override equals() for Substructures

[fkaiserbio]

• we need to define a suitable equals() method for LeafSubstructure, BranchSubstructure, etc...
• argument is: a residue should equal its copy (for that all atoms must be equal etc...)

[cleberecht]

I would promote the idea of a deep equals deepEquals() method and a shallow equals equals() method. The deep equals method can recursively compare all substructures of the called substructure. The equals method should only compare the most relevant attributes that important for the identity at the current depth. Details are given in this stack overflow post and in the object java docs.

[cleberecht]

Affected classes:

RegularAtom

• [x] equals() using identifer, atomNameString and position

UncertainAtom

• [x] equals() inheriting equals from RegularAtom

AtomContainer

• [x] equals() based on LeafIdentifier
• [ ] deepEquals()

Nucleotide

• [x] equals() based on LeafIdentifier
• [ ] deepEquals()

Residue

• [x] equals() based on LeafIdentifier
• [ ] deepEquals()

Chain

• [ ] equals()
• [ ] deepEquals()

StructuralModel

• [ ] equals()
• [ ] deepEquals()

StructuralMotif

• [ ] equals()
• [ ] deepEquals()

Edit 1: Commit f6de9c2 revamps equals for leaf structures

[cleberecht]

Since version 0.3.1 this is fixed with the implementation of structures.