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Re: [Cdk-user] Question on Tabular Display of 2D Structures
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From: Rajarshi G. <rg...@in...> - 2009-04-29 20:27:14
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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. On Apr 29, 2009, at 12:54 PM, Beesley, Angela wrote: > 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...@li... > [mailto:cdk...@li...] On Behalf Of > cdk...@li... > Sent: Wednesday, April 29, 2009 1:02 PM > To: cdk...@li... > Subject: Cdk-user Digest, Vol 35, Issue 15 > > Send Cdk-user mailing list submissions to > cdk...@li... > > 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...@li... > > You can reach the person managing the list at > cdk...@li... > > 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...@in...> > Subject: Re: [Cdk-user] Question on descriptors > To: "Beesley, Angela" <Ang...@un...> > Cc: cdk...@li... > Message-ID: <999...@in...> > 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...@in...> > 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...@li... > 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...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> 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. |