doc strings and comments

Author: skfegan

CodeEntropy/entropy.py

@@ -12,17 +12,19 @@ def __init__(self):
         """
         Initializes the class with relevant information.
 
-        Args:
-            run_manager: Manager for universe and selection operations.
-            args: Argument namespace containing user parameters.
-            universe: MDAnalysis universe representing the simulation system.
-            data_logger: Logger for storing and exporting entropy data.
         """
         self._molecule_groups = None
 
     def grouping_molecules(self, universe, grouping):
         """
         Grouping molecules by desired level of detail.
+
+        Args:
+            universe: MDAnalysis univers object for the system of interest.
+            grouping (str): how to group molecules for averaging
+
+        Returns:
+            molecule_groups (dict): molecule indices for each group.
         """
 
         molecule_groups = {}
@@ -33,11 +35,22 @@ def grouping_molecules(self, universe, grouping):
         if grouping == "molecules":
             molecule_groups = self._by_molecules(universe)
 
+        number_groups = len(molecule_groups)
+
+        logger.info(f"Number of molecule groups: {number_groups}")
+        logger.debug(f"Molecule groups are: {molecule_groups}")
+
         return molecule_groups
 
     def _by_none(self, universe):
         """
         Don't group molecules. Every molecule is in its own group.
+
+        Args:
+            universe: MDAnalysis universe
+
+        Returns:
+            molecule_groups (dict): molecule indices for each group.
         """
 
         # fragments is MDAnalysis terminology for molecules
@@ -48,17 +61,18 @@ def _by_none(self, universe):
         for molecule_i in range(number_molecules):
             molecule_groups[molecule_i] = [molecule_i]
 
-        number_groups = len(molecule_groups)
-
-        logger.info(f"Number of molecule groups: {number_groups}")
-        logger.debug(f"Molecule groups are: {molecule_groups}")
-
         return molecule_groups
 
     def _by_molecules(self, universe):
         """
         Group molecules by chemical type.
         Based on number of atoms and atom names.
+
+        Args:
+            universe: MDAnalysis universe
+
+        Returns:
+            molecule_groups (dict): molecule indices for each group.
         """
 
         # fragments is MDAnalysis terminology for molecules
@@ -75,6 +89,10 @@ def _by_molecules(self, universe):
                 names_j = fragments[molecule_j].names
                 number_atoms_j = len(names_j)
 
+                # If molecule_i has the same number of atoms and same
+                # atom names as molecule_j, then index i is added to group j
+                # The index of molecule_j is the group key, the keys are
+                # all integers, but may not be consecutive numbers.
                 if number_atoms_i == number_atoms_j and (names_i == names_j).all:
                     if molecule_j in molecule_groups.keys():
                         molecule_groups[molecule_j].append(molecule_i)
@@ -83,9 +101,4 @@ def _by_molecules(self, universe):
                         molecule_groups[molecule_j].append(molecule_i)
                     break
 
-        number_groups = len(molecule_groups)
-
-        logger.info(f"Number of molecule groups: {number_groups}")
-        logger.debug(f"Molecule groups are: {molecule_groups}")
-
         return molecule_groups