Hi All,
I've been working on a patch since March that greatly enhances the CDK
structure manipulation both in terms of usability and performance.
It is essentially backwards compatible with the current API (barring some
minor caveats) but to minimise issues I was planning a gradual introduction
where by initially it is turned on and off using an system/environment flag
and removing the flag and current implementation as a 3.0 release.
In summary you can now do this:
IAtomContainer mol = ...;
> for (IAtom atom : mol.atoms()) {
> int aidx = atom.getIndex(); // O(1) constant time!
> int deg = atom.getBondCount(); // O(1) constant time!
> // atoms know about their bonds O(|degree|)
> for (IBond bond : atom.bonds()) {
> int bidx = bond.getIndex(); // O(1) constant time!
> }
> }
I believe it should be relatively pain free to migrate however only testing
will tell. This is where we need your help! Please review the patch and
once applied please test you code with the new implementation (see info
below).
Further details/benchmarks: https://github.com/cdk/cdk/wiki/AtomContainer2
Patch: https://github.com/cdk/cdk/pull/368
Many Thanks,
John
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