From: Ola S. <ola...@fa...> - 2007-02-16 13:45:08
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Hi, I'd like to propose an addition for the Monomer class: myMonomer.getPolymer(); OK? /Ola |
From: Egon W. <e.w...@sc...> - 2007-02-16 13:58:07
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On Friday 16 February 2007, Ola Spjuth wrote: > I'd like to propose an addition for the Monomer class: > > myMonomer.getPolymer(); There are few things to this: 1. Yes, having that is very handy 2. Consider the symmetry with not having Atom.bonds() 3. the CDK 1.0 interfaces are in freeze 4. this requires code updates in several other methods too, including in other classes like Polymer, BioPolymer I'm not against this change, but it is not easily done. Ola, it would help if you have a ready-made patch. Everyone, input please. Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Rajarshi G. <rg...@in...> - 2007-02-16 14:08:15
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On Fri, 2007-02-16 at 14:55 +0100, Egon Willighagen wrote: > On Friday 16 February 2007, Ola Spjuth wrote: > > I'd like to propose an addition for the Monomer class: > > > > myMonomer.getPolymer(); Sorry for being slow, but what would getPolymer() return from a Monomer object? ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "355/113 -- Not the famous irrational number PI, but an incredible simulation!" |
From: Ola S. <ola...@fa...> - 2007-02-16 16:00:08
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A Polymer if the Monomer is contained in a Polymer, null otherwise. On Feb 16, 2007, at 15:07 , Rajarshi Guha wrote: > On Fri, 2007-02-16 at 14:55 +0100, Egon Willighagen wrote: >> On Friday 16 February 2007, Ola Spjuth wrote: >>> I'd like to propose an addition for the Monomer class: >>> >>> myMonomer.getPolymer(); > > Sorry for being slow, but what would getPolymer() return from a > Monomer object? > > ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > "355/113 -- Not the famous irrational number PI, > but an incredible simulation!" > > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Miguel R. <mig...@ya...> - 2007-02-16 17:14:50
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> A Polymer if the Monomer is contained in a Polymer, null otherwise. I think the idea is wrong. If I have understood right that would be the same for your case like you ask an atom getMolecule. For this we have a method molecule.contains(IAtom). This should be clearer in my opinion. Miquel ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com |
From: Ola S. <ola...@fa...> - 2007-02-18 23:03:36
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I understand your point but consider the following scenario in =20 Bioclipse: A user clicks on a Monomer. A selection with the Monomer object is =20 passed to Views (this is the SWT selection mechanism). Views act on =20 the selection. If we'd like to highlight a monomer in Jmol (and we =20 most certainly do), then Jmol requires monomer identification by =20 Monomer:Chain. I'll probably be able to work around the problem in Bioclipse anyway; =20= I wanted to avoid adding another layer on top of CDK but that is =20 perhaps necessary if we can't add required functionality due to a =20 design policy. I really don't understand the objection against a bidirectional =20 parent/child relationship in general but maybe it's because I work =20 too much with SWT. Cheers, .../Ola On Feb 16, 2007, at 18:15 , Miguel Rojas wrote: > >> A Polymer if the Monomer is contained in a Polymer, null otherwise. > I think the idea is wrong. If I have understood right that would be =20= > the same > for your case like you ask an atom getMolecule. > > For this we have a method molecule.contains(IAtom). What if you have no reference to the molecule? Loop over all =20 molecules? What if you have many? > > This should be clearer in my opinion. > > Miquel > > =09 > ______________________________________________ > LLama Gratis a cualquier PC del Mundo. > Llamadas a fijos y m=F3viles desde 1 c=E9ntimo por minuto. > http://es.voice.yahoo.com > > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Egon W. <e.w...@sc...> - 2007-02-19 08:19:17
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On Monday 19 February 2007, Ola Spjuth wrote: > I really don't understand the objection against a bidirectional > parent/child relationship in general but maybe it's because I work > too much with SWT. I don't object to the idea; actually, after 6 years of CDK, I think we should do this, just not now. The API of the core classes is frozen, making a change like this is practically not possible, for me at least, as it involved not just these two methods you propose, but a rewrite of methods in other classes too. Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Kai H. <Kai.Hartmann@Uni-Koeln.De> - 2007-02-19 08:35:06
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> myMonomer.getPolymer(); Is there always a 1:1 relationship between a Monomer and a Polymer? Might a user be interested to reuse an existing Monomer object as part of more than one Polymer object? Generally speaking, I don't think it is such a bad idea to have references to each other stored in both related objects - if one object is completely dependent on the other (e.g. Monomer does not exist without Polymer). Kai |