Removed all instances of # End Method comments as this is no longer standard practice

Author: harryswift01

CodeEntropy/ConformationFunctions.py

@@ -80,6 +80,3 @@ def assign_conformation(
         conformations[frame] = np.argmin(distances)
 
     return conformations
-
-
-# END assign_conformation

CodeEntropy/EntropyFunctions.py

@@ -53,9 +53,6 @@ def frequency_calculation(lambdas, temp):
     return frequencies
 
 
-# END frequency_calculation
-
-
 def vibrational_entropy(matrix, matrix_type, temp, highest_level):
     """
     Function to calculate the vibrational entropy for each level calculated from eq. (4)
@@ -110,9 +107,6 @@ def vibrational_entropy(matrix, matrix_type, temp, highest_level):
     return S_vib_total
 
 
-# END vibrational_entropy
-
-
 def conformational_entropy(
     data_container, dihedrals, bin_width, start, end, step, number_frames
 ):
@@ -166,9 +160,6 @@ def conformational_entropy(
     return S_conf_total
 
 
-# END conformational_entropy
-
-
 def orientational_entropy(neighbours_dict):
     """
     Function to calculate orientational entropies from eq. (10) in J. Higham, S.-Y.
@@ -211,6 +202,3 @@ def orientational_entropy(neighbours_dict):
     # implement a case for molecules with hydrogen bonds but to a lesser
     # extent than water
     return S_or_total
-
-
-# END orientational_entropy

CodeEntropy/GeometricFunctions.py

@@ -43,9 +43,6 @@ def get_beads(data_container, level):
     return list_of_beads
 
 
-# END
-
-
 def get_axes(data_container, level, index=0):
     """
     Function to set the translational and rotational axes.
@@ -126,9 +123,6 @@ def get_axes(data_container, level, index=0):
     return trans_axes, rot_axes
 
 
-# END
-
-
 def get_avg_pos(atom_set, center):
     """
     Function to get the average position of a set of atoms.
@@ -168,9 +162,6 @@ def get_avg_pos(atom_set, center):
     return avg_position
 
 
-# END
-
-
 def get_sphCoord_axes(arg_r):
     """
     For a given vector in space, treat it is a radial vector rooted at 0,0,0 and
@@ -243,9 +234,6 @@ def get_sphCoord_axes(arg_r):
     return spherical_basis
 
 
-# END
-
-
 def get_weighted_forces(
     data_container, bead, trans_axes, highest_level, force_partitioning=0.5
 ):
@@ -291,9 +279,6 @@ def get_weighted_forces(
     return weighted_force
 
 
-# END
-
-
 def get_weighted_torques(data_container, bead, rot_axes, force_partitioning=0.5):
     """
     Function to calculate the moment of inertia weighted torques for a given bead.
@@ -379,9 +364,6 @@ def get_weighted_torques(data_container, bead, rot_axes, force_partitioning=0.5)
     return weighted_torque
 
 
-# END
-
-
 def create_submatrix(data_i, data_j, number_frames):
     """
     Function for making covariance matrices.
@@ -411,9 +393,6 @@ def create_submatrix(data_i, data_j, number_frames):
     return submatrix
 
 
-# END
-
-
 def filter_zero_rows_columns(arg_matrix, verbose):
     """
     function for removing rows and columns that contain only zeros from a matrix
@@ -461,6 +440,3 @@ def filter_zero_rows_columns(arg_matrix, verbose):
         )
 
     return arg_matrix
-
-
-# END

CodeEntropy/LevelFunctions.py

@@ -48,9 +48,6 @@ def select_levels(data_container, verbose):
     return number_molecules, levels
 
 
-# END get_levels
-
-
 def get_matrices(
     data_container, level, verbose, start, end, step, number_frames, highest_level
 ):
@@ -155,9 +152,6 @@ def get_matrices(
     return force_matrix, torque_matrix
 
 
-# END get_matrices
-
-
 def get_dihedrals(data_container, level):
     """
     Define the set of dihedrals for use in the conformational entropy function.
@@ -233,6 +227,3 @@ def get_dihedrals(data_container, level):
                 dihedrals.append(atom_group.dihedral)
 
     return dihedrals
-
-
-# END get_dihedrals

CodeEntropy/main_mcc.py

@@ -420,8 +420,6 @@ def main():
                 with open(args.outfile, "a") as out:
                     print(molecule, "\t", level, "\tConformational\t", S_conf, file=out)
 
-                # End united atom vibrational and conformational calculations #
-
             if level in ("polymer", "residue"):
                 # Vibrational entropy at every level
                 # Get the force and torque matrices for the beads at the relevant level
@@ -540,8 +538,6 @@ def main():
             print(molecule, "\t Molecule\tTotal Entropy\t", S_molecule, file=out)
 
 
-# END main function
-
 if __name__ == "__main__":
 
     main()