Linting with flake8

Author: roncv

PyCEC/__init__.py

@@ -1,5 +1,5 @@
 """
-PyCEC: A Python implementation of the Center of Excess Charge (CEC) collective variable.
+PyCEC: A Python implementation of the Center of Excess Charge (CEC) CV.
 ================================================
 
 Documentation is available in the docstrings and
@@ -27,18 +27,17 @@
  test              --- Run PyCEC unittests
 """
 
-#export PYTHONPATH="${PYTHONPATH}:/biggin/b222/catz0163/pept/dynamics/pept_holo/pept_AF_H87P_D342P_v2/qmmm/analysis/PyCEC/PyCEC"
-
 # # For relative imports to work in Python 3.6
 # import os, sys; sys.path.append(os.path.dirname(os.path.realpath(__file__)))
 
 from pathlib import Path
 
+
 def _get_version() -> str:
     """Read VERSION.txt and return its contents."""
     path = Path(__file__).parent.resolve()
     version_file = path / "VERSION.txt"
     return version_file.read_text(encoding="utf-8").strip()
 
 
-__version__ = _get_version()
+__version__ = _get_version()

PyCEC/analysis/analysis.py

@@ -2,11 +2,10 @@
 from PyCEC.cec_system import CECSystem
 
 # MDAnalysis
-import MDAnalysis as mda # TODO: This needs to be fixed tbh, not efficient
+import MDAnalysis as mda  # TODO: This needs to be fixed tbh, not efficient
 from MDAnalysis.analysis.hydrogenbonds.hbond_analysis import HydrogenBondAnalysis as HBA
 
 from tqdm import tqdm
-import time
 
 from matplotlib import pyplot as plt
 import numpy as np
@@ -16,9 +15,9 @@ class CVAnalysis:
     """
     Class to analyse the collective variable of the CEC system.
     """
-
-    def __init__(self, universe, initial_resid, target_resid, other_resids=None,
-                 ligand=None, cyzone_dim=[8, 8, -8], frame_n=0):
+    def __init__(self, universe, initial_resid, target_resid,
+                 other_resids=None, ligand=None, cyzone_dim=[8, 8, -8],
+                 frame_n=0):
         # Attributes
         self.u = universe
         self.initial_resid = initial_resid
@@ -40,31 +39,29 @@ def __init__(self, universe, initial_resid, target_resid, other_resids=None,
     def get_traj_times(self):
         """
         Get the time of each frame in the trajectory.
-        
+
         """
         times = []
         for ts in self.u.trajectory:
             times.append(ts.time)
 
         return times
 
-
     def get_water_counts(self):
         """
         Iterate through the frames and get the water counts.
-        
+
         """
         water_counts = []
-        for ts in tqdm(self.u.trajectory, desc="Getting water counts..."): # tqdm progress bar
+        for ts in tqdm(self.u.trajectory, desc="Getting water counts..."):
             self.cv.set_frame(ts.frame)
             water_counts.append(len(self.cv.waters.atoms))
 
         return water_counts
 
-
     def get_water_counts_h(self):
         """
-        Iterate through the frames and get the water counts in a readable format.
+        Iterate through the frames and get water counts in a readable format.
 
         """
         water_counts = self.get_water_counts()
@@ -78,7 +75,7 @@ def get_water_counts_h(self):
         for i, t, w in water_c:
             print(f"Frame {i} at time {t} ps has {w} water molecules.")
 
-        #return water_c
+        # return water_c
 
 
 class WaterAnalysis:
@@ -94,7 +91,7 @@ def __init__(self, universe, initial_resid, target_resid, other_resids,
         self.other_resids = other_resids
         self.ligand = ligand
         self.cyzone_dim = cyzone_dim
-        self.frame_n = frame_n # TODO: is frame relevant here?
+        self.frame_n = frame_n  # TODO: is frame relevant here?
 
         # Trajectory information
         self.n_frames = len(self.u.trajectory)
@@ -109,39 +106,37 @@ def __init__(self, universe, initial_resid, target_resid, other_resids,
         self.waters = self.cv.waters
         self.waters_sele_str = self.cv.waters_sele_str
 
-
     def get_traj_times(self):
         """
         Get the time of each frame in the trajectory.
-        
+
         """
         times = []
         for ts in self.u.trajectory:
             times.append(ts.time)
 
         return times
 
-    def get_hydrogen_bonds(self, donors_sel=None, hydrogens_sel=None, acceptors_sel=None,
-                            distance_cutoff=3.5, angle_cutoff=120.0):
+    def get_hydrogen_bonds(self, donors_sel=None, hydrogens_sel=None,
+                           acceptors_sel=None, distance_cutoff=3.5,
+                           angle_cutoff=120.0):
         """
         Get the hydrogen bonds between the a pair of molecules.
-        
+
         """
         # Create the HBA object
         hba = HBA(universe=self.u, donors_sel=donors_sel,
                   hydrogens_sel=hydrogens_sel, acceptors_sel=acceptors_sel,
                   d_h_cutoff=distance_cutoff, d_h_a_angle_cutoff=angle_cutoff)
-        hba.run() # run the analysis
+        hba.run()  # run the analysis
 
