Merge branch 'fix_codacy_issues'

Author: blakeaw

pybilt/bilayer_analyzer/bilayer_analyzer.py

@@ -18,17 +18,13 @@
 from __future__ import print_function
 from builtins import object
 import numpy as np
-import warnings
 from six.moves import range
 try:
     import six.moves.cPickle as pickle
 except ImportWarning as warn:
     import pickle
-
 import os
-import multiprocessing
-import sys
-
+import ast
 # PyBILT imports
 from . import com_frame as cf
 from . import leaflet as lf
@@ -38,7 +34,7 @@
 from . import plot_protocols as pp
 from pybilt.common.running_stats import RunningStats
 from . import mda_data as md
-import MDAnalysis as mda
+
 # import the coordinate wrapping function--for unwrapping
 from pybilt.mda_tools.mda_unwrap_vectorized import wrap_coordinates, \
     wrap_coordinates_parallel
@@ -509,7 +505,7 @@ def parse_input_script(self, input_script_name):
                 if key in ['structure', 'trajectory', 'selection']:
                     second_term = line.replace(key, '', 1).strip()
                     if key == 'selection':
-                        second_term = eval(second_term)
+                        second_term = ast.literal_eval(second_term)
                     commands[key] = second_term
                 else:
                     if key in self._valid_commands:
@@ -856,28 +852,19 @@ def _build_leaflets_orientation(self):
                     'lower': lf.Leaflet('lower')}
         l = 0
         for lipcom in com_frame.lipidcom:
-            sel_str = "resname {} and resid {}".format(lipcom.type, lipcom.resid)
-            # residue = self._mda_data.mda_universe.select_atoms(sel_str)
             resname = lipcom.type
             resid = lipcom.resid
             tail_str = "resname {} and resid {} and name {}".format(resname, resid,self.rep_settings['leaflets']['orientation_atoms'][resname][0])
             tail = self._mda_data.mda_universe.select_atoms(tail_str)
-            # print(tail, len(tail))
             tail_v = tail.center_of_mass()
             head_str = "resname {} and resid {} and name {}".format(resname, resid,self.rep_settings['leaflets']['orientation_atoms'][resname][1])
             head = self._mda_data.mda_universe.select_atoms(head_str)
             head_v = head.center_of_mass()
-            # print(tail_v)
-            # print(head_v)
             vec = head_v - tail_v
-            # print(vec)
             norm = self.settings['norm']
             norm_vec = np.zeros(3)
             norm_vec[norm] = 1.0
             cost = np.dot(vec, norm_vec)/np.sqrt(np.dot(vec, vec))
-            # print(tail_str, head_str)
-            # print(tail_v, head_v, cost)
-            # print(" ")
             pos = ""
             if cost > 0.0:
                 pos = 'upper'
@@ -917,10 +904,6 @@ def __next__(self):
         builds the necessary objects (e.g. COMFrame) and then executes the
         analysis of each analysis that was initialized in the setup.
 
-        Args:
-            nprocs (int): An integer specifying the number of cores to use in
-            multithreaded parallelelization.
-
         """
         if self._current_frame > self._last_frame:
             raise StopIteration()
@@ -971,7 +954,7 @@ def __next__(self):
             self._oldcoords = oldcoord
             # print (wrapcoord)
             if self._analysis_protocol.use_objects['com_frame']:
-            # now build the COMFrame
+                # now build the COMFrame
                 self.reps['com_frame'] = cf.COMFrame(frame, self._mda_data.bilayer_sel,
                                              wrapcoord,
                                              name_dict =

pybilt/bilayer_analyzer/com_frame.py

@@ -378,7 +378,7 @@ def coordinates(self, wrapped=True, leaflet=None):
                     if wrapped:
                         coords.append(item.com)
                     else:
-                        coords.append(item.com_unwrap)            
+                        coords.append(item.com_unwrap)
         return np.array(coords)
 
     def masses(self):

pybilt/bilayer_analyzer/vector_frame.py

@@ -5,10 +5,6 @@
 from builtins import object
 import MDAnalysis as mda
 import numpy as np
-from mpl_toolkits.mplot3d import axes3d
-import pybilt.plot_generation.plot_generation_functions as pgf
-import matplotlib.pyplot as plt
-import sys
 from six.moves import range
 
 class LipidVec(object):
@@ -152,8 +148,8 @@ def __init__(self, mda_frame, mda_bilayer_selection, ref_atoms):
         # initialize all the LipidVec objects
         for dummy_i in range(nlipids):
             self.lipidvec.append(LipidVec())
-        #atom indices in mda selection/frame
-        index = mda_bilayer_selection.indices
+        # atom indices in mda selection/frame
+        # index = mda_bilayer_selection.indices
         # loop over the residues (lipids) and get the centers of mass
         ## do the wrapped coordinates
 

pybilt/com_trajectory/COMTraj.py

@@ -28,10 +28,8 @@
 import multiprocessing as mp
 from scipy.spatial import Voronoi
 from scipy.spatial import Delaunay
-#import copy
-
-#import running stats class
-from pybilt.common.running_stats import *
+# import running stats class
+from pybilt.common.running_stats import RunningStats, gen_running_average
 # import the coordinate wrapping function--for unwrapping
 from pybilt.mda_tools.mda_unwrap import wrap_coordinates,wrap_coordinates_parallel
 from six.moves import range
@@ -834,7 +832,7 @@ def thickness_frames(frames, fstart, fend, leaflets, nlipids, plane, norm):
             comclo = fr.lipidcom[idl].com
             distxy = 10000.0
             distz = 0.0
-            mindex = 0
+            # mindex = 0
             zlom = 0.0
             zhim = 0.0
             xavgm = 0.0
@@ -1344,7 +1342,7 @@ def calc_membrane_thickness(self):
                 comclo = fr.lipidcom[idl].com
                 distxy = 10000.0
                 distz = 0.0
-                mindex = 0
+                # mindex = 0
                 zlom = 0.0
                 zhim = 0.0
                 xavgm = 0.0
@@ -1509,7 +1507,7 @@ def check_clustering(self, leaflet="both",group="all", dist=15.0):
                     #get neighbors of the start
                     #mindex=0
                     for j in range(len(masterlistf)):
-                    #for elem in masterlistf:
+                        #for elem in masterlistf:
                         elem = masterlistf[j]
                         incluster = elem[1]
                         #    print "second incluster ",incluster

pybilt/lipid_grid/lipid_grid.py

@@ -16,14 +16,11 @@
 from __future__ import division
 from __future__ import print_function
 from builtins import object
+from six.moves import range
 import numpy as np
-import sys
 from scipy.ndimage.filters import gaussian_filter
 # pybilt imports
 from pybilt.common.running_stats import RunningStats
-from six.moves import range
-
-
 
 def grid_curvature(x_vals, y_vals, zgrid):
     """Compute the Mean and Gaussian curvature across a grid.
@@ -654,7 +651,7 @@ def write_pdb(self, pdb_name, leaflet='both', z_grid_upper=None,
 
         # Open up the file to write to
         pdb_out = open(pdb_name, "w")
-        npoints = (self.nbins_x*self.nbins_y)*len(do_leaflet)
+        # npoints = (self.nbins_x*self.nbins_y)*len(do_leaflet)
         # First line to write is the box dimensions
         box = self.frame.box
         box_data = "CRYST1  {:06.3f}  {:06.3f}  {:06.3f}".format(box[0],