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
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
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
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:
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/
>
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
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
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
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
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
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