Re: [Rdkit-discuss] MolFromXYZ?

On 1/17/2015 8:57 AM, Naeem Attari wrote: Hi, Is it possible to generate rdkit mol object only from xyz coordinates? It would be useful to connect rdkit with other tools. If you can't transform your xyz coordinates into pdb ATOM line, then probably not. Dima

Re: [Rdkit-discuss] New RDKit drawing code

On 2/14/2015 4:23 AM, Markus Sitzmann wrote: Hi Greg and all the others involved, That looks really nice! +1 ...And don't give any code to Noel anymore, it all ends up in JavaScript :-) (who would have thought 10 years ago that would make any sense). Still doesn't, really. The problem is

Re: [Rdkit-discuss] Memory management during conformer generation

On 6/26/2015 9:48 AM, az wrote: Thanks Jean-Paul You're right that I eat up a lot of memory with large files but I think its not the whole story. If it were, my memory should come back each time a new file is being read (jobs=[]), no ? No. It's a feature of garbage collection: your memory

Re: [Rdkit-discuss] Memory management during conformer generation

On 6/27/2015 5:45 AM, Greg Landrum wrote: ... That's assuming that the futures code (which I don't know) isn't doing anything odd behind the scenes to hold onto references. Or every mol in supplier holds a pointer to c++ dll that python vm doesn't quite know how to garbage-collect, which keeps

Re: [Rdkit-discuss] highlightColor in Draw.MolsToGridImage()

On 7/17/2016 5:29 AM, Greg Landrum wrote: > > > On Sat, Jul 16, 2016 at 9:37 PM, DmitriR > wrote: > (2) For the SVG rendering, is there perhaps a way to change the with > (weight) of the stroke? > For smaller images, the default bond width

Re: [Rdkit-discuss] highlightColor in Draw.MolsToGridImage()

On 7/17/2016 8:17 AM, Brian Kelley wrote: > Svg can actually be styled with css to change properties. It might > be worthwhile to start adding proper ids to our svg elements for more > flexibility. As long as my code for generating CSS can figure out the ids from Mol's atoms and bonds... Dima

Re: [Rdkit-discuss] Fwd: 2D drawing with atoms labeled by index

OK, my turn: that went out too soon. It seems to me that jypiter, ipython, or whatever, has no idea how render MIME type image/svg+xml. It can display an "SVG" object, but the bit that turned image/svg+xml into "SVG" does not understand XML namespaces (that's been around since at least 2009).

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

Re: [Rdkit-discuss] Are atom and bond indexes deterministic?

oveH/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] Dividing inputstream over threads

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/listi

Re: [Rdkit-discuss] Dividing inputstream over threads

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] 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. --

Re: [Rdkit-discuss] GETAWAY descriptor returning non-numeric values

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] PDB file that can be read in Gromacs

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] 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