From: Rajarshi G. <rg...@in...> - 2008-05-05 14:43:28
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I was looking into the case of the aromaticity problem with substituted pyridine derived from a SMILES string. What I see is that after explicit atom typing, the ring nitrogen gets an atom type of N.planar3 when the molecule is obtained from a SMILES string. But when the molecule is built explicitly (via CDK source code writer) the ring nitrogen is N.sp2. As a result, in the former case the pi electron count is of by one causing armaticity detection to fail. So it would seem that the problem the problem is in atom typing. Can anybody confirm this? - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Chemistry professors never die, they just fail to react. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfHQQACgkQZqGSLFHnnoSmuQCgnh80iLopeHjLyK0urVynxri8 cOwAn2ap95PkeG+TxRZTMMtm850V5Qel =RPde -----END PGP SIGNATURE----- |
From: Rajarshi G. <rg...@in...> - 2008-05-05 15:07:53
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 5, 2008, at 10:43 AM, Rajarshi Guha wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi, I was looking into the case of the aromaticity problem with > substituted pyridine derived from a SMILES string. What I see is that > after explicit atom typing, the ring nitrogen gets an atom type of > N.planar3 when the molecule is obtained from a SMILES string. But > when the molecule is built explicitly (via CDK source code writer) > the ring nitrogen is N.sp2. > > As a result, in the former case the pi electron count is of by one > causing armaticity detection to fail. > > So it would seem that the problem the problem is in atom typing. Can > anybody confirm this? Digging more into this, since the SMILES parser is not setting bond order information explicitly (all bonds appear to be single bonds), the nitrogen detection method in the CDK atom type matcher assigns the ring nitrogen N.planar3 It seems that the confusion is between pyrrole and pyridine - in general, cases where the ring nitrogen should have a hydrogen and cases where it should not. Now if I update the code to ensure that h-count is non-zero (to take into account pyrrole et al), then the pyridine case works fine. But then the pyrrole test case (and 3 other related cases such as indole0 in the atom type tests fails. Looking at the structure that is used to test pyrrole, it appears there is no explicit hydrogen. Is that correct? I've always thought that pyrrole should have an explicit H on the ring nitrogen. - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfIq0ACgkQZqGSLFHnnoT0PACgoookRw7RYS6A6QcrncyxXeGa Jc8AoPEQbEnzt/rGD0XceGt6ps5skRb3 =8Xju -----END PGP SIGNATURE----- |
From: Rajarshi G. <rg...@in...> - 2008-05-05 19:30:38
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 5, 2008, at 11:49 AM, Andreas Schüller wrote: > I agree that the pyrrole nitrogen should be protonated. But it > shouldn't matter whether the hydrogen is given implicitly or > explicitly. Hmm, I still have problems with this approach, since the identification of implicit H's implies atom typing. But if atom typing takes into account implicit H's, we have a circular problem > So the difficulty is how to determine whether a nitrogen contained > in a ring is N.planar3 or N.sp2. Given the two smiles n1cccc1 and > n1ccccc1 for pyrrole and pyridine the only information given are > the atom symbols, the connectivity and the aromaticity. To be pedantic, we do not have aromaticity. Rather, we have hybridization > One solution for atom typing now is to perform a ring detection or > substructure matching on a 5-membered ring. If the nitrogen is part > of a 5-ring, its configuration should be N.planar3, otherwise > N.sp2. If there are more than one nitrogens in a 5-ring, only one > of them should be N.planar3, the rest should be N.sp2. The same > applied to oxygens and sulfurs. This sounds good - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Alcohol, an alternative to your self - 'Alcohol' by the Bare Naked Ladies -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfYEsACgkQZqGSLFHnnoQVSwCfX0B9P/LzOtlKh2svoTLD3tVa FoMAniKbazpFV8RT8N7t2Ye3w4ZLSRaI =tA7l -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-05-05 19:37:59
|
On Mon, May 5, 2008 at 9:30 PM, Rajarshi Guha <rg...@in...> wrote: > On May 5, 2008, at 11:49 AM, Andreas Schüller wrote: > > I agree that the pyrrole nitrogen should be protonated. But it > > shouldn't matter whether the hydrogen is given implicitly or > > explicitly. > > Hmm, I still have problems with this approach, since the > identification of implicit H's implies atom typing. But if atom > typing takes into account implicit H's, we have a circular problem Correct. Atom typing cannot take into account implicit hydrogen. > > So the difficulty is how to determine whether a nitrogen contained > > in a ring is N.planar3 or N.sp2. Given the two smiles n1cccc1 and > > n1ccccc1 for pyrrole and pyridine the only information given are > > the atom symbols, the connectivity and the aromaticity. > > To be pedantic, we do not have aromaticity. Rather, we have > hybridization Yeah... implicit chemistry is just lovely. > > One solution for atom typing now is to perform a ring detection or > > substructure matching on a 5-membered ring. If the nitrogen is part > > of a 5-ring, its configuration should be N.planar3, otherwise > > N.sp2. If there are more than one nitrogens in a 5-ring, only one > > of them should be N.planar3, the rest should be N.sp2. The same > > applied to oxygens and sulfurs. > > This sounds good Sounds reasonable, but: unit tests please. PubChem CIDs for the simplest examples of each case, please. Or InChI... Rajarshi, did I tell you about @cdk.inchi yet? Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-05-05 21:14:34
