[Rdkit-discuss] FYI: google code shutting down
Dear all, Google has decided to shut down Google Code: http://google-opensource.blogspot.ch/2015/03/farewell-to-google-code.html This doesn't have a huge impact on the RDKit since the only current information that's still hosted there is the wiki (and a lot of that is pretty out of date). Google has a tool available for getting data out of the google code wiki and translating it to the flavor of MarkDown that github uses. I will look into that over the next few weeks and get the bits that are still useful and current transferred. Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. -greg -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Oracle, pypl and rdkit
Hi Jan and TJ, Thank you very much for your comments. Yes, I'm going to use fingerprints, but I was hoping to use UTL_RAW bitwise operation to handle them (we'll see how this goes). What worries me that invoking structure matching via PYPL for each molecule would be slow, do you see any way of doing it batchwise? (for example, using oracle's table functions) Best wishes, Michal On 13 March 2015 at 07:50, Jan Holst Jensen j...@biochemfusion.com wrote: Hi Michal and TJ, The nice thing about Postgres extensions is that they are loaded directly into the session's process space. Therefore the overhead is minimal, almost non-existing. Not so with Oracle cartridges/extensions that are loaded in a separate process, the extproc process. The overhead per call into PYPL is on the order of tens of microseconds, which could be a lot or not, depending on how many calls you do and what kind of calls. I have tried to do a naïve SSS search with PYPL and HasSubstructMatch() on a database of 70 000 compounds (seventy thousand) and it took several minutes to complete so it was not really usable. If you need any kind of speed you need to use fingerprints to find an initial hit list, and you need to pass fingerprints in bulk to PYPL to avoid too much call overhead. Do consecutive pypl calls always share the same interpreter? On Oracle 10g and 11g, yes. I do have a disclaimer that it might not be the case if you run shared server, but in my experience even shared server ensures that each session gets its own private instance of an interpreter (its own extproc process). And, if you run a multi-threaded extproc configuration then there are no guarantees, but I don't know anyone who does that. On 12c I just don't know yet. The little I have done with it seems to indicate that it behaves like 10 and 11, so looking good so far. Cheers -- Jan On 2015-03-13 00:43, TJ O'Donnell wrote: I've implemented a suite of rdkit functions for postgres using plpython https://github.com/tjod/rdchord and the overhead is minimal since most of the heavy lifting of substructure searching is done by rdkit. I think the same would be true of oracle. --- TJ O'Donnell On Thu, Mar 12, 2015 at 4:24 PM, Michal Krompiec michal.kromp...@gmail.com wrote: Hello, has anybody tried to implement substructure searching in an Oracle database using PYPL and RDKit? Is it just a matter of writing a wrapper function for molecule.HasSubstructMatch(pattern) or is the overhead of calling pypl each time too costly timewise? Do consecutive pypl calls always share the same interpreter? Best wishes, Michal -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] FYI: google code shutting down
On 2015-03-13 01:25, Greg Landrum wrote: Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. Documentation has a tendency to go out of date whether it's in wiki format or not. What's the proposed alternative: not have any documentation online at all? Dimitri -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] FYI: google code shutting down
I vote for setting up readthedocs.org automatic documentation generation, plus some sphinx API docs. All we need to do then is to keep track of changes and create solid docstrings. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-03-13 15:43 GMT+01:00 David Hall li...@cowsandmilk.net: well, presumably the documentation not in the wiki would continue to be online. http://rdkit.org/docs/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/cppapi/index.html None of those are the wiki and tend to be more up-to-date. -David On Mar 13, 2015, at 10:39 AM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 2015-03-13 01:25, Greg Landrum wrote: Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. Documentation has a tendency to go out of date whether it's in wiki format or not. What's the proposed alternative: not have any documentation online at all? Dimitri -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] FYI: google code shutting down
well, presumably the documentation not in the wiki would continue to be online. http://rdkit.org/docs/index.html http://rdkit.org/docs/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/cppapi/index.html http://rdkit.org/docs/cppapi/index.html None of those are the wiki and tend to be more up-to-date. -David On Mar 13, 2015, at 10:39 AM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 2015-03-13 01:25, Greg Landrum wrote: Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. Documentation has a tendency to go out of date whether it's in wiki format or not. What's the proposed alternative: not have any documentation online at all? Dimitri -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] FYI: google code shutting down
You mean like the docs that are already there? The links that David provided are to docs that are built on Sphinx. Those are also available, without the API documentation from ReadTheDocs ( https://readthedocs.org/projects/rdkit/) My solution for keeping the docs as up-to-date as possible is to include doctests in them. This isn't perfect, but it's the best I've found. -greg On Fri, Mar 13, 2015 at 3:52 PM, Maciek Wójcikowski mac...@wojcikowski.pl wrote: I vote for setting up readthedocs.org automatic documentation generation, plus some sphinx API docs. All we need to do then is to keep track of changes and create solid docstrings. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-03-13 15:43 GMT+01:00 David Hall li...@cowsandmilk.net: well, presumably the documentation not in the wiki would continue to be online. http://rdkit.org/docs/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/cppapi/index.html None of those are the wiki and tend to be more up-to-date. -David On Mar 13, 2015, at 10:39 AM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 2015-03-13 01:25, Greg Landrum wrote: Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. Documentation has a tendency to go out of date whether it's in wiki format or not. What's the proposed alternative: not have any documentation online at all? Dimitri -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] FYI: google code shutting down
My bad. I knew it's Sphinx generated, although had no idea it's in sync with Github :) There is also no mention of it on github (a badge would be nice) - Pull Request coming. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-03-13 16:10 GMT+01:00 Greg Landrum greg.land...@gmail.com: You mean like the docs that are already there? The links that David provided are to docs that are built on Sphinx. Those are also available, without the API documentation from ReadTheDocs ( https://readthedocs.org/projects/rdkit/) My solution for keeping the docs as up-to-date as possible is to include doctests in them. This isn't perfect, but it's the best I've found. -greg On Fri, Mar 13, 2015 at 3:52 PM, Maciek Wójcikowski mac...@wojcikowski.pl wrote: I vote for setting up readthedocs.org automatic documentation generation, plus some sphinx API docs. All we need to do then is to keep track of changes and create solid docstrings. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-03-13 15:43 GMT+01:00 David Hall li...@cowsandmilk.net: well, presumably the documentation not in the wiki would continue to be online. http://rdkit.org/docs/index.html http://rdkit.org/docs/api/index.html http://rdkit.org/docs/cppapi/index.html None of those are the wiki and tend to be more up-to-date. -David On Mar 13, 2015, at 10:39 AM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: On 2015-03-13 01:25, Greg Landrum wrote: Github does offer the option of setting up a wiki for a project, I haven't done this for the RDKit since it doesn't seem that necessary (and it seems that the information in wikis has a tendency to rot) but if anyone has strong opinion otherwise, we can get something set up. Documentation has a tendency to go out of date whether it's in wiki format or not. What's the proposed alternative: not have any documentation online at all? Dimitri -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
