One of the areas we are still struggling with are default values and implicit assumptions. These need to get firmed up in CML as defaults in the schema. In many cases they are unknown and can be stamped as "known unknowns" (in the Rumsfeld taxonomy of knowledge). In other cases it may be less clear
Here are some typical examples
atom:
* formalCharge. Can we assume the default is 0? This would assert that if the attribute was absent it is known to be zero? This can be set in the schema
* occupancy. Similarly can we assume the default is 1.0?
* x2 (and all other coordinates). Here it is extremely dangerous to assume any value, so it is a known unknown. Can we use Double.NaN as marking unset? And then can a user can definitely write:
if (atom.getX2() == Double.NaN) {
System.out.println("atom x2 not known: ");
}
* hydrogenCount. Here it is also unreasonable to assume that a missing value tells us anything, so it is a known unknown. How do we do that? There is no "null" value for an int or NaN so we either have to box it as Integer or use some special value (e.g. negative infinity) or use an additional variable to indicate state of knowledge.
There are more complex issues such as "how can we estimate the hydrogen count from an incomplete specification" but I'll leave those for now.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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