Re: [Rdkit-discuss] missing MolFromSmiles error output in Jupyter
On 10/16/2019 1:50 PM, Andrew Dalke wrote: ... I would expect to see a "SyntaxError: invalid character in identifier" as Python doesn't recognize left-handed or right-handed double quotes in a way that doesn't cause an error. Instead, the MolFromSmiles() appears to be evaluated. Is that a c++ method (hint, hint)? Dima ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDB file that can be read in Gromacs
On Thu, 14 Mar 2019 13:19:00 -0600 Phuong Chau wrote: > Could anyone tell me any possible solution to solve this problem? 1. Go to ligand expo search @ http://ligand-expo.rcsb.org/ld-search.html 2. Search for UNL and consider the topology of an "unknown ligand". The solution is to fiter your substances to ones that are actually known. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Dividing inputstream over threads
On Mon, 21 Jan 2019 09:43:48 +0100 Markus Sitzmann wrote: > There is no need for objects with SQLAlchemy, SQLAlchemy's Core and > its expression language is pretty excellent without objects ... I spent weeks last year rewriting code that I myself wrote back when I believed that... When I wrote it originally, as I was getting deeper in, SQLAlchemy changed my mind. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Dividing inputstream over threads
On Sun, 20 Jan 2019 12:03:50 +0100 Shojiro Shibayama wrote: > ... I guess SQLalchemy > in python might be good, but I'm not sure. Hope that you'll find out > a good library of SQL OR mapper for python. SQLalchemy creates a fairly specific ecosystem that you have to buy into for it to make sense. When you don't have objects, only a table of properties, OR mapper is just bloat. With parallel processing your bottleneck is going to be database inserts. One option is write out CSV file(s) from each thread/job, concatenate them in the final node, and then bulk-import into the database: typically CSV (or other such format) bulk import is orders of magnitude faster than inserting one SQL statement at a time. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] InChI to Mol to InChi
On Mon, 17 Dec 2018 14:23:32 +0100 JEAN-MARC NUZILLARD wrote: ... > returns DIFFERENT. > > Removing the EmbedMolecule step returns EQUAL. > > How could I change that? You could try generating multiple conformers instead and checking if one of them returns EQUAL. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] GETAWAY descriptor returning non-numeric values
On Fri, 30 Nov 2018 05:32:13 +0100 Greg Landrum wrote: > I don’t think you should be getting NaNs, and that’s worth looking into, > but they are technically numeric values : that’s the double value younger > when you divide by zero. NaNs are great because you can tell "invalid result" from 0, or some other number that's perfectly valid per se, just out of bounds in your particular corner case. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
On Wed, 3 Oct 2018 06:21:06 +0200 Greg Landrum wrote: > The atom ordering in the RDKit molecule created from a SMILES or Mol block > will always be the same and will corresponds to the ordering of the atoms > in the input ... provided your molecule has no protons and/or you don't removeH/addH in the process. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PDBBlock file
On 7/5/2018 1:39 PM, Paolo Tosco wrote: As the PDB format includes no stereochemistry, no coordinates are needed, and by default they are zero, as the molecule does not have a conformation yet. Hmm. One could argue that PDB format *is* 3D coordinates, so a block with all zeroes is quite pointless. And of course counter-intuitive. Dima -- 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