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 5, 2008, at 3:37 PM, Egon Willighagen wrote: > On Mon, May 5, 2008 at 9:30 PM, Rajarshi Guha <rg...@in...> > wrote: >> On May 5, 2008, at 11:49 AM, Andreas Schüller wrote: >>> I agree that the pyrrole nitrogen should be protonated. But it >>> shouldn't matter whether the hydrogen is given implicitly or >>> explicitly. >> >> Hmm, I still have problems with this approach, since the >> identification of implicit H's implies atom typing. But if atom >> typing takes into account implicit H's, we have a circular problem > > Correct. Atom typing cannot take into account implicit hydrogen. Hmm, it looks like the code in CDKAtomTypeMatcher makes calls to getHydrogenCount() which returns the count of implicit H's - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Q: Why did the mathematician name his dog "Cauchy"? A: Because he left a residue at every pole. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfeK8ACgkQZqGSLFHnnoSEDACg1ZnPM2wWnn0t9vsqCRLn5Zz6 yt0An17Z1hOrWDQOtOe93MqDQzruxFbN =Ev9d -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-05-05 21:18:21
|
On Mon, May 5, 2008 at 11:14 PM, Rajarshi Guha <rg...@in...> wrote: > Hmm, it looks like the code in CDKAtomTypeMatcher makes calls to > getHydrogenCount() which returns the count of implicit H's Ooops!... when did I sneak in that bit of code ?!?! Will fix that right away... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-05-05 21:25:09
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 5, 2008, at 5:18 PM, Egon Willighagen wrote: > On Mon, May 5, 2008 at 11:14 PM, Rajarshi Guha <rg...@in...> > wrote: >> Hmm, it looks like the code in CDKAtomTypeMatcher makes calls to >> getHydrogenCount() which returns the count of implicit H's > > Ooops!... when did I sneak in that bit of code ?!?! > > Will fix that right away... I'm in the process of fixing it and trying to incorporate Andreas' suggestion - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- AIBOHPHOBIA - the fear of palindromes. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfezAACgkQZqGSLFHnnoSS5ACg3NTgc9fCHYNTLuDsGPlsRvtU GFEAoMUPCEOynYFw+WqXSYwCrxynsGFf =7Uqr -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-05-05 21:36:12
|
Rajarshi, On Mon, May 5, 2008 at 11:25 PM, Rajarshi Guha <rg...@in...> wrote: > > Will fix that right away... > > I'm in the process of fixing it and trying to incorporate Andreas' > suggestion I already commited something... :( I did include Andreas suggestion... not exact, but the idea. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Andreas S. <a.s...@ch...> - 2008-05-05 22:27:47
|
Hey Egon, I didn't actually check it, but the way I read your modifications I think there's going to be a problem in rings with more than one hetero atom. 5-rings with more than one hetero atom: Imidazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=152446 Pyrazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=152444 Triazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=121373 Osotriazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=67516 Tetrazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=67519 Oxazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=11533600 Isooxazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=11533601 Thiazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=26697065 Isothiazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=209631 Thiadiazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=119391 Oxadiazole http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=97428 6-rings with more than one hetero atom: Pyrimidine http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9260 Pyridazine http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9259 Triazine http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9262 etc... Andreas P.S. Egon, for some reason sourceforge.net doesn't accept my emails. Would you please forward this email to the list? Thanks. Egon Willighagen wrote: > Rajarshi, > > On Mon, May 5, 2008 at 11:25 PM, Rajarshi Guha <rg...@in...> wrote: >>> Will fix that right away... >> I'm in the process of fixing it and trying to incorporate Andreas' >> suggestion > > I already commited something... :( I did include Andreas suggestion... > not exact, but the idea. > > Egon > |
From: Andreas S. <a.s...@ch...> - 2008-05-07 21:55:31
|
