Thank you, Max! It worked nicely and looks like each array is a line in a nxn matrix.
Thanks again -- Henrique C. S. Junior ________________________________ From: Max Pinheiro Jr <[email protected]> Sent: Sunday, September 20, 2020 10:41 To: Henrique Castro <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [Rdkit-discuss] Example of the new Coulomb Matrix Feature in RDKit Dear Henrique, You can try something like this: import rdkit from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem.rdMolDescriptors import CalcCoulombMat smiles = 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C' caffeine = Chem.MolFromSmiles(smiles, sanitize=True) caffeine = Chem.AddHs(caffeine) AllChem.EmbedMolecule(caffeine) AllChem.UFFOptimizeMolecule(caffeine) CM = CalcCoulombMat(caffeine) list(CM[0]) The CM object contains a list of Coulomb matrices calculated for the molecule that I think it is generated by randomizing the arrangement of atoms, but I am not totally sure. It seems that you need first to optimize the molecule to get its 3D conformation, and then you can pass this object as input to the CalcCoulombMat function. One way to access the values of each Coulomb Matrix is by transforming it into a list or a NumPy array. I hope this can help you. Max Pinheiro Jr --------------------------------------------- Postdoctoral researcher Aix-Marseille Université, France Institut de Chimie Radicalaire Em dom., 20 de set. de 2020 às 14:58, Henrique Castro <[email protected]<mailto:[email protected]>> escreveu: Dear colleagues, how are you? I have almost zero experience with RDKit, so forgive me for such a basic request. Could anyone provide me an example of the new Coulomb Matrix generator in RDKit? I intend to iterate through my organometallic molecules stored in a pandas DataFrame. Thank you in advance -- Henrique C. S. Junior _______________________________________________ Rdkit-discuss mailing list [email protected]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=02%7C01%7C%7C7e948d47163446be4cdd08d85d6ade1a%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637362060851793028&sdata=0L%2B6VVi80RoyjdKc%2FZ%2Fgy3rsCT%2BfrlFonRvsvygUXG4%3D&reserved=0>
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