"""
Bonds
=====
PROPKA representation of bonds.
"""
import math
import json
import pkg_resources
import propka.calculations
# TODO - replace the info/warning imports with logging functionality
from propka.lib import info
# TODO - should these constants be defined higher up in the module?
# TODO - I don't know what some of these constants mean
DISULFIDE_DISTANCE = 2.5
FLUORIDE_DISTANCE = 1.7
HYDROGEN_DISTANCE = 1.5
DEFAULT_DISTANCE = 2.0
BOX_SIZE = 2.5
POS_MAX = 1e6
[docs]class BondMaker:
"""Makes bonds?
TODO - the documentation for this class needs to be improved.
"""
def __init__(self):
# predefined bonding distances
self.distances = {'S-S' : DISULFIDE_DISTANCE,
'F-F' : FLUORIDE_DISTANCE}
self.distances_squared = {}
for key in self.distances:
self.distances_squared[key] = (
self.distances[key] * self.distances[key])
h_dist = HYDROGEN_DISTANCE
self.default_dist = DEFAULT_DISTANCE
self.h_dist_squared = h_dist * h_dist
self.default_dist_squared = self.default_dist * self.default_dist
distances = (
list(self.distances_squared.values())
+ [self.default_dist_squared])
self.max_sq_distance = max(distances)
# protein bonding data
self.data_file_name = (
pkg_resources.resource_filename(__name__, 'protein_bonds.json'))
with open(self.data_file_name, 'rt') as json_file:
self.protein_bonds = json.load(json_file)
self.intra_residue_backbone_bonds = {'N': ['CA'], 'CA': ['N', 'C'],
'C': ['CA', 'O'], 'O': ['C']}
self.num_pi_elec_bonds_backbone = {'C': 1, 'O': 1}
self.num_pi_elec_conj_bonds_backbone = {'N': 1}
self.num_pi_elec_bonds_sidechains = {'ARG-CZ' : 1, 'ARG-NH1': 1,
'ASN-OD1': 1, 'ASN-CG' : 1,
'ASP-OD1': 1, 'ASP-CG' : 1,
'GLU-OE1': 1, 'GLU-CD' : 1,
'GLN-OE1': 1, 'GLN-CD' : 1,
'HIS-CG' : 1, 'HIS-CD2': 1,
'HIS-ND1': 1, 'HIS-CE1': 1,
'PHE-CG' : 1, 'PHE-CD1': 1,
'PHE-CE1': 1, 'PHE-CZ' : 1,
'PHE-CE2': 1, 'PHE-CD2': 1,
'TRP-CG' : 1, 'TRP-CD1': 1,
'TRP-CE2': 1, 'TRP-CD2': 1,
'TRP-CE3': 1, 'TRP-CZ3': 1,
'TRP-CH2': 1, 'TRP-CZ2': 1,
'TYR-CG' : 1, 'TYR-CD1': 1,
'TYR-CE1': 1, 'TYR-CZ' : 1,
'TYR-CE2': 1, 'TYR-CD2': 1}
self.num_pi_elec_conj_bonds_sidechains = {'ARG-NE': 1, 'ARG-NH2': 1,
'ASN-ND2': 1, 'GLN-NE2': 1,
'HIS-NE2': 1, 'TRP-NE1': 1}
self.num_pi_elec_bonds_ligands = {'C.ar': 1, 'N.pl3': 0, 'C.2': 1,
'O.2': 1, 'O.co2': 1, 'N.ar': 1,
'C.1': 2, 'N.1': 2}
self.num_pi_elec_conj_bonds_ligands = {'N.am': 1, 'N.pl3': 1}
self.backbone_atoms = list(self.intra_residue_backbone_bonds.keys())
self.terminal_oxygen_names = ['OXT', 'O\'\'']
self.boxes = {}
self.num_box_x = None
self.num_box_y = None
self.num_box_z = None
[docs] def find_bonds_for_protein(self, protein):
"""Bonds proteins based on the way atoms normally bond.
