RFC= request for comments
Hi all,
what is the hydrogen count when I type:
IAtom atom = new IAtom("C");
or, what happens when I have an atom container with 5 atoms, and I set the
H-count for only one of them. Are the values zero for the other four then?
The JavaDoc is not helpful here, though non-native fields simply default to
null. I tended to say that if a property is not explicitly set, it is
undefined, which matches the 'null' nicely. Native fields (int, double, etc)
do not have a null concept, and some work by Rajarshi yesterday addressed
this by explicitly stating a field was UNSET, by using Integer.MIN_VALUE and
Double.NaN.
This broke about 300 JUnit tests.
However, too many algorithms (atom typing, canonical labeler, to name some)
*do* expect a 0 default. For example, expect the above carbon to have zero
formal charge, and zero implicit hydrogens. But I am sure that other
algorithms expect something else.
I made a brief attempt to fix some code here and there to deal with unset
values, but I never had any chance... and I had to revert the changes and
make formalCharge and hydrogenCount now explicitly default to zero.
So, very importantly: what *are* the default values for all non-native fields
in the interfaces?! This needs to be defined *and* clearly stated in the API.
And if we go the UNSET route, this will require a whole lot of implementation
fixing!
Egon
--
CUBIC
blog: http://chem-bla-ics.blogspot.com/
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