Re: [Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

2017-06-20 Thread Ling Chan
Hello Janusz, Perhaps you have answered your own question? You can start with Smiles like "[H][SH3](C)[SH5]". Otherwise you could use the SetNumExplicitHs() function. For example, m = Chem.MolFromSmiles('CS') m.GetAtomWithIdx(1).SetNumExplicitHs(5) AllChem.SanitizeMol(m) print

[Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Paul Czodrowski
Dear RDKitters, When trying to re-run Greg's wonderful blog entry about the py3Dmol integration (https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-py3dmol-to-browse.html ), I'm getting a different behavior (check the attachment with a screenshot and the jupyter notebook). Any help would

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Paul Czodrowski
Dear Malitha, Dear RDKitters, thanks a lot for your investigations! Indeed, this issue seems somehow browser-related; please check the attachment which shows the output in a different browser (Firefox@openSUSE vs. IE11@Win7 from my previous mail). I’m now able to find a button-like widget but

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Malitha Kabir
Dear Paul, >From your response, I think your ipywidgets is working fine. Now, you are facing trouble with py3Dmol. py3Dmol basically generates JavaScript codes (3Dmol.js) and IPython injects those in web browser. So, will you kindly share what error printed in your browser console? Off topic:

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-20 Thread Greg Landrum
did you build boost serialize? On Mon, Jun 19, 2017 at 12:03 PM, JP wrote: > Hi Greg ! > > Unfortunately that didn't help (I delete everything in my build directory, > then): > > cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/ >

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Axel Pahl
Hi Paul, I just tried the example Notebook that you provided and it runs just as in Greg's blog post, i.e. with the interactive slider (see attached screenshot). This is the configuration I used (in Anaconda): python 3.5.3 rdkit 2017.03.2 notebook 5.0.0

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Paul Czodrowski
Dear Axel, thanks a lot for this very helpful information! The only difference I could figure out: Python 2.7.13 instead of Python 3.5.3 @RDKitters: Can this really cause such a different behavior? Cheers, Paul P.S.: I'm aware of http://www.python3statement.org/ ;) Von: Axel Pahl

Re: [Rdkit-discuss] ipywidgets & py3Dmol

2017-06-20 Thread Malitha Kabir
Dear Paul, Kindly consider a few pieces of information provided below. For your 2nd question: Widgets are rendered in web browsers. So, in my sense, Python 2.7.13 instead of Python 3.5.3 should not cause problem with widget rendering. Python 2.7.13 should work. My conda install uses Python

[Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

2017-06-20 Thread Janusz Petkowski
Dear RDKit Community, I have a quick question regarding a possibility of setting valence of an atom in rdkit. Let's say that I have a molecule like this (smiles notation): PPC or SSC and I would like to change the valence of one or more S or P atoms from default II for S or III for P to let's

[Rdkit-discuss] Definition of HBA differs from pipeline pilot

2017-06-20 Thread Hongbin Yang
Hi, Rdkiters, ? ?The definition of HBA in rdkit is (by Lipinski) : 32 HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),' + 33 '$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' + 34