diff --git a/__pycache__/RotTable.cpython-36.pyc b/__pycache__/RotTable.cpython-36.pyc index 98365b3695b6ee33d2f796c59a3503d3f62271be..a8064bb45dbaad46db289f9e730b7dd816423ae4 100644 Binary files a/__pycache__/RotTable.cpython-36.pyc and b/__pycache__/RotTable.cpython-36.pyc differ diff --git a/__pycache__/Traj3D.cpython-36.pyc b/__pycache__/Traj3D.cpython-36.pyc index a01f12cb0c29d22c424578f11642ea789f4f035a..b5c1da4e7f16d56be5828446b2f8423d03027c1c 100644 Binary files a/__pycache__/Traj3D.cpython-36.pyc and b/__pycache__/Traj3D.cpython-36.pyc differ diff --git a/individu.py b/individu.py index 18b2158c1619aa48cf6bfb811a9d606be46bbd4b..e9fdceca287cbc231c4a535f03f8967c514fdf20 100644 --- a/individu.py +++ b/individu.py @@ -1,7 +1,7 @@ from RotTable import RotTable from Traj3D import Traj3D import numpy as np -from math import sqrt +from math import sqrt, inf from random import random P1 = 0.015 @@ -14,26 +14,30 @@ class Individu(): def evaluate(self, brin): traj = Traj3D() - traj.compute(brin, self.table) + + numb_ajout = 3 + + fisrt_seq = brin[0:numb_ajout] + last_seq = brin[-numb_ajout:] + + traj.compute(last_seq + brin + fisrt_seq, self.table) traj_array = np.array(traj.getTraj()) - print(traj_array) - first_nucleotide = traj_array[0, 0:3] - last_nucleotide = traj_array[-1, 0:3] - print(first_nucleotide) - print(last_nucleotide) - distance = sqrt(sum((first_nucleotide - last_nucleotide) ** 2)) - diff_ideal_distance = abs(3.38 - distance) + list_distance = [] + + for i in range(numb_ajout): + first_nuc_coordonate = traj_array[numb_ajout+i, 0:3] + first_nuc_coordonate_compute = traj_array[-(numb_ajout-i), 0:3] + + last_nuc_coordonate = traj_array[-(2*numb_ajout-i), 0:3] + last_nuc_coordonate_compute = traj_array[i, 0:3] + + distance_first_nuc = np.linalg.norm(first_nuc_coordonate - first_nuc_coordonate_compute, ord=2) + distance_last_nuc = np.linalg.norm(last_nuc_coordonate - last_nuc_coordonate_compute, ord=2) - first_name = brin[0] - last_name = brin[-1] + list_distance += [distance_first_nuc, distance_last_nuc] - #rot_computed = self.table.rot_table[last_name+first_name] - #rot_traj = first_nucleotide - last_nucleotide - # print(rot_traj) - # print(rot_computed) - #diff_angle = sum(abs(rot_computed - rot_traj)) - self.score = 1/distance + self.score = 1/max(list_distance) def mutation(self, proba = P1): @@ -61,7 +65,7 @@ class Individu(): # print(test.score) -qqun=Individu(RotTable()) -qqun.table.rot_table={'AA': [35.576558502141, 7.433901511509349, -154], 'AC': [33.22048222654215, 5.25191751302917, 143], 'AG': [26.446029097301288, 6.052240462237622, -2], 'AT': [30.47045254036881, 1.333716025628036, 0], 'CA': [34.00734209585039, 33.70710613604862, -64], 'CC': [33.61019622767888, 3.713127032109607, -57], 'CG': [29.664061041382677, 6.725155507162601, 0], 'CT': [26.446029097301288, 6.052240462237622, 2], 'GA': [36.655773481637176, 10.45337581740701, 120], 'GC': [42.26984493493484, 3.5310453395352823, 180], 'GG': [33.61019622767888, 3.713127032109607, -57], 'GT': [33.22048222654215, 5.25191751302917, 143], 'TA': [36.951508786388914, -2.5174751178033303, 0], 'TC': [36.655773481637176, 10.45337581740701, -120], 'TG': [34.00734209585039, 33.70710613604862, -64], 'TT': [35.576558502141, 7.433901511509349, -154]} -qqun.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") -print(qqun.score) +# qqun=Individu(RotTable()) +# qqun.table.rot_table={'AA': [35.576558502141, 7.433901511509349, -154], 'AC': [33.22048222654215, 5.25191751302917, 143], 'AG': [26.446029097301288, 6.052240462237622, -2], 'AT': [30.47045254036881, 1.333716025628036, 0], 'CA': [34.00734209585039, 33.70710613604862, -64], 'CC': [33.61019622767888, 3.713127032109607, -57], 'CG': [29.664061041382677, 6.725155507162601, 0], 'CT': [26.446029097301288, 6.052240462237622, 2], 'GA': [36.655773481637176, 10.45337581740701, 120], 'GC': [42.26984493493484, 3.5310453395352823, 180], 'GG': [33.61019622767888, 3.713127032109607, -57], 'GT': [33.22048222654215, 5.25191751302917, 143], 'TA': [36.951508786388914, -2.5174751178033303, 0], 'TC': [36.655773481637176, 10.45337581740701, -120], 'TG': [34.00734209585039, 33.70710613604862, -64], 'TT': [35.576558502141, 7.433901511509349, -154]} +# qqun.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") +# print(qqun.score)