rdkit-discuss

[Rdkit-discuss] depiction of molecules with PandasTools AddMoleculeColumnToFrame

[Ines S. <ia...@ca...>]

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

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

[Greg L. <gre...@gm...>]

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 <ia...@ca...> 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

[Ines S. <ia...@ca...>]

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 <ia...@ca...> 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
>> 
>> 
> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot [1]
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [2]
> 
> 
> 
> Links:
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