Re: [Rdkit-discuss] Molecules not rendere in Dataframe

I posted basically the same question on Friday. I thought it was a Google Colab problem, but apparently it is a more general problem. On 4 Nov 2019, at 19.47, Markus Heller mailto:mhel...@admarebio.com>> wrote: Hi, In a Jupyter notebook, the following code does not show renderings of the mole

Re: [Rdkit-discuss] Molecules not rendere in Dataframe

Jan, I think this is the same issue you ran into in your example colab? On Mon, Nov 4, 2019 at 2:03 PM Markus Heller wrote: > Hi, > > > > In a Jupyter notebook, the following code does not show renderings of the > molecules in a Pandas dataframe: > > > > > > from rdkit import Chem > > from rdki

[Rdkit-discuss] Compiling Java Wrappers

Dear all, I wanted to use the RDKit Java wrappers to just learn and play around with RDKit in Java (and maybe one day be able to write a KNIME node myself). Unfortunately I am stuck already at the building process. Unfortunately, I am neither familiar with boost nor cmake, therefore I am sorry if

[Rdkit-discuss] Molecules not rendere in Dataframe

Hi, In a Jupyter notebook, the following code does not show renderings of the molecules in a Pandas dataframe: from rdkit import Chem from rdkit.Chem import PandasTools from rdkit.Chem.Draw import MolsToGridImage from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import rdDepictor rdDe

Re: [Rdkit-discuss] SMARTS Query Normalization?

We are currently using Mol files, they’re large especially when urlencoded, we would prefer smiles and smarts for queries, but we would need to be able to normalize them. As to sketchers Marvin JS seems to do a pretty good job with SMARTS. Webster From: Greg Landrum Sent: Friday, November 01,

Re: [Rdkit-discuss] AttributeError in loading Crippen module

Dear Goutam, Probably you’re getting this error because you did not import the module correctly. If you use "from rdkit.Chem import Crippen” and replace "rdkit.Chem.Crippen.MolLogP(mol)” with "Crippen.MolLogP(mol)”, it should work properly. Best regards, Lorenzo Fabbri, M.Sc.

[Rdkit-discuss] AttributeError in loading Crippen module

Dear Members, I want to calculate molar refractivity and logP values by using Crippen module of rdKit. https://www.rdkit.org/docs/source/rdkit.Chem.Crippen.html Could any one please help me how do I calculate the same. When I used the command, ligand_pdb = "test.pdb" mol=Chem.MolFromPDBFile(liga