From: Rajarshi G. <raj...@gm...> - 2010-07-21 21:21:04
|
Hi, I was trying to read a mol2 file containing multiple molecules, but it doesn't seem to be working. Given a set of molecules, converted to SDF and Mol2, reading the former gives me the correct number of molecules, but reading the latter gives me a *single* molecule - which consists of all molecules collected togetehr in one IAtomContainer. Example code is at http://gist.github.com/485155 Does anybody have any ideas why this is the case? -- Rajarshi Guha NIH Chemical Genomics Center |
From: Egon W. <ego...@gm...> - 2010-07-21 21:24:08
|
On Wed, Jul 21, 2010 at 11:20 PM, Rajarshi Guha <raj...@gm...> wrote: > Example code is at http://gist.github.com/485155 Note that this Gist tries to read the .sdf twice... > Does anybody have any ideas why this is the case? Did you check if the Mol2 reader supports reading of more than one file? I did not even know it supported that... I would guess the Mol2Reader just reads everything as one IAtomContainer... Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Rajarshi G. <raj...@gm...> - 2010-07-21 21:39:16
|
On Wed, Jul 21, 2010 at 5:23 PM, Egon Willighagen <ego...@gm...> wrote: > On Wed, Jul 21, 2010 at 11:20 PM, Rajarshi Guha <raj...@gm...> wrote: >> Example code is at http://gist.github.com/485155 > > Note that this Gist tries to read the .sdf twice... Oops. Even after correcting file name the problem remains > Did you check if the Mol2 reader supports reading of more than one > file? I did not even know it supported that... > > I would guess the Mol2Reader just reads everything as one IAtomContainer... Hmm, I was expecting that it did, but apparently not :( Patch coming in -- Rajarshi Guha NIH Chemical Genomics Center |
From: Egon W. <ego...@gm...> - 2010-07-21 21:42:25
|
On Wed, Jul 21, 2010 at 11:39 PM, Rajarshi Guha <raj...@gm...> wrote: > Patch coming in Cool :) BTW, there are still a few patches for CDK 1.2.x, with one new one since my last request, fixing SD properties reading... if you could find a bit of time... I'm also trying to regenerate the FPs for the builder3d, as that got broken once more... (that will be fixed with the HybridOnlyFP for once and for all, I think :) Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Rajarshi G. <raj...@gm...> - 2010-07-21 23:09:08
|
On Wed, Jul 21, 2010 at 5:41 PM, Egon Willighagen <ego...@gm...> wrote: > On Wed, Jul 21, 2010 at 11:39 PM, Rajarshi Guha <raj...@gm...> wrote: >> Patch coming in > > Cool :) OK, it's uploaded. If you could apply it to maste that'd be great > BTW, there are still a few patches for CDK 1.2.x, with one new one > since my last request, fixing SD properties reading... if you could > find a bit of time... Done -- Rajarshi Guha NIH Chemical Genomics Center |
From: Egon W. <ego...@gm...> - 2010-07-22 06:46:00
|
On Thu, Jul 22, 2010 at 1:09 AM, Rajarshi Guha <raj...@gm...> wrote: >> BTW, there are still a few patches for CDK 1.2.x, with one new one >> since my last request, fixing SD properties reading... if you could >> find a bit of time... > > Done There are still a few more patches I would like to release with 1.2.6: 3030167 Addition of a missing atom type: N.oxide (I replied to your comment) 3030166 Two atom type unit tests for SMILES from cdk-devel ML 2982677 Exception when IAtomContainer.clone() with IBond with 0 Atom The following we should take to the mailing list, I guess... 3018684 Add a constant to indicate library version Please check my comments, and see how I can make my patch acceptable for you... would it help if I added more functionality to the CDK class? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Rajarshi G. <raj...@gm...> - 2010-07-22 13:03:15
|
On Thu, Jul 22, 2010 at 2:45 AM, Egon Willighagen <ego...@gm...> wrote: > On Thu, Jul 22, 2010 at 1:09 AM, Rajarshi Guha <raj...@gm...> wrote: >>> BTW, there are still a few patches for CDK 1.2.x, with one new one >>> since my last request, fixing SD properties reading... if you could >>> find a bit of time... >> >> Done > > There are still a few more patches I would like to release with 1.2.6: > > 3030167 Addition of a missing atom type: N.oxide (I replied to your comment) > 3030166 Two atom type unit tests for SMILES from cdk-devel ML > 2982677 Exception when IAtomContainer.clone() with IBond with 0 Atom Went over these and they look good, so all applied > The following we should take to the mailing list, I guess... > > 3018684 Add a constant to indicate library version > > Please check my comments, and see how I can make my patch acceptable > for you... would it help if I added more functionality to the CDK > class? Your approach makes sense, but I still think a whole class extra class for a version string is a bit overkill. Lets see what the mailling list has to say? -- Rajarshi Guha NIH Chemical Genomics Center |