[Rdkit-discuss] 2D coord for hydrogens

or the hydrogens are poor on the 5-membered ring, and the two hydrogens on the NH2 are superimposed. (In practise I'm starting from a 3D SDF and trying to generate 2D coords for it, hence the need for CoordGen). What am I doing wrong? Regards, Mark -- Mark Mackey Chief Scientific Offic

Re: [Rdkit-discuss] 2D coord for hydrogens

Hi all, After further offline discussion with Paolo, it turns out that the behaviour I was seeing was due to a bug, which has now been fixed by Paolo and accepted. Thanks Paolo for sorting this out! Regards, Mark From: Paolo Tosco Sent: 27 August 2020 23:08 To: Mark Mackey Cc: rdkit-discuss

Re: [Rdkit-discuss] GPU Implementation of shape-based 3D overlap on rdkit?

ldn’t be that much of a net win. As a result, take all of the above with a grain of salt 😊. Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 157, Issue 2

he code looked clean enough but it was slow. Unfortunately from the RDKit point of view it's LGPL so can't be used as the basis of an RDKit shape algorithm. Regards, Mark From: Chris Swain Sent: 04 November 2020 15:56 To: rdkit-discuss@lists.sourceforge.net; Mark Mackey Subject: Re:

Re: [Rdkit-discuss] canonicalization of two aromatic molecules returning two different forms (kekule and aromatic)

Hi Paolo, Hmmm, I think this is displaying a bug (or at the very least unexpected behaviour) in the aromaticity code. The issue isn’t the aromaticity of the imidazole/dihydroimidazole, but the aromaticity of the pyridyl. Alexis’ second molecule is identical to the first except that one bond in

Re: [Rdkit-discuss] explicit H atoms

I believe it's not possible to represent the chirality of the attached molecule's ring fusion carbons without using an explicit H. Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

, b2) in B, break all bonds in B except b1 and b2. Keep the fragment containing b1 only if it also contains b2. Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223 858890mobile: +44 (0

[Rdkit-discuss] Reaction SMARTS ring properties

complex. Googling has shown that the problem is that the ring information is not automatically calculated for the SMARTS molecules, but I'm failing to work out what I need to call RDKit::MolOps::findSSSR on and when. All pointers appreciated. Regards, Mark Dr Mark Mackey Chief Scientific Off

Re: [Rdkit-discuss] Reaction SMARTS ring properties

Hi Greg, Argh, I’d missed that we hadn’t done the ring calculation on the reagents, and had been led astray by Googling the exception message. Adding the ring calculation does the trick - thanks very much for the help. Regards, Mark Dr Mark Mackey Chief Scientific Officer Cresset From

[Rdkit-discuss] Problem with depicting reaction SMARTS

quivalent "[c,nH1:1]>>[o:1]"): Exception in ChemicalReactionsCalculation::toSvg on "[c,n&H1:1]>>[o:1]" : bad query type1 This happens for pretty much any combination of "," and "&" operators inside the square brackets. Any ideas? Regar

Re: [Rdkit-discuss] Problem with depicting reaction SMARTS

Thanks Paolo – we’ll give that a try. Regards, Mark Dr Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK Tel: +44 (0)1223 858890 Mobile: +44 (0)7595099165 Email: m...@cresset-group.com<mailto:m...@cres