Args:
protein: the protein to search for bonds
"""
info('++++ Side chains ++++')
# side chains
for chain in protein.chains:
for residue in chain.residues:
if residue.res_name.replace(' ', '') not in ['N+', 'C-']:
self.find_bonds_for_side_chain(residue.atoms)
info('++++ Backbones ++++')
# backbone
last_residues = []
for chain in protein.chains:
for i in range(1, len(chain.residues)):
if (chain.residues[i-1].res_name.replace(' ', '')
not in ['N+', 'C-']):
if (chain.residues[i].res_name.replace(' ', '')
not in ['N+', 'C-']):
self.connect_backbone(chain.residues[i-1],
chain.residues[i])
last_residues.append(chain.residues[i])
info('++++ terminal oxygen ++++')
# terminal OXT
for last_residue in last_residues:
self.find_bonds_for_terminal_oxygen(last_residue)
info('++++ cysteines ++++')
# Cysteines
for chain in protein.chains:
for i in range(0, len(chain.residues)):
if chain.residues[i].res_name == 'CYS':
for j in range(0, len(chain.residues)):
if chain.residues[j].res_name == 'CYS' and j != i:
self.check_for_cysteine_bonds(chain.residues[i],
chain.residues[j])
[docs] def check_for_cysteine_bonds(self, cys1, cys2):
"""Looks for potential bonds between two cysteines.
Args:
cys1: one of the cysteines to check
cys1: one of the cysteines to check
"""
for atom1 in cys1.atoms:
if atom1.name == 'SG':
for atom2 in cys2.atoms:
if atom2.name == 'SG':
dist = propka.calculations.squared_distance(atom1,
atom2)
# TODO - is SS_dist_squared an attribute of this class?
if dist < self.SS_dist_squared:
self.make_bond(atom1, atom2)
[docs] def find_bonds_for_terminal_oxygen(self, residue):
"""Look for bonds for terminal oxygen.
Args:
residue - test residue
"""
for atom1 in residue.atoms:
if atom1.name in self.terminal_oxygen_names:
for atom2 in residue.atoms:
if atom2.name == 'C':
self.make_bond(atom1, atom2)
[docs] def connect_backbone(self, residue1, residue2):
"""Sets up bonds in the backbone
Args:
residue1: first residue to connect
residue2: second residue to connect
"""
self.find_bonds_for_residue_backbone(residue1)
self.find_bonds_for_residue_backbone(residue2)
for atom1 in residue1.atoms:
if atom1.name == 'C':
for atom2 in residue2.atoms:
if atom2.name == 'N':
if (propka.calculations.squared_distance(atom1, atom2)
< self.default_dist_squared):
self.make_bond(atom1, atom2)
[docs] def find_bonds_for_residue_backbone(self, residue):
"""Find bonds for this residue's backbone.
Args:
residue: reside to search for backbone bonds.
"""
for atom1 in residue.atoms:
if atom1.name in list(self.num_pi_elec_bonds_backbone.keys()):
atom1.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_backbone[atom1.name])
if atom1.name in (
list(self.num_pi_elec_conj_bonds_backbone.keys())
and len(atom1.bonded_atoms) > 1): # avoid N-term
atom1.num_pi_elec_conj_2_3_bonds = (
self.num_pi_elec_conj_bonds_backbone[atom1.name])
if atom1.name in self.backbone_atoms:
for atom2 in residue.atoms:
if atom2.name in (
self.intra_residue_backbone_bonds[atom1.name]):
self.make_bond(atom1, atom2)
[docs] def find_bonds_for_side_chain(self, atoms):
"""Finds bonds for a side chain.
