Convert dataframe to json.

I often use PANDAS for data analysis. PANDAS can handle data set as DataFrame like R language. It’s quite useful ;-). Today, I think about new web app. And I want to use MongoDB for data strage. MongoDB is No SQL database, and data format looks like Json. So, I want to convert Pandas DataFrameContinue reading “Convert dataframe to json.”

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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.”

Passport for compound.

I was interested in the title. “Compound Passport Service” http://dx.doi.org/10.1016/j.drudis.2015.06.011 AZ made passport for compound to manage compound rights tracking. The system can manage status of compounds, like ownership, permission and structure shared. I really impressed with the concept and system because I think that management of compound(and right) logistics is key factor in DrugContinue reading “Passport for compound.”

Render molecule as SVG via Flask.

I posted topics about rdkitjs before. The library can render molecule as SVG format. It was very useful for me. But, sometime I write webapp using python. So I want to draw molecule from python. There are a lots of web framework in python and my favorite is “Flask”. ;-) So, I tested render moleculeContinue reading “Render molecule as SVG via Flask.”

Draw molecule in RDKit

I really enjoyed OETK training. Thanks a lot y_sama and organiser of the training. And I told about rdkit with the TK specialist in break time. TK specialist asked me that can RDKit draw molecule with highlight substructure. I answered to him ‘yes… maybe…but I can’t show you example now…’. Now I searched Web andContinue reading “Draw molecule in RDKit”

How to visualize QSAR model.

I often discuss with other chemist(s) about QSAR. And sometime they told me …”QSAR is useful tool for drug discovery, but I don’t understand it. Because QSAR model (i.e. ML) is hard to understand why the compound is good ?” Hmm, I agree his opinion. SVM, NB, RF etc are very useful but these modelsContinue reading “How to visualize QSAR model.”