Small Bug Fix and Minor Improvements

Bug fixed for finding missing atoms.
Bug is not likely to have caused problems.
Only likely to affect reactions where lots of atoms were moving around.
Now prints a message once tasks are finished
Inline documentation improved.

AtomObjectBuilder.py

@@ -166,12 +166,31 @@ def check_mapped(self, mappedIDs, searchIndex, elementDict):
 
 
     def map_elements(self, atomObject, preAtomObjectDict, postAtomObjectDict):
+        """Map preAtom IDs to postAtomIDs by comparing neighbouring element symbols.
+
+        Compares the occurence of string chemical element symbols of a preAtom's neighbours 
+        to the known postAtom's neighbours. Creates a list of new mappedIDs and any missing IDs 
+        based on the neighbours of the known pre and postAtom pair.
+        Relies on compare_symmetric atoms to handle non-H atoms with >1 occurence.
+
+        Args:
+            self: This is a preAtom that has succesfully been mapped
+            atomObject: The known postAtom that has already been mapped to the preAtom
+            preAtomObjectDict: A dictionary of all preAtoms in the molecule
+            postAtomObjectDict: A dictionary of all the postAtoms in the molecule
+
+        Returns:
+            A partial mappedIDlist, partial missing pre and postAtom lists and additional atoms for the queue
+        """
+
         # Output variables
         mapList = []
         missingPreAtoms = []
         queueAtoms = []
 
         def allowed_maps(preAtom, postAtom):
+            '''Populate missing atoms prematurely instead of making misleading
+            maps based on element occurence'''
             # Checks if elements appear the same number of times in pre and post atoms
             # If they don't, mapping is not allowed to take place and atoms are moved to missing lists
             preElementOccurences = Counter(preAtom.mappedNeighbourElements)
@@ -205,7 +224,7 @@ def matchNeighbour(preAtom, postAtom, preAtomIndex, postAtomIndex, mapList, queu
             postAtom.mappedNeighbourIDs.pop(postAtomIndex)
             postAtom.mappedNeighbourElements.pop(postAtomIndex)
 
-        # Loop through neighbours for atom in one state and compare to neighbours of atom in other state
+        # Loop through neighbours for preAtom and compare to neighbours of postAtom
         for preIndex, neighbour in enumerate(self.mappedNeighbourElements):
             elementOccurence = atomObject.mappedNeighbourElements.count(neighbour)
 

AutoMapper.py

@@ -90,3 +90,5 @@
 elif tool == 'map':
     map_processor(directory, args.data_files[0], args.data_files[1], args.save_name[0], args.save_name[1], args.ba[:2], args.ba[2:], args.da, args.ebt, args.debug)
 
+# Print message to show AutoMapper is complete
+print('AutoMapper Task Complete')

MapProcessor.py

@@ -81,7 +81,7 @@ def map_processor(directory, preDataFileName, postDataFileName, preMoleculeFileN
     prePartialAtomsSet = keep_all_neighbours(preAtomObjectDict, preBondingAtoms, prePartialAtomsSet)
     postPartialAtomsSet = keep_all_neighbours(postAtomObjectDict, postBondingAtoms, postPartialAtomsSet)
 
-    # Keep delete atoms - IMPROVEMENT: Need to detect byproducts that are not deleted
+    # Keep delete atoms
     if preDeleteAtoms is not None:
         prePartialAtomsSet.update(preDeleteAtoms)
         postPartialAtomsSet.update(postDeleteAtoms)
@@ -91,6 +91,8 @@ def map_processor(directory, preDataFileName, postDataFileName, preMoleculeFileN
 
     # Check the edges aren't too close to atoms that change type
     preExtendEdgeDict = verify_edge_atoms(preEdgeAtoms, mappedIDList, preAtomObjectDict, postAtomObjectDict)
+
+    # Update mapped list and partial atom sets if edge atoms need extending
     mappedIDList, prePartialAtomsSet, postPartialAtomsSet = extend_edge_atoms(preExtendEdgeDict, mappedIDList, preAtomObjectDict, postAtomObjectDict, prePartialAtomsSet, postPartialAtomsSet)
 
     # Refind edge atoms after potential extension

PathSearch.py

@@ -51,7 +51,7 @@ def map_missing_atoms(missingPreAtomObjects, missingPostAtomObjects, mappedIDLis
             elementOccurence = missingPostAtomElements.count(preAtom.element)
 
             if elementOccurence == 0:
-                print(f"Couldn't find a match in post missing atom for {preAtom.atomID}")
+                print(f"Error: Couldn't find a match in post missing atom for {preAtom.atomID}. Please try again or map the atom manually.")
 
             elif elementOccurence == 1:
                 postIndex = missingPostAtomElements.index(preAtom.element)
@@ -171,8 +171,8 @@ def map_from_path(directory, preFileName, postFileName, elementsByType, debug, p
         # Enable inference if no new missing atoms were solved this loop
         if missingPreAtomCount == len(missingPreAtomList):
             inference = True
-        else:
-            infernce = False
+        else: # Disable inference if missing atoms were solved as other atoms may now be found without inference
+            inference = False
 
         timeoutCounter += 1
 

Test_Cases/Map_Tests/Caprolactam/automap.data

@@ -10,8 +10,8 @@ BondingIDs
 
 EdgeIDs 
 
-12
 9
+12
 
 Equivalences