example.py

#import libraries
import numpy as np
from Bio import PDB
from shapely.ops import unary_union
from mpl_toolkits.mplot3d import Axes3D
#imports from helper files
from knotLoad import connect_4th_alphas
from knotModify import apply_rotation_matrix
from knotIntersect import find_intersections
from knotIntersect import define_crossings
from knotIntersect import coordinates_to_lines
from plot import plot_lines_and_crossings
import random
def main():
    rotation_axis = 'x'
    # Defines angle at which rotation matrix will be applied
    rotation_angle = 90
    random.seed(50)
    connected_alpha_coords = []
    for i in range(9):
        connected_alpha_coords.append([random.randint(1,10),
                                       random.randint(1,10),
                                       random.randint(1,10)])
    #print(connected_alpha_coords)
    # Applies rotation matrix to connected chain of alpha carbons
    apply_rotation_matrix(connected_alpha_coords, rotation_axis, rotation_angle)
    # Creates line objects from coordinates. Used for plotting
    lines = coordinates_to_lines(connected_alpha_coords)
    # Finds intersections in 2D projection of alpha chain
    intersections = find_intersections(connected_alpha_coords)
    # Defines crossing types for each intersection.
    crossings = define_crossings(intersections)
    #print(crossings)
    # Plots line objects along with defined crossings and intersections
    plot_lines_and_crossings(lines, crossings)

if __name__ == "__main__":
    main()