Args:
atoms: list of atoms to check for bonds
"""
for atom1 in atoms:
key = '{0:s}-{1:s}'.format(atom1.res_name, atom1.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
atom1.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_sidechains[key])
if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()):
atom1.num_pi_elec_conj_2_3_bonds = (
self.num_pi_elec_conj_bonds_sidechains[key])
if not atom1.name in self.backbone_atoms:
if not atom1.name in self.terminal_oxygen_names:
for atom2 in atoms:
if atom2.name in (
self
.protein_bonds[atom1.res_name][atom1.name]):
self.make_bond(atom1, atom2)
[docs] def find_bonds_for_ligand(self, ligand):
"""Finds bonds for all atoms in the ligand molecule
Args:
ligand: ligand molecule to search for bonds
"""
# identify bonding atoms
self.find_bonds_for_atoms(ligand.atoms)
self.add_pi_electron_table_info(ligand.atoms)
[docs] def add_pi_electron_table_info(self, atoms):
"""Add table information on pi electrons
Args:
atoms: list of atoms for pi electron table information checking
"""
# apply table information on pi-electrons
for atom in atoms:
# for ligands
if atom.type == 'hetatm':
if atom.sybyl_type in self.num_pi_elec_bonds_ligands.keys():
atom.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_ligands[atom.sybyl_type])
if atom.sybyl_type in (
self.num_pi_elec_conj_bonds_ligands.keys()):
atom.num_pi_elec_conj_2_3_bonds = (
self.num_pi_elec_conj_bonds_ligands[atom.sybyl_type])
# for protein
if atom.type == 'atom':
key = '{0:s}-{1:s}'.format(atom.res_name, atom.name)
if key in list(self.num_pi_elec_bonds_sidechains.keys()):
atom.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_sidechains[key])
if key in list(self.num_pi_elec_conj_bonds_sidechains.keys()):
atom.num_pi_elec_conj_2_3_bonds = (
self.num_pi_elec_conj_bonds_sidechains[key])
if atom.name in list(self.num_pi_elec_bonds_backbone.keys()):
atom.num_pi_elec_2_3_bonds = (
self.num_pi_elec_bonds_backbone[atom.name])
if atom.name in list(
self.num_pi_elec_conj_bonds_backbone.keys()) and (
len(atom.bonded_atoms) > 1):
# last part to avoid including N-term
atom.num_pi_elec_conj_2_3_bonds = (
self.num_pi_elec_conj_bonds_backbone[atom.name])
[docs] def find_bonds_for_protein_by_distance(self, molecule):
"""Finds bonds for all atoms in the molecule.
Args:
molecule: molecule in which to find bonds.
Returns:
list of atoms
"""
#self.find_bonds_for_protein(molecule)
atoms = []
for chain in molecule.chains:
for residue in chain.residues:
if residue.res_name.replace(' ', '') not in ['N+', 'C-']:
for atom in residue.atoms:
atoms.append(atom)
self.find_bonds_for_atoms_using_boxes(atoms)
return atoms
[docs] def find_bonds_for_atoms(self, atoms):
"""Finds all bonds for a list of atoms
Args:
atoms: list of atoms in which to find bonds.
"""
no_atoms = len(atoms)
for i in range(no_atoms):
for j in range(i+1, no_atoms):
if atoms[i] in atoms[j].bonded_atoms:
continue
if self.check_distance(atoms[i], atoms[j]):
self.make_bond(atoms[i], atoms[j])
# di-sulphide bonds
if atoms[i].element == 'S' and atoms[j].element == 'S':
atoms[i].cysteine_bridge = True
atoms[j].cysteine_bridge = True
[docs] def check_distance(self, atom1, atom2):
"""Check distance between two atoms
Args:
atom1: first atom for distance check
atom2: second atom for distance check
Returns:
True if within distance, False otherwise
"""
sq_dist = propka.calculations.squared_distance(atom1, atom2)
if sq_dist > self.max_sq_distance:
return False
key = '{0:s}-{1:s}'.format(atom1.element, atom2.element)
h_count = key.count('H')
if sq_dist < self.h_dist_squared and h_count == 1:
return True
if sq_dist < self.default_dist_squared and h_count == 0:
return True
if key in self.distances_squared.keys():
if sq_dist < self.distances_squared[key]:
return True
return False
[docs] def find_bonds_for_molecules_using_boxes(self, molecules):
""" Finds all bonds for a molecular container.
Args:
molecules: list of molecules for finding bonds.
