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Merge pull request #110 from jensengroup/fix-97-speedup-box-bonding

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Fix and speedup box bonding
This commit is contained in:
Thomas Holder
2020-12-03 10:19:01 +01:00
committed by GitHub
parent 45aa08a79c c78345c75c
commit 31b41c32df
1 changed files with 52 additions and 65 deletions
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117
propka/bonds.py
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@@ -81,10 +81,6 @@ class BondMaker:
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
def find_bonds_for_protein(self, protein):
"""Bonds proteins based on the way atoms normally bond.
@@ -286,14 +282,29 @@ class BondMaker:
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
self._find_bonds_for_atoms(atoms[i], atoms[j])
def find_bonds_for_atoms_disjoint(self, atoms1, atoms2):
"""Finds all bonds between two disjoint sets of atoms.
Args:
atoms1: list of atoms
atoms2: list of atoms
"""
for atom1 in atoms1:
for atom2 in atoms2:
self._find_bonds_for_atoms(atom1, atom2)
def _find_bonds_for_atoms(self, atom1, atom2):
assert atom1 is not atom2
if atom1 in atom2.bonded_atoms:
return
if self.check_distance(atom1, atom2):
self.make_bond(atom1, atom2)
# di-sulphide bonds
if atom1.element == 'S' and atom2.element == 'S':
atom1.cysteine_bridge = True
atom2.cysteine_bridge = True
def check_distance(self, atom1, atom2):
"""Check distance between two atoms
@@ -344,62 +355,38 @@ class BondMaker:
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
box_size = max(BOX_SIZE, self.max_sq_distance**0.5 + 0.01)
boxes = {}
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():
x = math.floor(atom.x / box_size)
y = math.floor(atom.y / box_size)
z = math.floor(atom.z / box_size)
boxes.setdefault((x, y, z), []).append(atom)
for (x, y, z), value in boxes.items():
self.find_bonds_for_atoms(value)
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
for (dx, dy, dz) in [
(-1, -1, -1),
(-1, -1, 0),
(-1, -1, 1),
(-1, 0, -1),
(-1, 0, 0),
(-1, 0, 1),
(-1, 1, -1),
(-1, 1, 0),
(-1, 1, 1),
(0, -1, -1),
(0, -1, 0),
(0, -1, 1),
(0, 0, -1),
]:
try:
value2 = boxes[x + dx, y + dy, z + dz]
except KeyError:
continue
self.find_bonds_for_atoms_disjoint(value, value2)
@staticmethod
def has_bond(atom1, atom2):