Re: [Rdkit-discuss] Descriptor3d not exposed in python

Great, now it works perfectly! Envoyé de mon iPhone Le 11 oct. 2016 à 21:34, Greg Landrum > a écrit : Ah, right, I forgot to bring it over into rdkit.Chem.Descriptors. The functions are in rdkit.Chem.rdMolDescriptors: In [4]: from

Re: [Rdkit-discuss] Descriptor3d not exposed in python

Ah, right, I forgot to bring it over into rdkit.Chem.Descriptors. The functions are in rdkit.Chem.rdMolDescriptors: In [4]: from rdkit.Chem import rdMolDescriptors In [5]: rdMolDescriptors.CalcRadiusOfGyration? Docstring: CalcRadiusOfGyration( (Mol)mol [, (int)confId=-1 [,

Re: [Rdkit-discuss] Descriptor3d not exposed in python

Maybe I made a wrong request: from rdkit import Chem from rdkit.Chem import Descriptors from rdkit import rdBase print rdBase.rdkitVersion print rdBase.boostVersion m = Chem.MolFromSmiles('c1c1C(=O)O') print dir(Descriptors) print Descriptors.CalcRadiusOfGyration(m) output is:

Re: [Rdkit-discuss] Descriptor3d not exposed in python

file == Done updating pains files -- Configuring done -- Generating done -- Build files have been written to: /tmp/rdkit-20161011-53375-95rv1i ==> make Scanning dependencies of target inchi_support Scanning dependencies of target hc maybe the python files were not updated correctly, I will

Re: [Rdkit-discuss] Descriptor3d not exposed in python

Guillaume, Are you sure that the 3D descriptors built? If you don't have the eigen library installed ("conda install -c conda-forge eigen" if you are using anaconda python), the 3D descriptor build will be automatically disabled. If eigen is not present, when you run cmake, you will see a message

[Rdkit-discuss] Jupyter: "I forgot to remember to forget you"

This is a Jupyter quirk that cost me some hours and caused me some grief. So beware! Please see the attached image and Jupyter notebook. Note the following block of code, which has been succeeding for me for days, even when "Run All Cells" is carried out: my_mols = [mol.RDK_mol for mol in mols]

[Rdkit-discuss] Descriptor3d not exposed in python

Dear all, I'm trying to use 3D descriptors in Python after compiling without issue, there is no new descriptors available in Python, is it normal? Best regards, Guillaume Envoyé de mon iPhone ** DISCLAIMER This email and

Re: [Rdkit-discuss] Rendering of aromatics

Thanks ! Jean-Marc Le 11/10/2016 à 10:57, Greg Landrum a écrit : Here's the explanation of the RDKit's aromaticity model: https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#aromaticity -greg On Tue, Oct 11, 2016 at 9:28 AM, Jean-Marc Nuzillard

Re: [Rdkit-discuss] Rendering of aromatics

Thanks, Greg. Indeed, passing "kekulize=False" to MolsToGridImage works. -P. On Tue, Oct 11, 2016 at 1:56 AM, Greg Landrum wrote: > HI Peter, > > On Tue, Oct 11, 2016 at 12:31 AM, Peter S. Shenkin > wrote: > >> >> Please see the attached image for

Re: [Rdkit-discuss] Rendering of aromatics

Here's the explanation of the RDKit's aromaticity model: https://github.com/rdkit/rdkit/blob/master/Docs/Book/RDKit_Book.rst#aromaticity -greg On Tue, Oct 11, 2016 at 9:28 AM, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > Hi, > > maybe I am a bit off topic but I would not have

Re: [Rdkit-discuss] Rendering of aromatics

Hi, maybe I am a bit off topic but I would not have said that the nitrogen containing ring is aromatic. Of course, if all bonds are forced to be aromatic when they are not necessarily, you may end up with inconsistencies. A nitrogen in an aromatic ring should bear a positive charge when it