Source code for mmtfPyspark.utils.distanceBox
#!/user/bin/env python
'''distanceBox.py:
This code is a modification from BioJava's distanceBox class
References
----------
- `BioJava distanceBox <https://github.com/biojava/biojava/blob/359dce819e7678879ae41301b11fa268f92e81d1/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java>`_
'''
__author__ = "Mars (Shih-Cheng) Huang"
__maintainer__ = "Mars (Shih-Cheng) Huang"
__email__ = "marshuang80@gmail.com"
__version__ = "0.2.0"
__status__ = "Done"
import numpy as np
from collections import defaultdict
[docs]class DistanceBox(object):
offset = [
0 + (0 * 10000) + (0 * 1000000000),
-1 + (-1 * 10000) + (-1 * 1000000000),
-1 + (-1 * 10000) + (0 * 1000000000),
-1 + (-1 * 10000) + (1 * 1000000000),
-1 + (0 * 10000) + (-1 * 1000000000),
-1 + (0 * 10000) + (0 * 1000000000),
-1 + (0 * 10000) + (1 * 1000000000),
-1 + (1 * 10000) + (-1 * 1000000000),
-1 + (1 * 10000) + (0 * 1000000000),
-1 + (1 * 10000) + (1 * 1000000000),
0 + (-1 * 10000) + (-1 * 1000000000),
0 + (-1 * 10000) + (0 * 1000000000),
0 + (-1 * 10000) + (1 * 1000000000),
0 + (0 * 10000) + (-1 * 1000000000),
0 + (0 * 10000) + (1 * 1000000000),
0 + (1 * 10000) + (-1 * 1000000000),
0 + (1 * 10000) + (0 * 1000000000),
0 + (1 * 10000) + (1 * 1000000000),
1 + (-1 * 10000) + (-1 * 1000000000),
1 + (-1 * 10000) + (0 * 1000000000),
1 + (-1 * 10000) + (1 * 1000000000),
1 + (0 * 10000) + (-1 * 1000000000),
1 + (0 * 10000) + (0 * 1000000000),
1 + (0 * 10000) + (1 * 1000000000),
1 + (1 * 10000) + (-1 * 1000000000),
1 + (1 * 10000) + (0 * 1000000000),
1 + (1 * 10000) + (1 * 1000000000)
]
def __init__(self, binWidth):
self.inverseBinWidth = 1.0 / binWidth
self.hashMap = defaultdict(list)
[docs] def add_point(self, point, pointName):
i = np.rint(float(point[0]) * self.inverseBinWidth)
j = np.rint(float(point[1]) * self.inverseBinWidth)
k = np.rint(float(point[2]) * self.inverseBinWidth)
location = i + (j * 10000) + (k * 1000000000)
self.hashMap[location].append(pointName)
[docs] def get_neighbors(self, point):
i = np.rint(float(point[0]) * self.inverseBinWidth)
j = np.rint(float(point[1]) * self.inverseBinWidth)
k = np.rint(float(point[2]) * self.inverseBinWidth)
location = i + (j * 10000) + (k * 1000000000)
box = self.get_box_two(location)
return box
[docs] def get_box_two(self, location):
box_two = []
for off in self.offset:
if (location + off) in self.hashMap:
box_two += self.hashMap[location + off]
return box_two
[docs] def getIntersection(self, distanceBox):
intersection = []
checkedLocations = set()
for location in self.hashMap.keys():
overlap = False
for off in self.offset:
loc = location + off
if loc in distanceBox.hashMap:
overlap = True
break
if overlap:
for off in self.offset:
loc = location + off
if loc in checkedLocations:
continue
checkedLocations.add(loc)
if loc in self.hashMap:
intersection += self.hashMap[loc]
return intersection
