Rendering molecular image tooltips on Bokeh #RDKit #memo #visualization

Recently there many plotting tools for python package! I can’t follow everything… I mainly use seaborn and matplotlib. These tools are nice for rendering beautiful chart but if I would like to interactive plot, I need to switch plotting tools. So I started learn another tools and today I used Bokeh. (Reader already know bokeh,Continue reading “Rendering molecular image tooltips on Bokeh #RDKit #memo #visualization”

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Compare the view point of different QSAR models #RDKit #visualize #chemoinformatics

Some days ago, I posted how to visualize SVG images horizontally and ngboost for QSAR problem. It worked well. And I found that different models showed different performance. So my question is that which point each model detects important for molecular properties. Fortunately rdkit has GetSimilarityMapForModel method which can render the probe molecule with model’sContinue reading “Compare the view point of different QSAR models #RDKit #visualize #chemoinformatics”

Draw molecules as SVG in horizontal layout #Drawing #RDKit #memo

As you know, Greg posted cool code about new drawing code options of rdkit 202003. You can read details of them in following URLhttp://rdkit.blogspot.com/2020/04/new-drawing-options-in-202003-release.html It’s really cool! New version of rdkit can render molecule with many options in high quarity. In the post, molecules are rendered as SVG image one molecule per one cell. IContinue reading “Draw molecules as SVG in horizontal layout #Drawing #RDKit #memo”

Rendering molecular orbital on Jupyter notebook #psikit #py3dmol #rdkit #memo

@fmkz___ and I( @iwatobipen ) are developing psikit which is a thin wrapper of psi4 and rdkit. I hope the package integrates quantum chemistry (Psi4) and chemoinformatics (RDKit). By using psikit, user can make molecular orbital data very convinienlry. Rendering MO is useful for understanding molecular electrostatic shape and nature, but sometime it is difficultContinue reading “Rendering molecular orbital on Jupyter notebook #psikit #py3dmol #rdkit #memo”

Embed interactive plot in jupyter notebook with panel #chemoinformatics #RDKit #memo #panel

As you know Jupyter notebook is very useful tool for data scientist. It can analyze scientific data with nice view. And there are lots of packages for data visualization. And I often use matplotlib and seaborn for my task. However few days ago, I found an interesting package named Panel which is high level appContinue reading “Embed interactive plot in jupyter notebook with panel #chemoinformatics #RDKit #memo #panel”

Draw RDKit mol/reaction object on HTML without static png image #RDKit #memo

I think this post might not useful for many people. Just for my memorandum. When I make web app, I use draw SVG function for rdkit object rendering. But from last my post and Greg’s gist, I could learn draw png image without writing static png files. So I wonder that can I draw PNGContinue reading “Draw RDKit mol/reaction object on HTML without static png image #RDKit #memo”

Model interporation with new drawing code of RDKit #RDKit #Machine learning #chemoinformatics

Following code does not use new drawing code but it revised one of my old post. :) I think, everyone who visits my blog has already read Gregs nice blog post about the drawing similarity map with new code. If you don’t read it I recommend to read it soon. URL is below. ;)http://rdkit.blogspot.com/2020/01/similarity-maps-with-new-drawing-code.html NowContinue reading “Model interporation with new drawing code of RDKit #RDKit #Machine learning #chemoinformatics”

Visualise dataset using seaborn.

I often use scatter plot to analyse relationship of 2 valuables. There are a lots of tools for visualise dataset. Now, I challenged to use seaborn. Seaborn is python library based on matplotlib. And easy to make cool visualisation. Following snippet, I read sample data from rdkit install folder and plot MolWt vs LogP usingContinue reading “Visualise dataset using seaborn.”