Hi, It is me again!, I was trying to calculate fingerprints and used the example from the web:
Molecule molecule = new molecule(); Bitset fingerprint = Fingerprinter.getFingerprint(molecule); I get the following error: "non-static method getFingerprint (org.openscience.cdk.interfaces.IAtom Container) cannot be referenced from a static context" What am I doing wrong? Thxs. Angela -----Original Message----- From: cdk-user-boun...@lists.sourceforge.net [mailto:cdk-user-boun...@lists.sourceforge.net] On Behalf Of cdk-user-requ...@lists.sourceforge.net Sent: Thursday, April 30, 2009 1:02 PM To: cdk-user@lists.sourceforge.net Subject: Cdk-user Digest, Vol 35, Issue 17 Send Cdk-user mailing list submissions to cdk-user@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/cdk-user or, via email, send a message with subject or body 'help' to cdk-user-requ...@lists.sourceforge.net You can reach the person managing the list at cdk-user-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Cdk-user digest..." Today's Topics: 1. Re: substructure searching (Rajarshi Guha) 2. Re: Question on Tabular Display of 2D Structures (Egon Willighagen) ---------------------------------------------------------------------- Message: 1 Date: Thu, 30 Apr 2009 00:54:07 -0400 From: Rajarshi Guha <rg...@indiana.edu> Subject: Re: [Cdk-user] substructure searching To: Loren Lenzen <loren.len...@sial.com> Cc: cdk-user@lists.sourceforge.net Message-ID: <e017fc33-87e8-4c39-89ec-6ecc05ce4...@indiana.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes On Apr 29, 2009, at 6:05 PM, Loren Lenzen wrote: > > Rajarshi, thanks for your help on the SMARTSQueryTool. > > I tried to look back at the history of the SQT and UIT, but am unclear > on the algorithm used. Is it Ullman, VF2, Hanser, or a mishmash? The > description of UIT in the Javadoc says Hanser, but based on recent > blog postings, it seems as though SQT might use Ullman, and I was > under the impression that SQT is a wrapper of UIT. Right now, SQT is a wrapper around UIT which employs the Hanser algorithm The vflib branch, currently in review, will be an alternative to the UIT, and will support Ullman and VF2. My plan is to switch the SQT to use the VF2 algorithm implemented in the vflib branch (alernatively, SQT can be updated to allow a user to use UIT, VF2 or Ullman). > Does SQT.matches(IAtomContainer atomContainer) return after a single > match or does it find all matches first? It identifies all matches > If the latter, would there be any problems extending the method to a > type like SQT.matches(IAtomContainer atomContainer, boolean > forceInitialization, boolean singleMatch) where the method would > immediately return True on finding a single match if set to True? I suppose that might be possible, but would likely require hacking on the UIT to return after the first match. Not having much experience with the guts of the UIT, I'm not eager to do this, though it is probably not a lot of work ------------------------------------------------------------------- Rajarshi Guha <rg...@indiana.edu> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------ Message: 2 Date: Thu, 30 Apr 2009 08:21:42 +0200 From: Egon Willighagen <egon.willigha...@gmail.com> Subject: Re: [Cdk-user] Question on Tabular Display of 2D Structures To: Rajarshi Guha <rg...@indiana.edu> Cc: "Beesley, Angela" <angela.bees...@unilever.com>, cdk-user@lists.sourceforge.net Message-ID: <6aeb064b0904292321t704b1ffen37cb6d14349a1...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Wed, Apr 29, 2009 at 10:26 PM, Rajarshi Guha <rg...@indiana.edu> wrote: > I haven't touched that code is some time and I think the code is old > enough, that the renderer API has totally changed. Gilleain should be > better able to help out. > > PS. Another issue is that CDK 1.2.x (and master) don't contain the > latest renderer code, AFAIK, which is a pain. I tried to update Bioclipse with CDK 1.2.1 and current JChemPaint yesterday, but it needs some tweaking... I am in the process of setting up a series of patches, slowly, as we want to get Bioclipse 2.0.0 (Mid May) out of the door first, but will start doing that right after that... maybe earlier... The above Bioclipse update made a start... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------ ------------------------------------------------------------------------ ------ Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf ------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user End of Cdk-user Digest, Vol 35, Issue 17 **************************************** ------------------------------------------------------------------------------ Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
