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Traj3D.py

+#For computing
+import mathutils
+import math
+
+#For drawing
+import numpy as np
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+from matplotlib import collections  as mc
+
+
+class Traj3D:
+    """Represents a 3D trajectory"""
+
+    # Vertical translation (elevation) between two di-nucleotides
+    __MATRIX_T = mathutils.Matrix.Translation((0.0, 0.0, 3.38/2.0, 1.0))
+
+    def __init__(self):
+        self.__Traj3D = {}
+
+    def getTraj(self):
+        return self.__Traj3D
+
+    def compute(self, dna_seq, rot_table):
+
+        # Matrice cumulant l'ensemble des transformations géométriques engendrées par la séquence d'ADN
+        total_matrix = mathutils.Matrix()
+
+        # On enregistre la position du premier nucléotide
+        self.__Traj3D = [mathutils.Vector((0.0, 0.0, 0.0, 1.0))]
+
+        matrices_Rz = {}
+        matrices_Q = {}
+        # On parcourt la sequence, nucléotide par nucléotide
+        for i in range(1, len(dna_seq)):
+            # On lit le dinucleotide courant
+            dinucleotide = dna_seq[i-1]+dna_seq[i]
+            # On remplit au fur et à mesure les matrices de rotation
+            if dinucleotide not in matrices_Rz:
+                matrices_Rz[dinucleotide] = mathutils.Matrix.Rotation(math.radians(rot_table.getTwist(dinucleotide)/2), 4, 'Z')
+                matrices_Q[dinucleotide] = \
+                    mathutils.Matrix.Rotation(math.radians((rot_table.getDirection(dinucleotide)-90)), 4, 'Z') \
+                    @ mathutils.Matrix.Rotation(math.radians((-rot_table.getWedge(dinucleotide))), 4, 'X') \
+                    @ mathutils.Matrix.Rotation(math.radians((90-rot_table.getDirection(dinucleotide))), 4, 'Z')
+
+
+            # On calcule les transformations géométrique selon le dinucleotide courant, et on les ajoute à la matrice totale
+            total_matrix =  total_matrix @ \
+                self.__MATRIX_T \
+                @ matrices_Rz[dinucleotide] \
+                @ matrices_Q[dinucleotide] \
+                @ matrices_Rz[dinucleotide] @ \
+                self.__MATRIX_T
+
+            # On calcule la position du nucléotide courant en appliquant toutes les transformations géométriques à la position du premier nucléotide
+            self.__Traj3D.append(total_matrix @ self.__Traj3D[0])
+
+
+    def draw(self, filename):
+        xyz = np.array(self.__Traj3D)
+        self.__Traj3D = []
+        x, y, z = xyz[:,0], xyz[:,1], xyz[:,2]
+        fig = plt.figure()
+        ax = fig.add_subplot(111, projection='3d')
+        ax.plot(x,y,z)
+        plt.show()
+        plt.savefig(filename)