Hi Dmitry, I am happy to put layout code into the core CDK, or JCP, or wherever. If anyone has any suggestions or wishes for what it should be able to do, do let me know.
One thing that would be nice (but difficult) would be to take implicit hydrogens and other text into account when laying out. The tricky part is that you generally only know the size of text when you are at a particular stage of drawing. This also affects dihydrogen, ammonia, etc as you mention. The size is generally calculated without regard to the text, and this can lead to zero-sized bounding boxes. gilleain On 7/28/11, Dmitry Katsubo <dmitry.kats...@gmail.com> wrote: > Hi Nina, > > Thanks for you reply. Sorry for some delay with the answer... > > Thank you for nice demo of rendering the molecule set. From the link to > maillist I've found the class that does the job: > >> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-jchempaint/src/main/java/ambit2/jchempaint/CompoundImageTools.java > > and also nice work is presented here: > > http://gilleain.blogspot.com/2010/09/molecule-layouts.html > https://sourceforge.net/mailarchive/message.php?msg_id=26495170 > > Are there any plans to contribute any "layouting" code to jchempaint? If > not, maybe I can re-use the maven module, that contains > CompoundImageTools / GridMoleculeSetLayout class? > > I have also run the following related issue. When trying to render the > molecule like below: > > InChI=1/H2/h1H > InChI=1/H2N/h1H2/q-1 > > chemicalMoleculeRenderer.paint() returns the rectangular with zero > height and width. Is there any "correct" way to render "simple" > molecules like that? > > The relative message is: > https://sourceforge.net/mailarchive/message.php?msg_id=27010062 > > Thanks! > > On 02.06.2011 7:22, Nina Jeliazkova wrote: >> On 2 June 2011 01:38, Dmitry Katsubo <dmitry.kats...@gmail.com> wrote: >>> I definitely missed that, but perhaps I've joined just shortly >>> afterwards or it was in jcpempaint maillist (which I need to be >>> subscribed too): >>> >> https://sourceforge.net/mailarchive/forum.php?thread_name=4d8097d191b34_300c11a312c6527%40zx81.mail&forum_name=cdk-jchempaint >> http://apps.ideaconsult.net:8080/ambit2/depict?search=CCC.CCC.CCCCCCCC.CCCCCC >> >>> Looks great. Is the source open? >> >> Yes, it's quite old project ( ambit.sourceforge.net ) and there is a >> recent paper >> http://www.jcheminf.com/content/3/1/18 >> >>> Perhaps you can point me directly to the message you refer: if it >>> contains the implementation hints, I will start from that. >> >> Several messages here, where I was struggling with the same problem. >> >> http://sourceforge.net/mailarchive/forum.php?forum_name=cdk-devel&max_rows=25&style=ultimate&viewmonth=201010&viewday=26 >> >> Best regards, >> Nina > > > -- > With best regards, > Dmitry > > ------------------------------------------------------------------------------ > Got Input? Slashdot Needs You. > Take our quick survey online. Come on, we don't ask for help often. > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > http://p.sf.net/sfu/slashdot-survey > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
