Re: [Rdkit-discuss] CIPLabeler ranks

; No, the new code does not calculate those ranks. > There may be alternatives though; what are you interested in using the CIP > ranks for? > > -greg > > > On Thu, Dec 15, 2022 at 3:45 PM Juuso Lehtivarjo < > juuso.lehtiva...@gmail.com> wrote: > >> Hi,

[Rdkit-discuss] CIPLabeler ranks

Hi, According to my tests with the new CIPLabeler, it seems that it does not store the CIP ranking to any property, such as the _CIPRank prop that was filled in the legacy AssignStereochemisty, am I correct? Is it possible to retrieve this information somehow? Cheers, Juuso

Re: [Rdkit-discuss] double bond in a ring

Hi Greg and Shani, Please correct me if I understood something wrong, but isn't Shani trying to create 3D coordinates in that example code? To me this looks like the old issue with respecting double bond stereochemistry in embedding, which should have been fixed with #4346? Oddly enough, the

Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems

Hi, encountered this too. At least for me the problem was self-built cmake that did not automatically support https/ssl, which caused the empty downloads. The solution was to re-build cmake using the following instructions: https://github.com/ruslo/hunter/issues/328#issuecomment-198672048

Re: [Rdkit-discuss] Highlight atom according to property value when drawing molecule

Hi Changge, for guidelines, check out this blog post: http://rdkit.blogspot.fi/2015/02/new-drawing-code.html Also, you can set the highlight radius with "highlightAtomRadii" parameter. Cheers, Juuso On Thu, May 17, 2018 at 1:53 PM, Changge Ji wrote: > Dear Rdkit Users, >

Re: [Rdkit-discuss] Assigning formal charges

dentify all neutral N > atoms with a valence of 4 and add a positive charge to them > > Here's an example gist showing what I mean: > https://gist.github.com/greglandrum/7f546d1e35c2df537c68a64d887793b8 > > I hope this helps, > -greg > > > > On Wed, Aug 9, 2017 at 11

[Rdkit-discuss] Assigning formal charges

Hi All, and sorry if this has been previously answered. Found lots of threads close to this subject but not exactly what I'm looking for. I often encounter mol-files that have protonated atom species such as NH3+, with all protons explicitly present, but without charge lines. This leads to

Re: [Rdkit-discuss] looking for feedback on new python API documentation format

Hi Greg, Here's my user case: usually I want to find out the details of a certain class/function I already know of, but I may not have a clue to which module that class/function belongs to. This is where the alphabetical index of epydoc is often quite handy. Of course a proper search within the

[Rdkit-discuss] Operations dependent on Kekulization

Dear RDKit users, Interpreting the default sanitization order (in http://www.rdkit.org/docs/RDKit_Book.html), I assume that SetAromaticity must be preceded with Kekulization (otherwise, why to Kekulize at all if atoms and bonds are to be marked as aromatic anyway). However, I wonder if any of the

[Rdkit-discuss] Substructure by atom indices

Hi All, Is there a python function (or any simple way whatsoever) to create a substructure mol object from another one based on the given atom indices? In C++ this could apparently be done with getMolFragsWithQuery, but that does not seem to be much used in python wrappers... Best, Juuso

Re: [Rdkit-discuss] Map atomindex between mol2D and canonical smile

Dear Guillaume, if you are dealing with 1H NMR data, this might be problematic, as there is no canonicalization for hydrogens in SMILES (or InChi, for that matter). So e.g. for a CH2 with differing NMR shifts on the protons the stereochemical assignments are inevitably lost. If this is not a