tag:blogger.com,1999:blog-17889588.post5924816512475211291..comments2024-03-13T07:14:55.283+01:00Comments on chem-bla-ics: The Blue Obelisk Shoulders for Translational CheminformaticsEgon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-17889588.post-30124906015448899142011-10-20T06:55:12.139+02:002011-10-20T06:55:12.139+02:00I don't know how often.I don't know how often.Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-6784502973903469032011-10-19T22:29:36.749+02:002011-10-19T22:29:36.749+02:00Hi Noel - I got off topic in showing that Open Bab...Hi Noel - I got off topic in showing that Open Babel (correctly, IMO) handles a superset of OpenSMILES. My point is that there should be an arrow from RDKit to OpenSMILES.<br /><br />Greg Landrum has been part of OpenSMILES discussion for years, and changed part of RDKit to reflect that consensus. Not that he had to change much - OpenSMILES codified the best practices of what toolkits like Open Babel and RDKit already did. <br /><br />Every SMILES parser on the planet should handle OpenSMILES as input and generate OpenSMILES as output. <br /><br />Which makes me wonder about Egon's comment "you can in fact read OpenSMILES often with the CDK SMILES parser too" -- what part of OpenSMILES is not supported by CDK's SMILES parser?Andrew Dalkehttps://www.blogger.com/profile/17091314849699854287noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-79127544608614024962011-10-19T15:30:45.397+02:002011-10-19T15:30:45.397+02:00I consider non-implementation of the spec any exam...I consider non-implementation of the spec any examples where OB does not correctly read OpenSMILES, or where OB writes a SMILES string which is not valid OpenSMILES.<br /><br />(I think this discussion should either move to the opensmiles or openbabel mailing lists...)Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-7372942581604461412011-10-19T13:00:49.477+02:002011-10-19T13:00:49.477+02:00Open Babel's SMILES reader supports "[C--...Open Babel's SMILES reader supports "[C--]", which is valid Daylight SMILES syntax but invalid OpenSMILES syntax.<br /><br />Open Babel's SMILES reader supports "[C-H]" which a valid Daylight SMILES but again an invalid OpenSMILES.<br /><br />OpenSMILES does not support these forms because 1) no one uses it, and 2) it makes parsers more complicated.<br /><br />Well, almost no one uses it. RDKit had a data set which used "--". Greg has since updated all of the RDKit SMILES data so they are OpenSMILES compatible. (Hence an arrow from RDKit to OpenSMILES is appropriate.)<br /><br />In practice, OpenSMILES codifies the behavior that every tool already does, so it's hard to tell if a program is specifically influenced by OpenSMILES based on its output.Andrew Dalkehttps://www.blogger.com/profile/17091314849699854287noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-40669896197511253502011-10-19T10:13:41.169+02:002011-10-19T10:13:41.169+02:00There's no such option. But the OpenSMILES spe...There's no such option. But the OpenSMILES spec does not cover radicals.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-41090211923717667532011-10-19T10:10:09.325+02:002011-10-19T10:10:09.325+02:00Noel, is there also an option to output strict Ope...Noel, is there also an option to output strict OpenSMILES, with, say, -oosmi ?Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-64887090685584687042011-10-19T10:09:04.513+02:002011-10-19T10:09:04.513+02:00I forgot about that. So we "implement the Ope...I forgot about that. So we "implement the OpenSMILES specification, along with an extension for radicals". How does that sound?Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-22854071301496063902011-10-19T09:55:30.478+02:002011-10-19T09:55:30.478+02:00They report they do:
http://openbabel.org/docs/de...They report they do:<br /><br />http://openbabel.org/docs/dev/FileFormats/SMILES_format.html<br /><br />So, this would be a bug, then.<br /><br />How can people reproduce it?Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-59224615868072912242011-10-19T09:49:29.800+02:002011-10-19T09:49:29.800+02:00In that case, Open Babel reads and writes SMILES w...In that case, Open Babel reads and writes SMILES which aren't allowed by OpenSMILES; a notable example being its radical notation. OpenSMILES is a restrictive subset of SMILES, and I don't think any OB code changed in order to support it.Andrew Dalkehttps://www.blogger.com/profile/17091314849699854287noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-17763981771637161822011-10-19T06:10:30.382+02:002011-10-19T06:10:30.382+02:00Andrew,
1. the links show how the tools interoper...Andrew,<br /><br />1. the links show how the tools interoperate, not the people. So, me having looked at (asked questions / commented on) OpenSMILES is irrelevant; CDK does not support SMILES formally.<br /><br />2. I don't know if RDKit supports OpenSMILES. They authors have been asked to inform me about missing links, so I do not know if RDKit specifically supports OpenSMILES or just SMILES.<br /><br />So, that explains why those links are not there.<br /><br />It should be said that since OpenSMILES is so close to the original SMILES, you can in fact read OpenSMILES often with the CDK SMILES parser too, and likely with the RDKit one too. I don't know about the details, and how much noise that causes...<br /><br />Students are welcome to apply with me for a project to use the OpenSMILES grammar to create a (new) OpenSMILES parser from scratch :)Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-329442432227764132011-10-19T00:57:24.336+02:002011-10-19T00:57:24.336+02:00Greg Landrum participates in OpenSMILES, so there ...Greg Landrum participates in OpenSMILES, so there should also be an RDKit->OpenSMILES link. You're on there too, so why not a CDK->OpenSMILES one?Andrew Dalkehttps://www.blogger.com/profile/17091314849699854287noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-82770341692235323802011-10-18T11:50:50.273+02:002011-10-18T11:50:50.273+02:00Yeah, lack of metadata in CrossRef and PubChem... ...Yeah, lack of metadata in CrossRef and PubChem... I'll add it manually...Egon Willighagenhttps://www.blogger.com/profile/07470952136305035540noreply@blogger.comtag:blogger.com,1999:blog-17889588.post-37741515989221701932011-10-18T11:47:14.876+02:002011-10-18T11:47:14.876+02:00That picture of yours is really great. It clearly ...That picture of yours is really great. It clearly illustrates the way in which open source software is developed within an ecosystem of other software, and how certain components (e.g. a cheminformatics toolkit) really enable further developments in the field.<br /><br />(BTW, don't forget the article number of the recent paper, 37!)Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.com