projet_court/src/geom.py

import math
import numpy as np

# A couple of obvious functions for vector manipulation.
# Lack of time caused this not to be OOP-implemented, or furthermore
# documented.

def vector_from_pos(a, b):
    xAB = b[0]-a[0]
    yAB = b[1]-a[1]
    zAB = b[2]-a[2]
    coord_AB = [xAB,yAB,zAB]
    return coord_AB

def vector_norm(v):
    norm = math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
    return norm

def dot_product(v1,v2):
    dot_product = v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]
    return(dot_product)

def position_vector(c):
    vector = vector_from_pos([0,0,0],c)
    return vector

def vectors_substr(v1, v2):
    return ([v1[0]-v2[0],
             v1[1]-v2[1],
             v1[2]-v2[2]])

def vector_angles(v1,v2):
    dot_prod = dot_product(v1,v2)
    norm_v1 = vector_norm(v1)
    norm_v2 = vector_norm(v2)
    term = dot_prod/(abs(norm_v1)*abs(norm_v2))
    rad_angle = math.acos(term)
    return rad_angle

def calc_dihedral(u1, u2, u3, u4):
    """ Calculate dihedral angle method. From bioPython.PDB
    (adapted to np.array)
    Calculate the dihedral angle between 4 vectors
    representing 4 connected points. The angle is in
    [-pi, pi].

    Adapted function of dihedral_angle_from_coordinates.py 
    by Eric Alcaide.
    Source : https://gist.github.com/EricAlcaide
    URL : https://gist.github.com/EricAlcaide/30d6bfdb8358d3a57d010c9a501fda56
    """
    #convert coords to numpy arrays
    u1 = np.array(u1)
    u2 = np.array(u2)
    u3 = np.array(u3)
    u4 = np.array(u4)
    
    a1 = u2 - u1
    a2 = u3 - u2
    a3 = u4 - u3

    v1 = np.cross(a1, a2)
    v1 = v1 / (v1 * v1).sum(-1)**0.5
    v2 = np.cross(a2, a3)
    v2 = v2 / (v2 * v2).sum(-1)**0.5
    porm = np.sign((v1 * a3).sum(-1))
    rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
    if not porm == 0:
        rad = rad * porm

    deg_angle = rad*(180/math.pi)
    return deg_angle