pair in ad_hoc_non_linking_pairs:
return False
skip_if_both = linking_setup.skip_if_both
skip_if_longer = linking_setup.update_skip_if_longer(amino_acid_bond_cutoff,
rna_dna_bond_cutoff,
inter_residue_bond_cutoff,
saccharide_bond_cutoff,
metal_coordination_cutoff,
sulfur_bond_cutoff,
other_bond_cutoff,
)
class1 = get_classes(atom1, important_only=True)
class2 = get_classes(atom2, important_only=True)
class1 = linking_setup.adjust_class(atom1, class1)
class2 = linking_setup.adjust_class(atom2, class2)
if ( linking_setup.sulfur_class(atom1, class1)=="sulfur" and
linking_setup.sulfur_class(atom2, class2)=="sulfur" ) :
class1 = 'sulfur'
class2 = 'sulfur'
lookup = [class1, class2]
lookup.sort()
if verbose: print 'lookup1',lookup,skip_if_both #.get(lookup, None)
if lookup in skip_if_both: return False
lookup = tuple(lookup)
if verbose: print 'lookup2',lookup
limit = skip_if_longer.get(lookup, None)
if limit is not None:
if ( atom1.element not in ad_hoc_first_row or
atom2.element not in ad_hoc_first_row):
limit += second_row_buffer**2 # not completely accurate
if verbose: print 'limit',limit
if distance:
d2 = distance**2
else:
d2 = get_distance2(atom1, atom2)
if verbose: print "d2",d2
if limit is not None and limit<d2:
if verbose: print 'limit < d2',limit,d2
return False
if use_only_bond_cutoff:
if verbose: print 'use_only_bond_cutoff',use_only_bond_cutoff
return True
#
if "common_rna_dna" in lookup and "common_amino_acid" in lookup:
return True
if "common_rna_dna" in lookup and "common_small_molecule" in lookup:
return True
if "common_amino_acid" in lookup and "common_small_molecule" in lookup:
return True
if "other" in lookup and "common_small_molecule" in lookup:
return True
#
# sulfur bridge
#
if verbose:
print atom1.quote(),linking_setup.sulfur_class(atom1, class1)
print atom2.quote(),linking_setup.sulfur_class(atom2, class2)
if ( linking_setup.sulfur_class(atom1, class1)=="sulfur" and
linking_setup.sulfur_class(atom2, class2)=="sulfur" ) :
return True
#
# saccharides
#
if verbose: print 'checking common_saccharide',lookup
if "common_saccharide" in lookup:
limit = saccharide_bond_cutoff*saccharide_bond_cutoff
if "metal" in lookup:
limit = metal_coordination_cutoff*metal_coordination_cutoff
if verbose: print 'd2,limit',d2,limit
if d2>limit:
return False
return True
#
# metals
#
if "common_element" in lookup:
if(atom1.element.strip().upper() in ad_hoc_single_metal_residue_element_types or
atom2.element.strip().upper() in ad_hoc_single_metal_residue_element_types
):
return True
else:
print 'lookup',lookup
print atom1.quote()
print atom2.quote()
assert 0
if "metal" in lookup:
return link_metals
#
# amino acids
#
if class1=="common_amino_acid" and class2=="common_amino_acid":
if verbose:
print "AMINO ACIDS",atom1.quote(), atom2.quote()
#
# other
#
if lookup==("other", "other"):
# non-standard residue to non-standard is too risky to do automatically ...
if verbose: print 'other, other returns True'
return True
elif "other" in lookup:
if verbose: print 'other returns True'
return True
if verbose: print 'drop through '*5
return False