I added test code for all those hetero cycles and the tests complete without problems. -Andreas Andreas Schüller wrote: > Hey Egon, > > I didn't actually check it, but the way I read your modifications I > think there's going to be a problem in rings with more than one hetero atom. > > 5-rings with more than one hetero atom: > > Imidazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=152446 > > Pyrazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=152444 > > Triazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=121373 > > Osotriazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=67516 > > Tetrazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=67519 > > Oxazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=11533600 > > Isooxazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=11533601 > > Thiazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=26697065 > > Isothiazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=209631 > > Thiadiazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=119391 > > Oxadiazole > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=97428 > > > 6-rings with more than one hetero atom: > > Pyrimidine > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9260 > > Pyridazine > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9259 > > Triazine > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9262 > > etc... > > Andreas > > P.S. Egon, for some reason sourceforge.net doesn't accept my emails. > Would you please forward this email to the list? Thanks. > > > > > > > Egon Willighagen wrote: >> Rajarshi, >> >> On Mon, May 5, 2008 at 11:25 PM, Rajarshi Guha <rg...@in...> wrote: >>>> Will fix that right away... >>> I'm in the process of fixing it and trying to incorporate Andreas' >>> suggestion >> I already commited something... :( I did include Andreas suggestion... >> not exact, but the idea. >> >> Egon >> > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Andreas Schüller PhD student in the research group of Prof. Dr. Gisbert Schneider Johann Wolfgang Goethe University Beilstein-endowed Chair for Chemoinformatics Building B - 3rd floor Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49 69 798 24879 Fax: +49 69 798 24880 http://www.modlab.de/ |
From: Rajarshi G. <rg...@in...> - 2008-05-07 19:32:26
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 6, 2008, at 2:58 PM, Andreas Schüller wrote: > I added test code for all those hetero cycles and the tests > complete without problems. It looks like aromaticity is not detected properly for imidazole if atom typing is done on the basis of hybridization is provided (i.e., not a Kekule structure). - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Finally I am becoming stupider no more - Paul Erdos' epitaph -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgiA5kACgkQZqGSLFHnnoQYlgCfeot4l+kmR/jYXE2U4Xs2l9sV avAAoJvuI+wCI9lmTTOvGcwBm7jBX+Gt =PXLp -----END PGP SIGNATURE----- |
From: Andreas S. <a.s...@ch...> - 2008-05-07 21:52:59
|
I've implemented those tests in CDKAtomTypeMatcherTest.java building the molecules from scratch with CDK. Only the atom type itself is checked, not other stuff such as hybridization. I've already started to implement those tests in SmilesParserTest.java checking for real molecules and the first errors arose. Not done with it yet... Andreas Rajarshi Guha wrote: > On May 6, 2008, at 2:58 PM, Andreas Schüller wrote: >> I added test code for all those hetero cycles and the tests complete >> without problems. > > It looks like aromaticity is not detected properly for imidazole if atom > typing is done on the basis of hybridization is provided (i.e., not a > Kekule structure). > > - ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > - ------------------------------------------------------------------- > Finally I am becoming stupider no more > - Paul Erdos' epitaph > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.8 (Darwin) > > iEYEARECAAYFAkgiA5kACgkQZqGSLFHnnoQYlgCfeot4l+kmR/jYXE2U4Xs2l9sV > avAAoJvuI+wCI9lmTTOvGcwBm7jBX+Gt > =PXLp > -----END PGP SIGNATURE----- > |
From: Rajarshi G. <rg...@in...> - 2008-05-07 21:54:42
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 7, 2008, at 5:53 PM, Andreas Schüller wrote: > I've implemented those tests in CDKAtomTypeMatcherTest.java > building the molecules from scratch with CDK. Only the atom type > itself is checked, not other stuff such as hybridization. One way to do it in the atom typer tests, is to build the molecule from scratch and set all bonds to single and set all the atoms in the ring to SP2. That should 'simulate' atom typing on aromatic SMILES - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- After a number of decimal places, nobody gives a damn. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgiJRoACgkQZqGSLFHnnoRK+QCgpL3Rdgs9kqXShiziUfVjMUQ0 yUQAoKfyMefcaNZTh4MYhfsn/t62SMLU =l1z+ -----END PGP SIGNATURE----- |
From: Andreas S. <a.s...@ch...> - 2008-05-05 22:28:53
|
