Re: [Rdkit-discuss] stereochemistry of S with degree 3

On Mon, 8 Feb 2016 16:05:46 +0100 Andrew Dalke wrote: > Hi! > > Could someone explain to this non-chemist what the chirality means > in the following? > > CN[S@@](=O)C1=CC=CC=C1 > > It comes from PubChem id 12194260 at >

[Rdkit-discuss] fmcs/python bug?

Hi, I have attached some hackish code making use of FMCS which shows some strange behaviour in the Python implementation of FMCS. When I run with python mcs.py c++ 60 I get the expected result (16 atoms in the match) regardless of the timeout I set (last argument; I guess 1s is the smallest

[Rdkit-discuss] mol files and justification of the atom symbol in the atom block

Hi, I just had a problem with the atom symbols in the atom block of a particular MOL/SDF file. Looks like RDKit expects those to be left justified within their 3 character field while I had a file where they were right justified. A look into CTFile Formats from Oct 2003 does not suggest that

[Rdkit-discuss] where are the sanitizing flags?

Hi, I am using the current development branch with Python and was wondering what namespace should be used to access the sanitizing flags. E.g. I have rdkit.Chem.SANITIZE_ALL rdkit.Chem.SanitizeFlags.SANITIZE_ALL which both point to rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL A

Re: [Rdkit-discuss] official Tripos MOL2 file format PDF document

On Tue, 11 Apr 2017 08:35:53 -0500 Francois BERENGER wrote: > Hello, > > Not directly related to rdkit, but if someone that have > the original PDF of this file format could place it > online permanently, that would be wonderful. What does "permanent" mean

Re: [Rdkit-discuss] origin of GetO3A?

On Thu, 25 May 2017 10:25:36 +0100 Paolo Tosco wrote: > Dear Hannes, > > the Open3DALIGN algorithm is described here: > > /Journal of Computer-Aided Molecular Design/ *2011*, /25/, 777-783 > doi > > Cheers, > p. Many thanks.

[Rdkit-discuss] origin of GetO3A?

Hi, I am just trying to figure out how the Open3DALIGN works (rdkit.Chem.rdMolAlign.GetO3A()). The original code seems to suggest that it uses M. Petitjean's SDM/RMS algorithm. Is that right? Many thanks, Hannes. --

Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

Without your more detailled explanation of what that term specifically means I was wondering too at first. But then I did the most obvious thing: search for it online and found https://scholar.google.com/scholar?q=%22in+silico+synthesis%22=en_sdt=0_vis=1=scholart . Looks to me other people use

[Rdkit-discuss] ReplaceSubstructs dependent on order in pattern?

Hi, in the following I want to replace a group of atoms with a label. It seems, however, that the atom order in the query pattern determines the product molecule. In the first case I get the label atom connected to ethyl while in the second I get two fragments. mol =