tag:blogger.com,1999:blog-17889588.post356907313904098420..comments2024-03-13T07:14:55.283+01:00Comments on chem-bla-ics: OPSIN used for a Bioclipse wizardEgon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-17889588.post-85369819316776093692011-02-17T22:10:52.873+01:002011-02-17T22:10:52.873+01:00This comment has been removed by the author.gilleainhttps://www.blogger.com/profile/14491887080861584059noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-58223166041638798812011-02-17T20:26:45.793+01:002011-02-17T20:26:45.793+01:00Oh, and please file your ideas as feature requests...Oh, and please file your ideas as feature requests at:<br /><br /> http://wishes.bioclipse.net/Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-68340429751600707292011-02-17T20:26:09.825+01:002011-02-17T20:26:09.825+01:00@Noel. Yeah, 'searching' in online databas...@Noel. Yeah, 'searching' in online databases is currently a bit of a miss right now. You can search on 'name' in PubChem and ChemSpider, but something like substructure search is indeed needed.<br /><br />BTW, I very much like the idea of searching on truncated InChIs...Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-46831608033569447312011-02-17T20:25:00.182+01:002011-02-17T20:25:00.182+01:00Kekule structures are just resonance structures. T...Kekule structures are just resonance structures. Those you can already do with Miguel's code, though I would need to figure out first how the API works... (would make an interesting section for my CDK book perhaps...)Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-91648785199221604002011-02-17T19:52:30.315+01:002011-02-17T19:52:30.315+01:00@baoilleach : Well, my suggestion was only half-se...@baoilleach : Well, my suggestion was only half-serious. I think it would be a bad idea to allow users to type in "C1000H2000" and lock the process forever :)<br /><br />Your suggestion has more merit, I think. Other 'small' spaces might be tautomers, as with Mark's recent CDK patch. Or Kekulé structures if I could work out how to adapt <a href="http://en.wikipedia.org/wiki/Edmonds's_matching_algorithm" rel="nofollow">Edmond's Path/Tree/Flower algorithm</a> (or some other method).gilleainhttps://www.blogger.com/profile/14491887080861584059noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-35524137904876304412011-02-17T18:28:41.873+01:002011-02-17T18:28:41.873+01:00I like that too.
@gilleain: Maybe you could do an...I like that too.<br /><br />@gilleain: Maybe you could do an InChI search on the Chemical Structure Identifier Resolver with the truncated InChI. Not quite what you are talking about, but maybe close...Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-45111891154568275332011-02-17T18:15:55.455+01:002011-02-17T18:15:55.455+01:00Great stuff - looks useful.
What would be truly f...Great stuff - looks useful.<br /><br />What would be truly fantastic (er, literally at the moment) would be a "New Molecule Set from Formula" wizard, that would generate the chemical space...<br /><br />Anyone with know-how in canonical checking or structure generation is welcome to help make this a reality :)gilleainhttps://www.blogger.com/profile/14491887080861584059noreply@blogger.com