I agree that the pyrrole nitrogen should be protonated. But it shouldn't matter whether the hydrogen is given implicitly or explicitly. So the difficulty is how to determine whether a nitrogen contained in a ring is N.planar3 or N.sp2. Given the two smiles n1cccc1 and n1ccccc1 for pyrrole and pyridine the only information given are the atom symbols, the connectivity and the aromaticity. One solution for atom typing now is to perform a ring detection or substructure matching on a 5-membered ring. If the nitrogen is part of a 5-ring, its configuration should be N.planar3, otherwise N.sp2. If there are more than one nitrogens in a 5-ring, only one of them should be N.planar3, the rest should be N.sp2. The same applied to oxygens and sulfurs. I guess one needs to implement a special treatment of 5-rings in order to perform atom typing correctly. Best wishes, Andreas Rajarshi Guha wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > On May 5, 2008, at 10:43 AM, Rajarshi Guha wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Hi, I was looking into the case of the aromaticity problem with >> substituted pyridine derived from a SMILES string. What I see is that >> after explicit atom typing, the ring nitrogen gets an atom type of >> N.planar3 when the molecule is obtained from a SMILES string. But >> when the molecule is built explicitly (via CDK source code writer) >> the ring nitrogen is N.sp2. >> >> As a result, in the former case the pi electron count is of by one >> causing armaticity detection to fail. >> >> So it would seem that the problem the problem is in atom typing. Can >> anybody confirm this? > > Digging more into this, since the SMILES parser is not setting bond > order information explicitly (all bonds appear to be single bonds), > the nitrogen detection method in the CDK atom type matcher assigns > the ring nitrogen N.planar3 > > It seems that the confusion is between pyrrole and pyridine - in > general, cases where the ring nitrogen should have a hydrogen and > cases where it should not. > > Now if I update the code to ensure that h-count is non-zero (to take > into account pyrrole et al), then the pyridine case works fine. But > then the pyrrole test case (and 3 other related cases such as indole0 > in the atom type tests fails. Looking at the structure that is used > to test pyrrole, it appears there is no explicit hydrogen. > > Is that correct? I've always thought that pyrrole should have an > explicit H on the ring nitrogen. > > - ------------------------------------------------------------------- > Rajarshi Guha <rg...@in...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > - ------------------------------------------------------------------- > All science is either physics or stamp collecting. > -- Ernest Rutherford > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.8 (Darwin) > > iEYEARECAAYFAkgfIq0ACgkQZqGSLFHnnoT0PACgoookRw7RYS6A6QcrncyxXeGa > Jc8AoPEQbEnzt/rGD0XceGt6ps5skRb3 > =8Xju > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Andreas Schüller PhD student in the research group of Prof. Dr. Gisbert Schneider Johann Wolfgang Goethe University Beilstein-endowed Chair for Chemoinformatics Building B - 3rd floor Siesmayerstr. 70 60323 Frankfurt am Main Germany Tel.: +49 69 798 24879 Fax: +49 69 798 24880 http://www.modlab.de/ |
From: Rajarshi G. <rg...@in...> - 2008-05-05 19:46:13
|
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 5, 2008, at 3:37 PM, Egon Willighagen wrote: >>> >>> One solution for atom typing now is to perform a ring detection or >>> substructure matching on a 5-membered ring. If the nitrogen is part >>> of a 5-ring, its configuration should be N.planar3, otherwise >>> N.sp2. If there are more than one nitrogens in a 5-ring, only one >>> of them should be N.planar3, the rest should be N.sp2. The same >>> applied to oxygens and sulfurs. >> >> This sounds good > > Sounds reasonable, but: > > unit tests please. > > PubChem CIDs for the simplest examples of each case, please. Or > InChI... > > Rajarshi, did I tell you about @cdk.inchi yet? haven't heard about this one. BTW, looks like the source links for each class need to be updated to the new SVN layout. Also is it possible to annotate the Javadocs for the non-test classes with their corresponding test classes? I recall you saying some thing about annotations not being accessible from Javadoc - ------------------------------------------------------------------- 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. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkgfY/IACgkQZqGSLFHnnoRfPQCdFTwT+f5nG3c3QT6b8jOeMyXs D90AnifXwYZlGFouBZ4mXCSrwPRFCTNO =lJq5 -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-05-05 21:05:51
|
On Mon, May 5, 2008 at 9:45 PM, Rajarshi Guha <rg...@in...> wrote: > On May 5, 2008, at 3:37 PM, Egon Willighagen wrote: > > did I tell you about @cdk.inchi yet? > > haven't heard about this one. Indicated that a unit test tests algorithms applicability for a particular molecule. > BTW, looks like the source links for each class need to be updated to the > new SVN layout. Please file a bug report. > Also is it possible to annotate the Javadocs for the > non-test classes with their corresponding test classes? I recall you saying > some thing about annotations not being accessible from Javadoc Correct. Nothing much I can do about that :( Well, other than some hand-crafted utility afterwards... Egon -- ---- http://chem-bla-ics.blogspot.com/ |