diff --git a/.vscode/settings.json b/.vscode/settings.json index 395ba2d31e295f66eef5e2bd3db334975a462037..31e7ddfdf3472dbdd1b04dd753c498bc2995fd54 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 bcee29580aa9f90f53a240c4dafd995d6596a82b..3d9a88fe9f137cfbed43954895bb74eed387bce1 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 eee71819327b28c570771dcdca2b603043a014b9..92cc9720555ee8c29c954b2ea9a40cfc814917aa 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 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 ecd80201694553fe02c71577fca8c84a37602d91..a01f12cb0c29d22c424578f11642ea789f4f035a 100644 Binary files a/__pycache__/Traj3D.cpython-36.pyc and b/__pycache__/Traj3D.cpython-36.pyc differ diff --git a/first_plot.png b/first_plot.png new file mode 100644 index 0000000000000000000000000000000000000000..0e536fb530ea40bc82a9395940755ad27a030609 Binary files /dev/null and b/first_plot.png differ diff --git a/individu.py b/individu.py index d01e39b7818e6f09edc0766db823cb1798909f5b..4653a5885ebb8c68d1ee001ce65ef39b2a736954 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)