Re: [Cdk-devel] PathTools...

[Egon W. <ego...@gm...>]

On Mon, Aug 11, 2008 at 3:40 PM, Rajarshi Guha <rg...@in...> wrote:
>> This is the list with classes currently in atomtypes... and a lot can
>> be copied into core:
>>
>> org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
>> org/openscience/cdk/tools/manipulator/BondManipulator.java
>> org/openscience/cdk/graph/PathTools.java
>> org/openscience/cdk/graph/SpanningTree.java
>> org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
>>
>> which will leave in atomtype:
>>
>> org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
>> org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
>> org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
>> org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
>>
>> which more move further down the dependency tree.
>
> Looks good.

Went ahead and already commited this earlier this morning.

> While you're looking at this, it would also be useful to include
> the atom type related dictionaries into the atomtype module and out of the
> core, extra modules (bug 2045603).

Right.

> Also, in commit r11983 I see that you moved CDKAtomTypeMatcher to core - why
> not keep that in atomtype? It's general purpose from the point of view of
> atom typing, but functionality-wise it is specific to atom typing

Because it is likely as core to chemoinformatics as the SpanningTree.
This move has the advantage that it removes one compilation step from
the 12 layers, speeding up compilation on multicore systems, and it
removes a lot of dependencies.

...

Egon

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