From: Egon W. <eg...@us...> - 2006-01-22 15:33:48
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On Saturday 21 January 2006 20:04, Egon Willighagen wrote: > On Saturday 21 January 2006 16:40, Christoph Steinbeck wrote: > JCP 2.1.7 (in jcp21 branch) has a bug fix for this. It has not been ported > to HEAD yet. I'll try to port it right now, as I actually need 2D layout > working again in HEAD... I just applied the two line fix, and just commited this to CVS. I've converted the ZINC SDF test file with 1000 compounds to a PDF with table, using Rajarshi's draw2.java [1], and most compounds look rather good. One annoyance are the sulphates and phosphates with one would expect to be drawn with 90 degrees angled, and the two double bonded oxygens to the sides. BTW, another good use of the ZINC test data set, see the cdk-qa ML. The result: http://www.woc.science.ru.nl/devel/egonw/zinc.pdf Egon 1.http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d -- eg...@us... Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Christoph S. <c.s...@un...> - 2006-01-23 09:07:32
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> This looks very good. >=20 > A general observation. In difficult cases I would prefer a diagram to b= e=20 > uninterpretable (or only interpretable with difficulty) than to be=20 > misinterpretable. Two common examples are (a) when two atoms are=20 > superimposed and (b) when a carbon has two ligands at 180 degrees. In=20 > the first instance can the atoms be slightly shifted even if the rings=20 > are messy? and in the second a bent bond, or a "C" or dot at the atom=20 > position. Peter, about a year or two ago, I've built in the function to resolve overlap. Not sure if it was switched on in this case (guess it should be on by def= ault.) Did you see any examples in the PDF (ZINC number?) where instance 1 happe= ns? Cheers, Chris --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: peter murray-r. <pm...@ca...> - 2006-01-23 15:49:03
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At 09:07 23/01/2006, Christoph Steinbeck wrote: >>This looks very good. >>A general observation. In difficult cases I=20 >>would prefer a diagram to be uninterpretable=20 >>(or only interpretable with difficulty) than to=20 >>be misinterpretable. Two common examples are=20 >>(a) when two atoms are superimposed and (b)=20 >>when a carbon has two ligands at 180 degrees.=20 >>In the first instance can the atoms be slightly=20 >>shifted even if the rings are messy? and in the=20 >>second a bent bond, or a "C" or dot at the atom position. > >Peter, > >about a year or two ago, I've built in the function to resolve overlap. >Not sure if it was switched on in this case=20 >(guess it should be on by default.) >Did you see any examples in the PDF (ZINC number?) where instance 1= happens? I thought I saw several. Mainly strange oxygen coordinations P. >Cheers, > >Chris > >-- >Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) >Head of the Research Group for Molecular Informatics >Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) >Z=FClpicher Str. 47, 50674 Cologne >Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 > >What is man but that lofty spirit - that sense of enterprise. >... Kirk, "I, Mudd," stardate 4513.3.. Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069=20 |
From: Christoph S. <c.s...@un...> - 2006-01-22 16:39:39
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Egon, Rajarshi, this PDF is fantastic! It really shows where the problems are. I love this pretty new world with all this relevant structures (ZINC, Pub= chem)=20 available for testing things! As soon as I can, I'll go into fixing these things. And kudos to Rajarshi for writing such a helpful piece of code. Cheers, Chris Egon Willighagen wrote: > On Saturday 21 January 2006 20:04, Egon Willighagen wrote: >=20 >>On Saturday 21 January 2006 16:40, Christoph Steinbeck wrote: >>JCP 2.1.7 (in jcp21 branch) has a bug fix for this. It has not been por= ted >>to HEAD yet. I'll try to port it right now, as I actually need 2D layou= t >>working again in HEAD... >=20 >=20 > I just applied the two line fix, and just commited this to CVS. I've co= nverted=20 > the ZINC SDF test file with 1000 compounds to a PDF with table, using=20 > Rajarshi's draw2.java [1], and most compounds look rather good. >=20 > One annoyance are the sulphates and phosphates with one would expect to= be=20 > drawn with 90 degrees angled, and the two double bonded oxygens to the = sides. > BTW, another good use of the ZINC test data set, see the cdk-qa ML. >=20 > The result: >=20 > http://www.woc.science.ru.nl/devel/egonw/zinc.pdf >=20 > Egon >=20 > 1.http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d >=20 --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: peter murray-r. <pm...@ca...> - 2006-01-22 17:35:14
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At 16:39 22/01/2006, Christoph Steinbeck wrote: >Egon, Rajarshi, > >this PDF is fantastic! >It really shows where the problems are. >I love this pretty new world with all this=20 >relevant structures (ZINC, Pubchem) available for testing things! >As soon as I can, I'll go into fixing these things. > >And kudos to Rajarshi for writing such a helpful piece of code. > >Cheers, > >Chris > >Egon Willighagen wrote: >>On Saturday 21 January 2006 20:04, Egon Willighagen wrote: >> >>>On Saturday 21 January 2006 16:40, Christoph Steinbeck wrote: >>>JCP 2.1.7 (in jcp21 branch) has a bug fix for this. It has not been= ported >>>to HEAD yet. I'll try to port it right now, as I actually need 2D layout >>>working again in HEAD... >> >>I just applied the two line fix, and just=20 >>commited this to CVS. I've converted the ZINC=20 >>SDF test file with 1000 compounds to a PDF with=20 >>table, using Rajarshi's draw2.java [1], and most compounds look rather= good. >>One annoyance are the sulphates and phosphates=20 >>with one would expect to be drawn with 90=20 >>degrees angled, and the two double bonded oxygens to the sides. >>BTW, another good use of the ZINC test data set, see the cdk-qa ML. >>The result: >> http://www.woc.science.ru.nl/devel/egonw/zinc.pdf >>Egon >>1.http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d This looks very good. A general observation. In difficult cases I would=20 prefer a diagram to be uninterpretable (or only=20 interpretable with difficulty) than to be=20 misinterpretable. Two common examples are (a)=20 when two atoms are superimposed and (b) when a=20 carbon has two ligands at 180 degrees. In the=20 first instance can the atoms be slightly shifted=20 even if the rings are messy? and in the second a=20 bent bond, or a "C" or dot at the atom position. P. >-- >Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) >Head of the Research Group for Molecular Informatics >Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) >Z=FClpicher Str. 47, 50674 Cologne >Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 > >What is man but that lofty spirit - that sense of enterprise. >... Kirk, "I, Mudd," stardate 4513.3.. > > >------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. Do you grep through log= files >for problems? Stop! Download the new AJAX search engine that makes >searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >http://sel.as-us.falkag.net/sel?cmdk&kid3432&bid#0486&dat1642 >_______________________________________________ >Cdk-devel mailing list >Cdk...@li... >https://lists.sourceforge.net/lists/listinfo/cdk-devel Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069=20 |
From: Rajarshi G. <rx...@ps...> - 2006-01-22 20:08:48
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On Sun, 2006-01-22 at 17:39 +0100, Christoph Steinbeck wrote: > Egon, Rajarshi, > > this PDF is fantastic! > It really shows where the problems are. > I love this pretty new world with all this relevant structures (ZINC, Pubchem) > available for testing things! > As soon as I can, I'll go into fixing these things. Thanks for the fix. I've updated the code so that you can specify how many molecule columns should be generated. I also put up some examples. I have to say, the SDG is very neat! The output (3 structure column) looks very professional! ------------------------------------------------------------------- Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- "I'd love to go out with you, but my favorite commercial is on TV." |