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De-lint bonds.py

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This commit is contained in:
Nathan Baker
2020-05-23 09:57:53 -07:00
parent e1656a4911
commit f2aef4ce4f
1 changed files with 18 additions and 18 deletions
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36
propka/bonds.py
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@@ -1,16 +1,10 @@
"""PROPKA representation of bonds."""
# TODO - is pickle still used?
import pickle
# TODO - eliminate use of sys
import sys
# TODO - eliminate use of os
import os
import math
import json
import pkg_resources
import propka.calculations
# TODO - replace the info/warning imports with logging functionality
from propka.lib import info, warning
from propka.lib import info
# TODO - should these constants be defined higher up in the module?
@@ -32,11 +26,11 @@ class BondMaker:
# predefined bonding distances
self.distances = {'S-S' : DISULFIDE_DISTANCE, 'F-F' : FLUORIDE_DISTANCE}
self.distances_squared = {}
for k in self.distances.keys():
self.distances_squared[k] = self.distances[k] * self.distances[k]
self.H_dist = HYDROGEN_DISTANCE
for key in self.distances:
self.distances_squared[key] = self.distances[key] * self.distances[key]
self.h_dist = HYDROGEN_DISTANCE
self.default_dist = DEFAULT_DISTANCE
self.H_dist_squared = self.H_dist * self.H_dist
self.h_dist_squared = self.h_dist * self.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)
@@ -74,6 +68,10 @@ 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):
"""Finds bonds proteins based on the way atoms normally bond in proteins.
@@ -289,7 +287,7 @@ class BondMaker:
return False
key = '%s-%s' % (atom1.element, atom2.element)
h_count = key.count('H')
if sq_dist < self.H_dist_squared and h_count == 1:
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
@@ -370,16 +368,17 @@ class BondMaker:
z: box z-coordinates
atom: the atom to place in a box
"""
for bx in [x, x+1]:
for by in [y, y+1]:
for bz in [z, z+1]:
key = (bx, by, bz)
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
def has_bond(self, atom1, atom2):
@classmethod
def has_bond(cls, atom1, atom2):
"""Look for bond between two atoms.
Args:
@@ -392,7 +391,8 @@ class BondMaker:
return True
return False
def make_bond(self, atom1, atom2):
@classmethod
def make_bond(cls, atom1, atom2):
"""Makes a bond between atom1 and atom2
Args: