plotting

Author: roncv

PyCEC/analysis/analysis.py

@@ -196,10 +196,11 @@ def get_residence_times(self):
 
     # Directory and title
     dir1 = '/biggin/b222/catz0163/pept/dynamics/pept_holo/pept_AF_H87P_D342P_v2/qmmm'
+    dir1 = '/Users/nfo24278/Documents/dphil/proton_transfer/PyCEC/simulations/pept_AF_H87P_D342P'
     title1 = 'PepT2 with AF H87P D342P'
 
     # Load the universe
-    u1 = mda.Universe(f'{dir1}/prod-s100.pdb', f'{dir1}/prod-s100.xtc')
+    u1 = mda.Universe(f'{dir1}/prod-s200.pdb', f'{dir1}/prod-s200.xtc')
 
     # # Initialise class
     # cv = CVAnalysis(u1, initial_resid=342, target_resid=56,

PyCEC/analysis/plotting.py

@@ -37,7 +37,7 @@ def plot_water_counts(self, save=False):
         plt.show()
 
     def plot_water_counts_line(self, save=False,
-                               filename='water_counts_line_hist',
+                               filename='water_counts_line_hist.png',
                                test=False, show=False):
         """
         Plot the water counts over time, with a histogram of frequency to the\
@@ -75,7 +75,7 @@ def plot_water_counts_line(self, save=False,
 
         # Save the plot
         if save:
-            fig.savefig("water_counts2.png", dpi=300)
+            fig.savefig(filename, dpi=300)
 
         # Show the plot
         if show:
@@ -118,7 +118,8 @@ def plot_water_counts_violinplot(self, save=False):
 
 if __name__ == "__main__":
     # Directory and title
-    dir1 = '/biggin/b222/catz0163/pept/dynamics/pept_holo/pept_AF_H87P_D342P_v2'
+    # dir1 = '/biggin/b222/catz0163/pept/dynamics/pept_holo/pept_AF_H87P_D342P_v2'
+    dir1 = '/Users/nfo24278/Documents/dphil/proton_transfer/PyCEC/simulations/pept_AF_H87P_D342P'
     title1 = 'PepT2 with AF H87P D342P'
 
     # Load the universe

PyCEC/analysis/residue_analysis.py

@@ -1,4 +1,8 @@
 import MDAnalysis as mda
+import matplotlib.pyplot as plt
+plt.rcParams["font.family"] = "serif"
+plt.rcParams["mathtext.fontset"] = "dejavuserif"
+
 
 class ResidueAnalysis:
     """
@@ -64,13 +68,28 @@ def get_two_torsions(self, dihedral1=[], dihedral2=[], verbose=False):
         for ts in self.u.trajectory:
             torsions1.append(selection1.dihedral.value())
             torsions2.append(selection2.dihedral.value())
+
+        # Combine the index numbers, times, and torsions
+        torsions_h = []
+        steps = []
+        for i, t, d1, d2 in zip(range(self.n_frames), self.times, torsions1, torsions2):
+            torsions_h.append([i, t, d1, d2])
+            steps.append(i)
+
+        # Plot the torsions on a 2D plot
+        fig, ax = plt.subplots(figsize=(7,5), dpi=200)
+        sca = ax.scatter(torsions1, torsions2, c=steps, cmap='cividis', s=15)
+        # Add colorbar
+        cbar = fig.colorbar(sca, label='Frame')
+        ax.set_xlabel(f'{dihedral1[0]}-{dihedral1[1]}-{dihedral1[2]}-{dihedral1[3]}  [deg]')
+        ax.set_ylabel(f'{dihedral2[0]}-{dihedral2[1]}-{dihedral2[2]}-{dihedral2[3]}  [deg]')
+        ax.set_title(f'Torsions: {dihedral1[0]}-{dihedral1[1]}-{dihedral1[2]}-{dihedral1[3]} and {dihedral2[0]}-{dihedral2[1]}-{dihedral2[2]}-{dihedral2[3]}')
+
+
+        # Save the plot
+        fig.savefig(f'{self.resid}_{dihedral1[0]}-{dihedral1[1]}-{dihedral1[2]}-{dihedral1[3]}_{dihedral2[0]}-{dihedral2[1]}-{dihedral2[2]}-{dihedral2[3]}.png')
 
         if verbose:
-            # Combine the index numbers, times, and torsions
-            torsions_h = []
-            for i, t, d1, d2 in zip(range(self.n_frames), self.times, torsions1, torsions2):
-                torsions_h.append([i, t, d1, d2])
-
             # Print the output out line by line
             for i, t, d1, d2 in torsions_h:
                 print(f"Frame {i} at time {t} ps is {d1:.1f} deg and {d2:.1f} deg.")
@@ -96,6 +115,7 @@ def get_rmsd(self, reference):
 
     # Directory and title
     dir1 = '/biggin/b222/catz0163/pept/dynamics/pept_holo/pept_AF_H87P_D342P_v2/qmmm'
+    dir1 = '/Users/nfo24278/Documents/dphil/proton_transfer/PyCEC/simulations/pept_AF_H87P_D342P'
     title1 = 'PepT2 with AF H87P D342P'
 
     # Load the universe