Re: [Rdkit-discuss] atomic contributions to molecular polarizability

Hi Jim, On Thu, Jan 10, 2019 at 11:59 PM James T. Metz via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > > I would like to calculate and be able to visualize the atomic > contributions > to the total molecular polarizability of small organic molecules. > Apparently > there is

Re: [Rdkit-discuss] atomic contributions to molecular polarizability

Carlos,     Thank you for your suggestion.  However, rather than wrestle with the technical details of obtaining polarizabilities from new quantum mechanics schemes, I am simply interested in extracting the atomic contributions that are apparently already available for adescriptor called apol

[Rdkit-discuss] atomic contributions to molecular polarizability

RDkit Discussion Group,     I would like to calculate and be able to visualize the atomic contributionsto the total molecular polarizability of small organic molecules.  Apparentlythere is a molecular descriptor, apol, that is the sum total from the atomiccontributions to polarizability

Re: [Rdkit-discuss] InChI -> Mol(2D) -> InChI

Hi Jean-Marc, The problem here is being caused by a bug/deficiency in the RDKit's 2D coordinate generation algorithm. The molecule described by the input InChI.has a trans double bond in the macrocycle and Compute2DCoords() isn't handling that correctly. Here are the coordinates you get for that

[Rdkit-discuss] InChI -> Mol(2D) -> InChI

Dear all, I wrote some time ago about adding 3D coordinates to atoms in a molecule that was created from an InChI string. The conversion of the molecule to InChI dis not produce the initial InChI due to the presence of an intracyclic double bond. I face them same problem with the generation