Re: [Rdkit-discuss] ETKDG in rdkit-blog

[Jean-Marc Nuzillard]

Hi Greg,

Sure, it works better with py3dmol installed...
Many thanks !

Jean-Marc



Le 23/02/2021 à 18:15, Greg Landrum a écrit :

Hi Jean-Marc,

Hmm, which version of py3dmol do you have installed?
I have v0.8.0:

$ conda list | grep 3dmol
py3dmol                   0.8.0                    py_0    conda-forge


-greg


On Tue, Feb 23, 2021 at 5:22 PM Jean-Marc Nuzillard 
mailto:jm.nuzill...@univ-reims.fr>> wrote:


Dear all,

I tried to reproduce the workflow in the recent blog post by Greg

https://greglandrum.github.io/rdkit-blog/conformers/exploration/2021/02/22/etkdg-and-distance-constraints.html



and everything was running fine up to

IPythonConsole.drawMol3D(m,confId=cids[1])

that returned:

AttributeError Traceback (most recent call last)
 in 
> 1 IPythonConsole.drawMol3D(m,confId=cids[1])

~\Anaconda3\envs\rdkit3\lib\site-packages\rdkit\Chem\Draw\IPythonConsole.py

in drawMol3D(m, view, confId, drawAs, bgColor, size)
  71 size = molSize_3d
  72   if view is None:
---> 73 view = py3Dmol.view(width=size[0], height=size[1])
  74   view.removeAllModels()
  75   try:

AttributeError: module 'py3Dmol' has no attribute 'view'

I am using a freshly installed rdkit 2020.09.4 from conda under
windows.
Is there something I can do to see the 3D structure?

Best,

Jean-Marc Nuzillard



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Re: [Rdkit-discuss] ETKDG in rdkit-blog

[Greg Landrum]

Hi Jean-Marc,

Hmm, which version of py3dmol do you have installed?
I have v0.8.0:

$ conda list | grep 3dmol
py3dmol   0.8.0  py_0conda-forge


-greg


On Tue, Feb 23, 2021 at 5:22 PM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:

> Dear all,
>
> I tried to reproduce the workflow in the recent blog post by Greg
>
> https://greglandrum.github.io/rdkit-blog/conformers/exploration/2021/02/22/etkdg-and-distance-constraints.html
>
> and everything was running fine up to
>
> IPythonConsole.drawMol3D(m,confId=cids[1])
>
> that returned:
>
> AttributeError Traceback (most recent call last)
>  in 
> > 1 IPythonConsole.drawMol3D(m,confId=cids[1])
>
> ~\Anaconda3\envs\rdkit3\lib\site-packages\rdkit\Chem\Draw\IPythonConsole.py
>
> in drawMol3D(m, view, confId, drawAs, bgColor, size)
>   71 size = molSize_3d
>   72   if view is None:
> ---> 73 view = py3Dmol.view(width=size[0], height=size[1])
>   74   view.removeAllModels()
>   75   try:
>
> AttributeError: module 'py3Dmol' has no attribute 'view'
>
> I am using a freshly installed rdkit 2020.09.4 from conda under windows.
> Is there something I can do to see the 3D structure?
>
> Best,
>
> Jean-Marc Nuzillard
>
>
>
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> Rdkit-discuss mailing list
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[Rdkit-discuss] ETKDG in rdkit-blog

[Jean-Marc Nuzillard]

Dear all,

I tried to reproduce the workflow in the recent blog post by Greg
https://greglandrum.github.io/rdkit-blog/conformers/exploration/2021/02/22/etkdg-and-distance-constraints.html

and everything was running fine up to

IPythonConsole.drawMol3D(m,confId=cids[1])

that returned:

AttributeError Traceback (most recent call last)
 in 
> 1 IPythonConsole.drawMol3D(m,confId=cids[1])

~\Anaconda3\envs\rdkit3\lib\site-packages\rdkit\Chem\Draw\IPythonConsole.py 
in drawMol3D(m, view, confId, drawAs, bgColor, size)

 71 size = molSize_3d
 72   if view is None:
---> 73 view = py3Dmol.view(width=size[0], height=size[1])
 74   view.removeAllModels()
 75   try:

AttributeError: module 'py3Dmol' has no attribute 'view'

I am using a freshly installed rdkit 2020.09.4 from conda under windows.
Is there something I can do to see the 3D structure?

Best,

Jean-Marc Nuzillard



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