From 51d6496b02f1626a9eb357e8b46518b63d366d76 Mon Sep 17 00:00:00 2001
From: Kappes Marques Rodrigo <rodrigo.kappes@student-cs.fr>
Date: Wed, 29 Jan 2020 14:34:16 +0100
Subject: [PATCH] Optimization sur evaluate
---
__pycache__/individu.cpython-37.pyc | Bin 4034 -> 3961 bytes
algogenetique.py | 7 +++++--
individu.py | 8 ++++----
population.py | 2 +-
4 files changed, 10 insertions(+), 7 deletions(-)
diff --git a/__pycache__/individu.cpython-37.pyc b/__pycache__/individu.cpython-37.pyc
index 35557e4070ba1d2d0c008c67f366796605baa71d..32b398e808901aa0ca8d048b9b3c1ebb2f6c5133 100644
GIT binary patch
delta 757
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diff --git a/algogenetique.py b/algogenetique.py
index 1a0fa83..c445a68 100644
--- a/algogenetique.py
+++ b/algogenetique.py
@@ -33,8 +33,11 @@ def main(N,tmax,pmutation, proportion):
if individu.score<mini:
best=individu
mini=individu.score
+
+ S2=[individu.score for individu in People.indiv]
+ avg = sum(S2)/len(S2)
L.append(mini)
- print(i,":",mini)
+ print(i,"avg:",avg,"best score:", mini)
plt.subplot(221)
plt.plot([i for i in range(tmax)], L)
@@ -56,7 +59,7 @@ def main(N,tmax,pmutation, proportion):
lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
brin = ''.join(lineList[1:])
-best,People = main(20,10,0.01,10)
+best,People = main(50,20,0.05,25)
test = Traj3D()
test.compute(brin, best.table)
test.draw("first_plot")
diff --git a/individu.py b/individu.py
index 1d2a706..9c46b88 100644
--- a/individu.py
+++ b/individu.py
@@ -29,12 +29,12 @@ class Individu():
last_seq = self.brin[-numb_ajout:]
traj.compute(last_seq + self.brin + fisrt_seq, self.table)
- traj_array = np.array(traj.getTraj())
+ traj_array = traj.getTraj()
list_distance = []
- begining = traj_array[0:2*numb_ajout, 0:3]
- end = traj_array[-2*numb_ajout:, 0:3]
+ begining = traj_array[0:2*numb_ajout]
+ end = traj_array[-2*numb_ajout:]
for i in range(numb_ajout):
@@ -98,7 +98,7 @@ class Individu():
table_rotation_not_seen.remove(doublet)
for coord in range(3):
- value = table_rotations[doublet][coord] + np.random.uniform( low = - self.table.orta()[doublet][coord + 3]/10, high = - self.table.orta()[doublet][coord + 3]/10)
+ value = table_rotations[doublet][coord] + np.random.normal(0, self.table.orta()[doublet][coord + 3]/15)
if value > self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3]:
value = self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3]
elif value < self.table.orta()[doublet][coord] - self.table.orta()[doublet][coord + 3]:
diff --git a/population.py b/population.py
index 28a8700..0769839 100644
--- a/population.py
+++ b/population.py
@@ -165,7 +165,7 @@ class Population:
for child in couple_enfant :
lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
brin = ''.join(lineList[1:])
- child.mutation(proba_mutation)
+ child.mutation_close_values(proba_mutation, number_of_mutations = 2)
child.evaluate()
newself.append(couple_enfant[0])
newself.append(couple_enfant[1])
--
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