Re: [Cdk-user] Order of returned molecules from SMARTSQuery does not respect query

2010-09-15 Thread Thomas G. Kristensen
Hi, Thanks for the reply. I've looked into the code and although it partially solves the problem, it does so by forcing the user to split the SMARTS query into each atom and manually bond them. I'm trying to use some SMARTS definitions from a commercial package directly without modifications

Re: [Cdk-user] Charges in mol2 files ignored?

2010-09-15 Thread Egon Willighagen
On Wed, Sep 15, 2010 at 12:30 PM, Thomas G. Kristensen t...@cs.au.dk wrote: I'm trying to parse molecules with formal charges from a mol2 file, but no matter what I try it seems the formal charges are ignored when using the Mol2Reader. Inspecting the source code I discovered that mol type,

[Cdk-user] CDK development release 1.3.6 available

2010-09-15 Thread Egon Willighagen
Hi again, I have just released a new CDK *development* version. Details and full changelog is available: http://chem-bla-ics.blogspot.com/2010/09/cdk-137-changes-authors-and-reviewers.html Users of the 1.3.x development releases are encouraged to upgrade; users of 1.2.x are advised to wait

Re: [Cdk-user] addAtom slow?

2010-09-15 Thread Egon Willighagen
Hi Sebastian, On Mon, Sep 13, 2010 at 2:44 PM, Sebastian Wolf sw...@ipb-halle.de wrote: When I profile my project I saw that the method org.openscience.cdk.AtomContainer.addAtom(IAtom) calls org.openscience.cdk.ChemObject.addListener(IChemObjectListener). In this method contains