         # Get counts
         counts = hba.count_by_time()
-        
-        return counts
-    
+
     def get_water_h_bonds(self, distance_cutoff=3.5, angle_cutoff=120.0):
         """
         Get the hydrogen bonds between the water molecules.
-        
+
         """
         # Get the hydrogen bonds
         counts = self.get_hydrogen_bonds(donors_sel=self.waters_sele_str,
@@ -150,30 +145,29 @@ def get_water_h_bonds(self, distance_cutoff=3.5, angle_cutoff=120.0):
                                          distance_cutoff=distance_cutoff,
                                          angle_cutoff=angle_cutoff)
         return counts
-    
+
     def plot_hbond_counts(self, counts, save=False):
         """
         Plot the hydrogen bond counts.
-        
+
         """
         fig, ax = plt.subplots()
         ax.plot(self.times, counts)
         ax.set_ylabel("Number of hydrogen bonds")
         ax.set_xlabel("Frame number")
         ax.set_title("Hydrogen bond counts over time")
-        
+
         if save:
             fig.savefig("hbond_counts.png", dpi=300)
-        
-        plt.show()
 
+        plt.show()
 
     def get_max_hbond_counts(self, counts):
         """
         Get the frames and times of the 10 frames with the most hydrogen bonds.
         """
         # Get the frames with the most hydrogen bonds
-        max_counts = sorted(counts, reverse=True)[:10] # get the 10 highest counts
+        max_counts = sorted(counts, reverse=True)[:10]  # get 10 highest counts
         print(f"\nMax counts: {max_counts}")
         max_frames = []
         for c in max_counts:
@@ -184,7 +178,7 @@ def get_max_hbond_counts(self, counts):
         print(f"Times of the frames with the most hydrogen bonds: {max_times}")
 
         return max_frames, max_times
-    
+
     def find_consistent_waters(self):
         """
         Find waters consistently included in the waters list.
@@ -198,8 +192,6 @@ def get_residence_times(self):
         pass
 
 
-
-
 if __name__ == "__main__":
 
     # Directory and title
@@ -225,4 +217,4 @@ def get_residence_times(self):
 
     counts = wa.get_water_h_bonds()
 
-    wa.plot_hbond_counts(counts, save=True)
+    wa.plot_hbond_counts(counts, save=True)

PyCEC/analysis/plotting.py

@@ -1,12 +1,7 @@
-from PyCEC.cec_system import CECSystem
 from PyCEC.analysis.analysis import CVAnalysis
 
 import matplotlib.pyplot as plt
 import numpy as np
-import os
-import pandas as pd
-
-from tqdm import tqdm
 
 import MDAnalysis as mda
 
@@ -41,12 +36,14 @@ def plot_water_counts(self, save=False):
 
         plt.show()
 
-    def plot_water_counts_line(self, save=False, filename='water_counts_line_hist', test=False, show=False):
-        """
-        Plot the water counts over time, with a histogram of frequency to the right of the main plot.
-        
+    def plot_water_counts_line(self, save=False,
+                               filename='water_counts_line_hist',
+                               test=False, show=False):
         """
+        Plot the water counts over time, with a histogram of frequency to the\
+              right of the main plot.
 
+        """
         if test:
             # Generate some random data
             water_counts = np.random.randint(0, 100, self.cv_analysis.n_frames)
@@ -55,7 +52,10 @@ def plot_water_counts_line(self, save=False, filename='water_counts_line_hist',
             water_counts = self.cv_analysis.get_water_counts()
 
         # Create a figure and a grid of subplots
-        fig, axs = plt.subplots(1, 2, gridspec_kw={'width_ratios': [4, 1], 'wspace': 0.02}, figsize=(10, 5))
+        fig, axs = plt.subplots(1, 2,
+                                gridspec_kw={'width_ratios': [4, 1],
+                                             'wspace': 0.02},
+                                figsize=(10, 5))
 
         # Line plot on the left
         axs[0].plot(self.cv_analysis.times, water_counts, c='b', dash_capstyle='round')
@@ -65,8 +65,9 @@ def plot_water_counts_line(self, save=False, filename='water_counts_line_hist',
         axs[0].ticklabel_format(style='plain')
 
         # Histogram on the right
-        axs[1].hist(water_counts, bins=self.cv_analysis.n_frames//10, orientation='horizontal', 
-                    color='b', edgecolor='white', lw=0.4)
+        axs[1].hist(water_counts, bins=self.cv_analysis.n_frames//10,
+                    orientation='horizontal', color='b', edgecolor='white',
+                    lw=0.4)
         axs[1].axis('off')
 
         # Adjust layout to prevent overlap
@@ -80,11 +81,10 @@ def plot_water_counts_line(self, save=False, filename='water_counts_line_hist',
         if show:
             plt.show()
 
-
     def plot_water_counts_boxplot(self, save=False):
         """
         Plot the boxplot of water counts.
-        
+
         """
         water_counts = self.cv_analysis.get_water_counts()
 
@@ -101,7 +101,7 @@ def plot_water_counts_boxplot(self, save=False):
     def plot_water_counts_violinplot(self, save=False):
         """
         Plot the violin plot of water counts.
-        
+
         """
         water_counts = self.cv_analysis.get_water_counts()
 
@@ -126,12 +126,11 @@ def plot_water_counts_violinplot(self, save=False):
 
     # Initialise class
     cv_analysis = CVAnalysis(u1, initial_resid=342, target_resid=56,
-                    other_resids=[53, 57, 61, 622],
-                    ligand=[1, 2], cyzone_dim=[8, 8, -8],
-                    frame_n=160)
+                             other_resids=[53, 57, 61, 622], ligand=[1, 2],
+                             cyzone_dim=[8, 8, -8], frame_n=160)
 
     # Create the CVPlotting object
     cv_plotting = CVPlotting(cv_analysis)
 
     # Plot the water counts over time
-    cv_plotting.plot_water_counts_line(save=True, test=True)
+    cv_plotting.plot_water_counts_line(save=True, test=True)