Dear Rajarshi: Thanks for your prompt reply to my previous question, I managed to calculate AlogP correctly and to run the DescriptorEngine fine. As I said I am starting with cdk and with java in general, hence my struggling. I was trying to compile and run the example that you have in your web page regarding tabular display of 2D structures, I downloaded the jgrapht library and it is in my classpath. I also have the StructureDiagramGenerator class. However there are a few things that I don't understand from the program, here are the questions:
1. The program requires to import org.openscience.cdk.renderer.Renderer2D, I don't seem to have this but instead I have "org.penscience.cdk.renderer.Java2DRenderer" is this the same? 2. If so, I need to change line 121 to "Java2Drender renderer;" and line 130 to "renderer=new Java2DRenderer;", don't I? 3. On line 123 it appears "getAtomAt(i)", is this "getAtom(i)"? 4. On line 170 it appears: renderer.paintMolecule(this.mol,(Graphics2D)g,true); ... this shows an error, can I change it to: renderer.paintMolecule(this.mol,(Graphics2D)g); ...this seems to be ok. 5. On line 292, where st2d is declared, the error message shows "class st2d is public should be declared in a file name st2d.java". Do I need to download st2d.java? 6. Problems on line 321 and 322. It appears: IAtomContainer [] c = ChemFileManipulator......., this generates and error, can I chage it to: List<IAtomContainer> c = ChemFileManipulator......, this seems to be ok. Sorry if these questions are too basic! I am picking up more and more everyday. Cheers, 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: Wednesday, April 29, 2009 1:02 PM To: cdk-user@lists.sourceforge.net Subject: Cdk-user Digest, Vol 35, Issue 15 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: Question on descriptors (Rajarshi Guha) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Apr 2009 09:26:33 -0400 From: Rajarshi Guha <rg...@indiana.edu> Subject: Re: [Cdk-user] Question on descriptors To: "Beesley, Angela" <angela.bees...@unilever.com> Cc: cdk-user@lists.sourceforge.net Message-ID: <99967940-9e15-4ac8-adfb-9d2b2f827...@indiana.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes On Apr 27, 2009, at 12:25 PM, Beesley, Angela wrote: > Hi, > > I am very new on cdk and on java in general so I am struggling a bit > with the syntaxis and construction of commands. I managed to read a > .sdf file and calculate smiles, now I am trying to calculate AlogP > values, however all values return 0.0, I think that I have a problem > with explicit hydrogens. The descriptor will add explicit H's > This is what i've done: > > IChemObjectBuilder builder = > NoNotificationChemObjectBuilder.getInstance(); > IMolecule molecule = builder.newMolecule(); > molecule.addAtom(builder.newAtom("C")); > molecule.addAtom(builder.newAtom("C")); > molecule.addAtom(builder.newAtom("O")); > molecule.addAtom(builder.newAtom("C")); You don't seem to be adding any bonds between these atoms and hence the atom typing will not be correct > CDKAtomTypeMatcher matcher = > CDKAtomTypeMatcher.getInstance(molecule.getBuilder()); > for (IAtom atom : molecule.atoms()) { > IAtomType type = matcher.findMatchingAtomType(molecule, atom); > AtomTypeManipulator.configure(atom, type); } Consider using AtomContainerManipulator.perceiveAtomTypesAndConfigureAtoms to do it all at one go > Also, on using the calculation of Individual Descriptors I have no > problems (except the AlogP) but when using DescriptorEngine how can I > get the numerical values of each descriptor?, so far I have used: If you're not adding the bonds, I wonder about the validity of those descriptor values > DescriptorEngine engine = new > DescriptorEngine(DescriptorEngine.MOLECULAR); > engine.process(molecule); > but from then I don't know how to get each descriptor separately with > their corresponding names. For a given decsriptor get its DescriptorSpecification object and then use that as the key in the getProperty method of IAtomContainer. You can get the list of available specification objects via DescriptorEngine.getDescriptorSpecifications() ------------------------------------------------------------------- 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. ------------------------------ ------------------------------------------------------------------------ ------ 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 15 **************************************** ------------------------------------------------------------------------------ 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
