[Rdkit-discuss] [MSc] [PhD] [Post-Doc] Computational Chemistry Research Group.

Hello, Are you passionate about computational chemistry, eager to explore chemical space, thrilled by deep learning, and fascinated by aromatic molecules? If so, we have the perfect opportunity for you! The Poranne Research Group, at the Technion - Israel Institute of Technology, is currently rec

[Rdkit-discuss] mol to smiles code

Hello all, I hope you all are doing well. I am struggling trying to find the code where all the smile to mol and mol to smile translation happens. Can someone point me in the right direction? kind regards, eduardo ___ Rdkit-discuss mailing list Rdkit-d

[Rdkit-discuss] Varying ring size substructure match.

Hello, I hope you are all doing well. I'm looking for a smart pattern that can match rings of different sizes at the same time. The intention is to match something like naphthalene and azulene with the same pattern. Is that possible? Best, Eduardo ___ R

[Rdkit-discuss] [bug] ResonanceMolSupplier not working as expected

Dear all, I hope you all are doing well. I've been trying to enumerate all Kekule structures, and apparently it should be done with ResonanceMolSupplier. In this email apparently, this snippet works: from rdkit import Chem > from rdki

[Rdkit-discuss] Multiprocessing data loading

Hi everyone, I have a question regarding parallel data loading with RDKit, Regarding Chem.MultithreadedSDMolSupplier *By** default a single reader thread is used to extract records from the > file and a single writer thread is used to process them. Note that due to > multithreading the output ma

[Rdkit-discuss] RDKit in Google Colab

Hello, I have used RDKit in a Google collab before (a few months ago). However, when I tried today, I got the following error message: ImportError: /usr/local/lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/local/lib/python3.7/site-packages/rdkit/Chem/../../../../libRDKit

[Rdkit-discuss] molecular propierties from MolFile, multiprocessing and SDMolSupplier

Hi all, I hope you are doing well. I have some questions: 1. Is there any way to read and write molecular properties in MolBlocks? mol = Chem.MolFromSmiles("C") mol.SetProp("Name", "methane") mol.SetProp("Formula", "CH4") Chem.MolToMolBlock(mol) Expected behavior: ``` RDKit 2D

[Rdkit-discuss] SMARTS pattern

Greetings!! I hope this email finds you well. I need a SMARTS pattern that matches this molecule fragment [image: image.png] The first pattern I used was: [*;R2]~1~[*;R2]~[*;R2]~[*;R2]~[*;R2]~[*;R2]~1 However, it also matches this fragment. This is not the expected behavior but it agrees with th

[Rdkit-discuss] sanitize mol fail

Hi all, I'm trying to read this mol2 file but rdkit fails. I've read the molecule with sanitize=False, then SanitizeMol, and it raises this exception: ```AtomKekulizeException: non-ring atom 0 marked aromatic ``` Do you have any how to solve this?? Kind regards, Eduardo # created with PyMOL 2.3

[Rdkit-discuss] Can't load mol2 file.

Hi RDKiters, Hope you are well. I'm having trouble loading these molecules. Do you know any walk around?? Bests, Eduardo In: rdkit.__version__ Out: '2020.09.5' In: Chem.MolFromMOL2File('file.mol2') Out: None In:Chem.MolFromPDBBlock(pdb_block) Out: (Molecule successfully loaded but missing conne

[Rdkit-discuss] Isotope labeling

Hi RDKit community. How do I could remove isotope labels? Is there a way so I could avoid converting to and from smarts?? Best, Eduardo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-d

[Rdkit-discuss] About chirality in mol file

Hi, I'm reading a sdf file with racemates using RDKit and when I try to FindMolChiralCenter all the chiral center are listed the same. Any idea? PD: when I load the sdf with datawarrior all the chiral information are load property. ___ Rdkit-discuss maili

[Rdkit-discuss] PandasTools

Hi RDKit users: I have a couple of moleculas that must be load using the sanitize=False flag. Then do a partial sanitization for make some calculations. When I use PandaTools.LoadSDF the molecules with the sanitize trouble don't load so I copy PandaTools to my working folder and modified it chang

[Rdkit-discuss] MolSanitizerError

Hi I'm working in a script for processing autodock vina screening output. I got problem with protonated molecules as the molecule attached. Any idea how I can load molecule with a given protonated state. Attached is the RDKit error and the sdf file. Best s, Eduardo LIG119-outrdkit.rar Description

[Rdkit-discuss] RMSD between molecules

Hi I'm trying to calculate the RMSD between conformers of the same molecules stores in separate mol file. I figured out a way: m1= Chem.FromMolFile('1.mol') m2= Chem.FromMolFile('2.mol') m1.AddConformer(M2.GetConformer(-1),1) AllChem.GetConformerRMS(m1,0,1) Is there another way?? ___

[Rdkit-discuss] Documentation as pdf

Please is any documentation for the 2020.3 available as a PDF or any format that work offline?? ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss