(CC'ing the list as I hadn't in my original reply)
Dear Janusz,
this is what I would do:
>>> from rdkit import Chem
>>> mol = Chem.MolFromSmiles('SSC')
>>> print Chem.MolToSmiles(mol)
CSS
>>> print Chem.MolToSmiles(mol, allHsExplicit=True)
[CH3][S][SH]
>>> a = mol.GetAtomWithIdx(1)
>>> print (a.
Hi,
Many applications have multiple definitions of HBA/D from simple heteroatom
counts to sophisticated SMARTS definitions, as long as they are documented and
referenced I’d vote for keeping all definitions. It certainly helps if you want
to go back and try to repeat published work.
Cheers,
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/
> -DBoost_NO_SYSTEM_PATHS=ON ..
>
> and make as us
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 Chem.AddHs
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
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
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: Th
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,
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 2.7.1
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 [mailto:ax
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
ip
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