From f55549beac1de70270b692660680dab63d0e8e43 Mon Sep 17 00:00:00 2001
From: Gauthier Roy <gauthierroy83@gmail.com>
Date: Tue, 28 Jan 2020 15:16:42 +0100
Subject: [PATCH] fix in the distance
---
.vscode/settings.json | 2 +-
RotTable.py | 10 +++++-----
Traj3D.py | 6 ++++++
__pycache__/RotTable.cpython-36.pyc | Bin 2085 -> 2132 bytes
__pycache__/Traj3D.cpython-36.pyc | Bin 1976 -> 1976 bytes
first_plot.png | Bin 0 -> 2412 bytes
individu.py | 17 ++++++-----------
7 files changed, 18 insertions(+), 17 deletions(-)
create mode 100644 first_plot.png
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 395ba2d..31e7ddf 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,3 +1,3 @@
{
- "python.pythonPath": "D:\\Programmes\\Anaconda3\\python.exe"
+ "python.pythonPath": "/Users/gauthierroy/anaconda3/bin/python"
}
\ No newline at end of file
diff --git a/RotTable.py b/RotTable.py
index bcee295..3d9a88f 100644
--- a/RotTable.py
+++ b/RotTable.py
@@ -53,16 +53,16 @@ class RotTable:
###################
def getTwist(self, dinucleotide):
- return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][0]
+ return self.rot_table[dinucleotide][0]
def getWedge(self, dinucleotide):
- return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][1]
+ return self.rot_table[dinucleotide][1]
def getDirection(self, dinucleotide):
- return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][2]
+ return self.rot_table[dinucleotide][2]
###################
-table1 = RotTable()
-print(table1.orta())
+#table1 = RotTable()
+#print(table1.orta())
diff --git a/Traj3D.py b/Traj3D.py
index eee7181..92cc972 100644
--- a/Traj3D.py
+++ b/Traj3D.py
@@ -65,3 +65,9 @@ class Traj3D:
ax.plot(x,y,z)
plt.show()
plt.savefig(filename)
+
+# from RotTable import RotTable
+# table = RotTable()
+# test = Traj3D()
+# test.compute("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA", table)
+# test.draw("first_plot")
\ No newline at end of file
diff --git a/__pycache__/RotTable.cpython-36.pyc b/__pycache__/RotTable.cpython-36.pyc
index dbb2e4134f6503a6df95598a7c5505e659fc5c85..98365b3695b6ee33d2f796c59a3503d3f62271be 100644
GIT binary patch
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diff --git a/__pycache__/Traj3D.cpython-36.pyc b/__pycache__/Traj3D.cpython-36.pyc
index ecd80201694553fe02c71577fca8c84a37602d91..a01f12cb0c29d22c424578f11642ea789f4f035a 100644
GIT binary patch
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diff --git a/first_plot.png b/first_plot.png
new file mode 100644
index 0000000000000000000000000000000000000000..0e536fb530ea40bc82a9395940755ad27a030609
GIT binary patch
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diff --git a/individu.py b/individu.py
index d01e39b..4653a58 100644
--- a/individu.py
+++ b/individu.py
@@ -13,21 +13,15 @@ class Individu():
traj = Traj3D()
traj.compute(brin, 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)
- first_name = brin[0]
- last_name = brin[-1]
-
- 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 + diff_angle)
+ self.score = 1/(diff_ideal_distance )
def mutation(self):
@@ -37,4 +31,5 @@ class Individu():
table = RotTable()
test = Individu(table)
test.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA")
+print(table.rot_table)
print(test.score)
--
GitLab