Re: [Rdkit-discuss] Generating a pdf file with a grid of molecules

2022-10-06 Thread Alfredo Quevedo 
Thank you very much Aishvarya for the suggestion. I will explore the 
mol2grid library,



kind regards


Alfredo



On 6/10/22 09:37, Aishvarya Tandon wrote:


Hi Alfredo,


I can suggest some alternate ways which might be helpful since you 
want to do a visual inspection primarily.



 1. If not having the final output as a multi-page PDF is ok, you can
use "mol2grid" library
(https://mols2grid.readthedocs.io/en/latest/contents.html
).
There's an option to save the output as a HTML file.
 2. A hack if you are using Jupyter notebook (and really want a PDF
output) could be to download the notebook with output as a PDF.
 3. DataWarrior is another open-source software if you want to explore
something outside Python (https://openmolecules.org/datawarrior/
) to inspect molecules.


Cheers!
Aishvarya

*From:* Alfredo Quevedo 
*Sent:* Thursday, October 6, 2022 3:10:20 AM
*To:* RDKit Discuss
*Subject:* [Rdkit-discuss] Generating a pdf file with a grid of molecules

Hello,

I am trying to out a .pdf file containing a grid of molecules with the 
corresponding labels below. For that, I am following these steps:


1- Prepare a dataframe reading a csv file containing the smiles and 
molecule names,


2- use /PandasTools.AddMoleculeColumnToFrame(df,smilesCol='smiles')/ 
to obtain the df containin a column with the molecules,


3- I can see the molecules in the notebook using: 
/PandasTools.FrameToGridImage(df,legendsCol='name', molsPerRow=3)/


However I would like to output all the molecules to a multipage .pdf 
file for visual inspection.


Any hint on how I can produce that file is greatly appreciated,

kind regards

Alfredo


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*Dr. Alfredo Quevedo,*
Faculty of Chemical Sciences,
National University of Córdoba,
Argentina.
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Re: [Rdkit-discuss] Generating a pdf file with a grid of molecules

2022-10-06 Thread Aishvarya Tandon 
Hi Alfredo,


I can suggest some alternate ways which might be helpful since you want to do a 
visual inspection primarily.


  1.  If not having the final output as a multi-page PDF is ok, you can use 
"mol2grid" library (https://mols2grid.readthedocs.io/en/latest/contents.html).
There's an option to save the output as a HTML file.
  2.  A hack if you are using Jupyter notebook (and really want a PDF output) 
could be to download the notebook with output as a PDF.
  3.  DataWarrior is another open-source software if you want to explore 
something outside Python (https://openmolecules.org/datawarrior/) to inspect 
molecules.

Cheers!
Aishvarya

From: Alfredo Quevedo 
Sent: Thursday, October 6, 2022 3:10:20 AM
To: RDKit Discuss
Subject: [Rdkit-discuss] Generating a pdf file with a grid of molecules


Hello,

I am trying to out a .pdf file containing a grid of molecules with the 
corresponding labels below. For that, I am following these steps:

1- Prepare a dataframe reading a csv file containing the smiles and molecule 
names,

2- use PandasTools.AddMoleculeColumnToFrame(df,smilesCol='smiles') to obtain 
the df containin a column with the molecules,

3- I can see the molecules in the notebook using: 
PandasTools.FrameToGridImage(df,legendsCol='name', molsPerRow=3)

However I would like to output all the molecules to a multipage .pdf file for 
visual inspection.

Any hint on how I can produce that file is greatly appreciated,

kind regards

Alfredo
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