Re: [Rdkit-discuss] RDKit "cannot create mol from SMILE" error
This all explains a lot. Thanks very much, Brian and Peter! On Wed, Jan 18, 2017 at 6:05 PM, Peter S. Shenkin <shen...@gmail.com> wrote: > In addition to Brian's observation, there is also a "C1" early in the > SMILES, but no corresponding X1 to make a ring bond before or after it. > > It appears that you might be reading the second half of a SMILES for some > reason. My guess is that the (C=C1) is associated with a preceding atom > that was not read. > > -P > > On Wed, Jan 18, 2017 at 6:32 PM, Brian Kelley <fustiga...@gmail.com> > wrote: > >> That doesn't look like a valid SMILES to me, I don't think a think a >> smiles string can start with a parenthesis ( branch ). >> >> >> Brian Kelley >> >> On Jan 18, 2017, at 6:18 PM, Larson Danes <lgda...@gmail.com> wrote: >> >> Hi all, >> >> I'm using the following query in postgresql (with the rdkit extension >> installed): >> >> "select casrn from mols where m @> CAST(? AS mol)" >> >> >> This returns "ERROR: could not create molecule from SMILES '...' " on >> occasion. One such SMILE that causes this error regularly is >> '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific >> error message anywhere. I've looked and haven't had luck finding any. >> >> Any information about this error message is much appreciated. >> >> >> Thanks, >> >> >> Larson >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> >> -- >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> > -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit "cannot create mol from SMILE" error
Hi all, I'm using the following query in postgresql (with the rdkit extension installed): "select casrn from mols where m @> CAST(? AS mol)" This returns "ERROR: could not create molecule from SMILES '...' " on occasion. One such SMILE that causes this error regularly is '(C=C1)[N+]([O-])=O'. I'm curious if there's documentation on this specific error message anywhere. I've looked and haven't had luck finding any. Any information about this error message is much appreciated. Thanks, Larson -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] rdkit-postgresql cartridge not included in repository install?
Hi all, I was able to get the rdkit-postgresql cartridge working in a conda virtual env after installing everything (rdkit, postgresql, rdkit-postgresql cartridge) on a linux VM after getting help in this <https://sourceforge.net/p/rdkit/mailman/message/35428322/> thread. The gist of the problem I'm trying to solve now is this: get rdkit running as a server via the postgresql cartridge and call it from a web application. To do this, I assume I need to use rdkit and the postgresql cartridge outside of the conda virtual environment. After installing rdkit from repository as per the documentation, I proceeded to install postgresql from apt. Then, I created my database, started it, and attempted to create the rdkit extension. I was then greeted with a familiar error: "No such file 'rdkit.control'". My first attempt at a solution was to install the rdkit-postgresql cartridge from conda. I did so, and moved the relevant (all) files into the directory in which postgresql was looking for 'rdkit.control' and 'rdkit--3.4.sql' and so on. This was met with failure as there was one library that I was not able to locate and move (in the conda install, github, or with apt-file) which was something along the lines of "libAvalon.so.1". My question, then, is what is the process for getting the rdkit-postgresql cartridge up and running outside of a conda virtual environment (in a linux environment)? And, probably more to the point, is this the best option for the webserver use case? Any help here is greatly appreciated. Thanks all, Larson Danes -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
