[Rdkit-discuss] Question of substructure "neighborhood"

Dear RDKit experts, Substructure search is working well these days. RDKit is wonderful. For subsequent QM calcs., I would like to get the "next atom over" or the "one-atom-neighborhood" surrounding a substructure. The result would be something bigger than the original substructure with open

Re: [Rdkit-discuss] Question on substructure search

can get the intended result like this pat = Chem.MolFromSmarts("*=C1*C=C*1") mol = Chem.MolFromSmiles("C=C1SC=CS1") mol.HasSubstructMatch(pat) Pat On Tue, Jun 13, 2023 at 4:49 PM Storer, Joey (J) via Rdkit-discuss mailto:rdkit-discuss@lists.sourceforge.net>> wrote

[Rdkit-discuss] Question on substructure search

Hi RDKit masters, rdkit.__version__ = 2023.03.1 I am trying to match structures with a double bond in a 5-membered ring. [cid:image001.png@01D99E14.494E8F00] Then checking if this works in the sulfur case: [cid:image002.png@01D99E14.494E8F00] [cid:image003.png@01D99E14.494E8F00] Thanks for

[Rdkit-discuss] Color bonds with value

Hi all, I would like to color all bonds with a value. Does anyone have a snippet for this? Many thanks! Joey Storer Dow Inc. Core R General Business ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

[Rdkit-discuss] Atom sequence in 3D coordinates (H's at the end)

Dear All, I have experienced a few consistency problems in 3D coordinate output with H's not always at the end of the coordinate list. RDKit mostly does this by default except in a few cases every few thousand and even with simple organics. How can I check/verify/enforce "H's at the end" on

[Rdkit-discuss] XYZ to mol ???

Dear all, For molecular modeling workflows and interoperability with QM/MM etc., Can RDKit gain a Chem.XyzToMol(xyz) functionality? Thanks for considering this. Joey Storer Dow, Inc. General Business ___ Rdkit-discuss mailing list

[Rdkit-discuss] Install RDKit (Docker, rapids, rdkit=2020.03.2) ?/

Hi, I am trying to run the following Docker file and the container fails to install rdkit. Other incarnations install either the 2019 version or even the 2017 version. # FROM rapidsai/rapidsai:0.12-cuda10.1-runtime-ubuntu18.04 ARG ENVNAME=rapids ENV ENVNAME=$ENVNAME RUN source activate