"""
for name in molecules.conformation_names:
self.find_bonds_for_atoms_using_boxes(
molecules.conformations[name].atoms)
[docs] def find_bonds_for_atoms_using_boxes(self, atoms):
"""Finds all bonds for a list of atoms.
Args:
atoms: list of atoms for finding bonds
"""
box_size = BOX_SIZE
xmin = POS_MAX
xmax = -1.0 * POS_MAX
ymin = POS_MAX
ymax = -1.0 * POS_MAX
zmin = POS_MAX
zmax = -1.0 * POS_MAX
for atom in atoms:
if atom.x > xmax:
xmax = atom.x
if atom.y > ymax:
ymax = atom.y
if atom.z > zmax:
zmax = atom.z
if atom.x < xmin:
xmin = atom.x
if atom.y < ymin:
ymin = atom.y
if atom.z < zmin:
zmin = atom.z
xlen = xmax - xmin
ylen = ymax - ymin
zlen = zmax - zmin
self.num_box_x = max(1, int(math.ceil(xlen/box_size)))
self.num_box_y = max(1, int(math.ceil(ylen/box_size)))
self.num_box_z = max(1, int(math.ceil(zlen/box_size)))
self.boxes = {}
for x in range(self.num_box_x):
for y in range(self.num_box_y):
for z in range(self.num_box_z):
self.boxes[(x, y, z)] = []
for atom in atoms:
x = math.floor((atom.x - xmin)/box_size)
y = math.floor((atom.y - ymin)/box_size)
z = math.floor((atom.z - zmin)/box_size)
self.put_atom_in_box(x, y, z, atom)
for value in self.boxes.values():
self.find_bonds_for_atoms(value)
[docs] def put_atom_in_box(self, x, y, z, atom):
"""Put an atom in a box.
Args:
x: box x-coordinates
y: box y-coordinates
z: box z-coordinates
atom: the atom to place in a box
"""
for box_x in [x, x+1]:
for box_y in [y, y+1]:
for box_z in [z, z+1]:
key = (box_x, box_y, box_z)
try:
self.boxes[key].append(atom)
except KeyError:
pass
[docs] @staticmethod
def has_bond(atom1, atom2):
"""Look for bond between two atoms.
Args:
atom1: first atom to check
atom2: second atom to check
Returns:
True if there is a bond between atoms
"""
if atom1 in atom2.bonded_atoms or atom2 in atom1.bonded_atoms:
return True
return False
[docs] @staticmethod
def make_bond(atom1, atom2):
"""Makes a bond between atom1 and atom2
Args:
atom1: first atom to bond
atom2: second atom to bond
"""
if atom1 == atom2:
return
if not atom1 in atom2.bonded_atoms:
atom2.bonded_atoms.append(atom1)
if not atom2 in atom1.bonded_atoms:
atom1.bonded_atoms.append(atom2)
[docs] def generate_protein_bond_dictionary(self, atoms):
"""Generate dictionary of protein bonds.
Args:
atoms: list of atoms for bonding
"""
for atom in atoms:
for bonded_atom in atom.bonded_atoms:
resi_i = atom.res_name
name_i = atom.name
resi_j = bonded_atom.res_name
name_j = bonded_atom.name
if not name_i in (
self.backbone_atoms
or not name_j in self.backbone_atoms):
if not name_i in (
self.terminal_oxygen_names
and not name_j in self.terminal_oxygen_names):
if not resi_i in list(self.protein_bonds.keys()):
self.protein_bonds[resi_i] = {}
if not name_i in self.protein_bonds[resi_i]:
self.protein_bonds[resi_i][name_i] = []
if not name_j in self.protein_bonds[resi_i][name_i]:
self.protein_bonds[resi_i][name_i].append(name_j)
if not resi_j in list(self.protein_bonds.keys()):
self.protein_bonds[resi_j] = {}
if not name_j in self.protein_bonds[resi_j]:
self.protein_bonds[resi_j][name_j] = []
if not name_i in self.protein_bonds[resi_j][name_j]:
self.protein_bonds[resi_j][name_j].append(name_i)