Hi All,
This has been on my todo list since the last developer hangout. In the most
recent release (1.14.15) the cloning of stereo elements was added. For the
cloning a deep copy is returned as expected but for the shallow I mimicked the
behaviour of the bonds. The purpose of this mail is to ensure the behaviour is
known and also see if it is what is expected.
Here is the copy constructor behaviour https://gist.github.com/4136504
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IAtomContainer a = new AtomContainer();
a.addAtom(new Atom("C"));
a.addAtom(new Atom("C"));
a.addBond(new Bond(a.getAtom(0), a.getAtom(1), SINGLE));
// copy constructor
IAtomContainer b = new AtomContainer(a);
b.removeAtom(0); // atom at index 0 is removed from b, a is not affected
b.getBond(0).setOrder(DOUBLE); // bond order is change in both a and b
b.getBond(0).addAtom(new Atom("H")); // as the bond is the same instance this
is now
ITetrahedralChiralAtomParityEtc element = ...; // access stereo elements
element.setStereo(CLOCKWISE); // a,b both have stereo changed
Thinking about the front end uses it might make more sense to shallow copy the
bonds/stereo elements as well as the container or even make the copy
constructor perform a deep copy. Most cases I've seen where a method has needed
a copy they tend create there own method, specific to their needs or use a full
clone when it isn't needed. So, does the behaviour shown above make sense?
Perhaps the copy constructor should be a deep copy constructor… maybe there
should be a 'deepCopy()' method (everyone knows clone is evil and should not be
used).
There is of course no right answer but having seen a lot defensive cloning and
copy pasted reimplementations it might be that the currently implementation
isn't that useful.
Please let me know your thoughts.
Many thanks,
John
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