Hi Axel,
It's probably most straightforward to use the function
AllChem.TransformMol() to scale the coordinates.
Here's an example of applying the function to scale all the coordinates by
a factor of 2:
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import rdMolTransforms
In [5]: from r
Thanks. It's really a obvious error.I ran it in jupyter via browser. Both
docker/ubuntu and windows were tested and found that jupyter won't give error.
Ipython or python in terminal(cmd) would show this error.
Why not raise a python error or warning?
Hongbin Yang
From: Greg LandrumDate
> I ran it in jupyter via browser. Both docker/ubuntu and windows were
> tested and found that jupyter won't give error. Ipython or python in
> terminal(cmd) would show this error.
>
>
That problem is related to how Jupyter interacts with python kernels. It's
not an RDKit issue. If you check the
What Curt says is true if you just start the jupyter notebook and import
the RDKit.
However, if you also import the Jupyter integration (using "from
rdkit.Chem.Draw import IPythonConsole"), then you should also see the C++
error messages and warnings show up in the console:
[image: Inline image 1]
Hi Greg,
thanks a lot.
That is exactly what I was looking for!
RDKit rules!
Kind regards,
Axel
On 19.09.2016 09:35, Greg Landrum wrote:
Hi Axel,
It's probably most straightforward to use the function
AllChem.TransformMol() to scale the coordinates.
Here's an example of applying the functio
Dear All,
I would like to kekulize the molecule, but only conserve the aromaticity
knowledge of C6 (benzene like) type rings
So what to need to do after this command?
Chem.rdmolops.Kekulize(mol, clearAromaticFlags=True)
Should I need to store benzene like location before the Kekulize proc
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