[Cdk-devel] SMARTS and rings [was hi]

[Rajarshi G. <rg...@in...>]

On Sun, 2007-04-08 at 19:11 +0530, sushil ronghe wrote:

>     
>  public boolean matches(IAtom atom) {
>          if (RING_SIZE==1){ 
>               return atom.getFlag(CDKConstant.ISINRING);  // why the CDKConstant.ISINRING is not boolean value.            

The constant itself is an integer, the return value is boolean. Why
should the constant be boolean?

> I have also convinced about the fact that we have to go above the
> ringsize of 8.

Agreed.

> NOw we can have the method directly like getRingSizes() or
> atom.getFlag(CDKConstant.RingSizes);

I would rather not tack on another function to the IAtom interface.

Following Egon's suggestion I've committed a SMARTSQueryTool class which
allows an easier way to use SMARTS matching than directly calling the
parser and handling the UniversalIsomorphismTester to get matching atoms
etc

For your case, as you're developing the parser, this class probably
should not affect your work on the parser itself.

However, it does perform pre-processing of the target molecule. As a
result, if you use the query tool class, the target atomContainer will
be modified so that atoms in a ring will have a property,
CDKConstants.RING_SIZE whose value is a List of the sizes of each ring
the atom is a member of. 

So in the parser code you can do

List ringSizes = atom.getProperty(CDKConstants.RING_SIZE);

For example usage of the query tool class see
http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.html

Regarding the RingAtom class - I'll hold of adding that till you're done
on your side and then we can add the your stuff.

PS. Please cc to the list and use meaningful subject lines

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Rajarshi Guha <rg...@in...>
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After a number of decimal places, nobody gives a damn.