Re: [Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

2017-10-25 Thread Ines Smit 

That worked! Thanks Greg and everyone who worked on that, brilliant!
Ines

On 2017-10-25 07:09, Greg Landrum wrote:

Hi Ines,

This problem should go away if you update to the most recent version
of the RDKit.

-greg

On Tue, Oct 24, 2017 at 4:19 PM, Ines Smit  wrote:


Hello RDKitters/pandaskitters,

I'm trying to use the 'AddMoleculeColumnToFrame' in the Jupyter
notebook but the depiction of the molecule in dataframe isn't great,
the lines are jagged/low resolution. Displaying molecules inline in
the notebook (outside of the dataframe) works fine.

I've tried changing the PandasTools.molSize but it didn't help.

Here is my code:

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import PandasTools
import pandas as pd
from IPython.core.display import display, HTML

# Normal inline display of molecule is fine
Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')

# Add molecule to dataframe
my_df = pd.DataFrame(['COC1=C(OC)C(=O)C(C)=CC1=O'], columns =
['Smiles'])
PandasTools.AddMoleculeColumnToFrame(my_df,'Smiles','Molecule
picture')

# Depiction of molecule within dataframe is not so great
display(my_df)

# Using HTML I get the same jagged depiction.


HTML(PandasTools.PrintAsBase64PNGString(Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')))


I have these packages in my conda environment:
cairo 1.14.8
cffi 1.7.0
pandas 0.20.1
pillow 3.3.1
rdkit 2017.03.3

Am I missing something else? Any suggestions for what I could try?

Many thanks!
Ines
-- PhD student at the University of Cambridge



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Re: [Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

2017-10-24 Thread Greg Landrum 
Hi Ines,

This problem should go away if you update to the most recent version of the
RDKit.

-greg


On Tue, Oct 24, 2017 at 4:19 PM, Ines Smit  wrote:

> Hello RDKitters/pandaskitters,
>
> I'm trying to use the 'AddMoleculeColumnToFrame' in the Jupyter notebook
> but the depiction of the molecule in dataframe isn't great, the lines are
> jagged/low resolution. Displaying molecules inline in the notebook (outside
> of the dataframe) works fine.
>
> I've tried changing the PandasTools.molSize but it didn't help.
>
> Here is my code:
>
> from rdkit import Chem
> from rdkit.Chem.Draw import IPythonConsole
> from rdkit.Chem import PandasTools
> import pandas as pd
> from IPython.core.display import display, HTML
>
> # Normal inline display of molecule is fine
> Chem.MolFromSmiles('COC1=C(OC)C(=O)C(C)=CC1=O')
>
> # Add molecule to dataframe
> my_df = pd.DataFrame(['COC1=C(OC)C(=O)C(C)=CC1=O'], columns = ['Smiles'])
> PandasTools.AddMoleculeColumnToFrame(my_df,'Smiles','Molecule picture')
>
> # Depiction of molecule within dataframe is not so great
> display(my_df)
>
> # Using HTML I get the same jagged depiction.
> HTML(PandasTools.PrintAsBase64PNGString(Chem.MolFromSmiles('
> COC1=C(OC)C(=O)C(C)=CC1=O')))
>
> I have these packages in my conda environment:
> cairo 1.14.8
> cffi  1.7.0
> pandas0.20.1
> pillow3.3.1
> rdkit 2017.03.3
>
> Am I missing something else? Any suggestions for what I could try?
>
> Many thanks!
> Ines
> -- PhD student at the University of Cambridge
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
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