Rebase database test #196
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Rebase database test #196
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This function gives the boolean of whether two LogicOr objects are equivilant or not. I needed this for database checking
The function equivilant and isSpecificCaseOf for GroupAtom now checks the list of charges and atom label
The function isIsomorphic was meant to compare molecules to groups, therefore it respects wildcards (seeing as a molecule will never have an atom named Cs or Ct). However, this makes the function isIsomorphic not useful when tryint to compare two groups. I've created a new function isIdentical which will not respect wildcards and can tell if two groups are the same.
This function is used to check for malformed kinetic families. I have also removed the function isWellFormed from base.py because it is deprecated by this new function (and also didn't work due to the many changes we've been making). The new function checks for: -rule labels that have group names which do not exist in groups.py -rule adjLists that do not match with the corresponding adj list in groups.py -Each group must exist in the tree -Each group adjList must actually be a more specific case of it's parent's adjList
Coded another check in checkWellFormed to see if each node is unique inside of a family.
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I think this should have been other.charge. Fixing now.
(update: I now think the line below should have been other.charge 😊)
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Includes the new checks I've been making to make sure the database is well formed.