[Cdk-user] Re: [QSAR-devel] QSAR compatibility layers

[Peter Murray-R. <pm...@ca...>]

At 16:33 20/05/2004 +0200, Egon Willighagen wrote:
>On Thursday 20 May 2004 14:51, Peter Murray-Rust wrote:
> > [*] I mailed 2 questions to the CDK list about functionality (double and
> > cyclic bonds)- I assume they got there - if they didn't I will remail.  It
> > seems that discovering functionality is already a problem and we should
> > address it.
>
>I've responded on the second question, but could not quickly find the first
>one...

Thanks - wasn't sure it had got through as the archive isn't uptodate.

The questions included:
- is there a simple function to get cyclic bonds?
- what does layout do about known cis and trans double bonds?


>getAllDoubleBonds(Molecule molecule) is not explicitely in CDK, but is easily
>written as:
>
>AtomContainer bondSet = new AtomContainer();
>Bond[] bonds = molecule.getBonds();
>for (int i=0; i<bonds.length; i++) {
>     if (bonds[i].getOrder() == CDKConstants.BONDORDER_DOUBLE) {
>         bondSet.addBond(bonds[i]);
>     }
>}
>Bond[] allDoubleBonds = bondSet.getBonds();

Thanks.

P.


>Egon

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069