Re: [Cdk-devel] Interesting discussion about differences in CDK core classes API with others

[E.L. W. (Egon) <eg...@sc...>]

On Thursday 07 August 2003 17:28, Egon Willighagen wrote:
> below is a irc log of a chat I had this morning with Andrew Dalke. He is
> comparing application programming interfaces (API's) of several (open
> source?) chemical development kits, like CDK... It deals with some design
> decisions, and some other issues with the CDK core classes...

One of the problems that Andrew found, is the possibility to add a Bond
to a Molecule between two Atom's that are not part of the Molecule itself...
Which gives all sorts of problems with at least several algorithms in CDK
that assume that Atom's in a Bond in a Molecule are also Atom's in the 
Molecule themselves...

I've proposed a long standing wish of mine to have a drop-in replacement
for the standard CDK core classes which are *meant* not to do any sanity
checks...

This, I've begon... try:

ant dist-core-debug

This will create a cdk-core-debug.jar, which, at your convience, you can
1. rename to cdk-core.jar, and have it overwrite the normal cdk-core.jar
2. change your CLASSPATH to reference to cdk-core-debug.jar instead
    of cdk-core.jar

At this moment only one sanity check is done, but feel free to add more...
(by means of updating the patch src/patches/cdk-core.debug)

Egon