Re: [Rdkit-discuss] install on macosx with Python 3.8

2021-06-24 Thread Francois Berenger
On 25/06/2021 02:57, Michal Krompiec wrote: Hello, Is it possible to install RDKit on MacOSX in a Python 3.8 environment? There is no conda binary for 3.8, so I tried homebrew. But the following gives me an error message (brew doesn't like the --with-python3 argument): brew install rdkit

[Rdkit-discuss] How can I remove all angle potentials from a force field before EM?

2021-06-24 Thread Neale, Christopher Andrew via Rdkit-discuss
Hello, I am trying to embed one chemical on another and have them fit as well as possible given the common substructure. I am (sometimes) having trouble with chiral centers. It’s automated, so I don’t want to hand-define things. The position restraints we introduce via ff.AddDistanceConstraint

Re: [Rdkit-discuss] install on macosx with Python 3.8

2021-06-24 Thread Maciek Wójcikowski
Hi Michał, Conda-forge is your solution - you probably checked legacy rdkit channel. Best, Maciek czw., 24 cze 2021, 19:59 użytkownik Michal Krompiec < michal.kromp...@gmail.com> napisał: > Hello, > Is it possible to install RDKit on MacOSX in a Python 3.8 environment? > There is no conda

Re: [Rdkit-discuss] install on macosx with Python 3.8

2021-06-24 Thread Peter St. John
There should be a conda binary for mac / python 3.8 with conda-forge, just follow the first command listed here: https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda On Thu, Jun 24, 2021 at 11:59 AM Michal Krompiec wrote: > Hello, > Is it possible to install RDKit on MacOSX

[Rdkit-discuss] install on macosx with Python 3.8

2021-06-24 Thread Michal Krompiec
Hello, Is it possible to install RDKit on MacOSX in a Python 3.8 environment? There is no conda binary for 3.8, so I tried homebrew. But the following gives me an error message (brew doesn't like the --with-python3 argument): brew install rdkit --with-python3 --without-numpy So I did just "brew

Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

2021-06-24 Thread Paolo Tosco
Hi JP, the problem is caused by the reaction SMARTS that standardizes pyridine *N*-oxides being not very specific and also hitting your molecule, which is not actually an *N*-oxide but rather a *N*-hydroxypyridinium ion. I will submit a PR to fix the reaction pattern; in the meantime you can fix

Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

2021-06-24 Thread JP Ebejer
Apologies I took my sweet time to reply, I went down the standardization rabbit-hole and went through most of the material (thanks Matthew and Francois, but also links from other notebooks). The recording of the OpenScience session is excellent and crystal clear as usual Greg. I enjoyed that. I