Re: [Rdkit-discuss] para-stereochemistry

2021-05-26 Thread Jean-Marc Nuzillard
Dear Paolo, According to https://goldbook.iupac.org/terms/view/P04921 your interpretation is certainly the correct one. I still have to find how this r/s assignment is determined. Many thanks again, Jean-Marc Le 26/05/2021 à 22:40, Paolo Tosco a écrit : Dear Jean-Marc, I believe it

Re: [Rdkit-discuss] para-stereochemistry

2021-05-26 Thread Paolo Tosco
Dear Jean-Marc, I believe it indicates what the IUPAC Gold Book refers to as pseudoasymmetry. Let’s see if others agree with my interpretation. Cheers, P. > On 26 May 2021, at 22:28, Jean-Marc Nuzillard > wrote: > > I believed I sent a message with the same title a few minutes ago, but >

[Rdkit-discuss] para-stereochemistry

2021-05-26 Thread Jean-Marc Nuzillard
I believed I sent a message with the same title a few minutes ago, but apparently something went wrong. Reading the RDKit book about function FindMolChiralCenters(), I saw that it provides a better handling of para-stereochemisry. This concept is not familiar to me. Google did not help and sent

[Rdkit-discuss] para-stereochemistry

2021-05-26 Thread Jean-Marc Nuzillard
Dear all, the RDKit Book mentions, about function FindPotentialStereo(), the improved handling of "para-stereochemistry". Google sends me back to the the RDKit book when I search for this keyword. So,

Re: [Rdkit-discuss] Create an asymmetric carbon.

2021-05-26 Thread Jean-Marc Nuzillard
Hi Paolo, the SetChiralTag() function is exactly what I missed. Many thanks for your help, Best regards, Jean-Marc Le 26/05/2021 à 18:21, Paolo Tosco a écrit : Hi Jean-Marc, You can use Chem.Atom.SetChiralTag(): from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole

Re: [Rdkit-discuss] Create an asymmetric carbon.

2021-05-26 Thread Paolo Tosco
Hi Jean-Marc, You can use Chem.Atom.SetChiralTag(): from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole IPythonConsole.drawOptions.addAtomIndices = True IPythonConsole.ipython_useSVG=True m = Chem.AddHs(Chem.MolFromSmiles('CCO')) m [image: image.png] a = m.GetAtomWithIdx(6)

[Rdkit-discuss] Create an asymmetric carbon.

2021-05-26 Thread Jean-Marc Nuzillard
Dear all, starting from ethanol with added Hs: >>> m = Chem.AddHs(Chem.MolFromSmiles('CCO')) the C atom of the CH2  group is indexed by "1" and is bound to H atoms indexed "6" and "7". Replacing the H atom indexed "6" by a deuterium atom >>> a = m.GetAtomWithIdx(6) >>> a.SetIsotope(2)

[Rdkit-discuss] rdkit and pip

2021-05-26 Thread Marco Stenta
Dear Colleagues, I recently came across this https://pypi.org/project/rdkit-pypi/ is pip going to be supported officially by the dev community? any plan? getting out of the conda dependency might be beneficial to get slightly slimmer docker images. Thanks cheers, m