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.”


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.”

mishima.syk#6 etc.

Today I presented at mishima.syk#6 about rdkitjs. I wrote very simple script using rdkitjs and d3js. This script can make scatter plot about fraction of Csp3 and molwt and when user mouse over the circle, rdkitjs return molecule image. Like this. I uploaded the script to github. I hope, participants enjoyed my presentation…. TheContinue reading “mishima.syk#6 etc.”

calculate 3d pharmacophore fingerprint in rdkit

I read document about RDKit for the first time in a while and found nice snippet. A 3D Pharmacophore finger print can be caluclated very easily. If dMat = None( default setting), fp means 2D Pharamcophore fingerprint, but now I passed dMat so the fingerprint has 3D information. Now 3D pharmacophore fingerprint in hand, itContinue reading “calculate 3d pharmacophore fingerprint in rdkit”


I often use flask for developing some web services. Because it’s very easy and powerful tool and python library. There are lot’s of extensions. Yesterday, @kzfm san gave me useful information for developing web services via node-js. I haven’t used node-js before, but I tried it. Node-js is very major tools and also it canContinue reading “nodejs-rdkit”

Fragmentation of molecules.

I often use molecular fragmentation for getting small drug like fragments from any data sources. RECAP, BRICS, or another algorithms are used to do it. RDKit is suite tool to do that. I often use the toolkit. Also I was interested in a tool that named “molBLOCKS” and tried to use it. If reader whoContinue reading “Fragmentation of molecules.”

View SDF using open source toolkit.

There are lots of commercial tools to visualize structures from SDF files. Also I often use Spotfire, etc in my lab, but not use in my house. In 2014RDKit-UGM open source SDF viewing tool was presented. Today I installed it and used. If reader who interested this tool, there is nice presentation in following link.Continue reading “View SDF using open source toolkit.”

After mishima.syk #4

Thank a lot for all attendance and presenters at mishima.syk #4 ! I enjoyed the event and party. All presentations were very interesting and exciting. ;-) I made brief introduction about cytoscape.js, and up loaded my slide and sample code to slide share and git hub. slide link code link My sample apps will needContinue reading “After mishima.syk #4”

Moleculer Similarity

Sometime, we discuss about molecular similarity. I think that meaning of similar is depend on a situation. For example, if aromatic pharmacophore is important, phenyl and pyridil maybe similar. But If molecular charge is important, phenyl ando pyridil maybe unsimilar. So, Having some metrics methodologies are useful. RDKit has interesting fingerprint called “Fraggle Fingerprint” It’sContinue reading “Moleculer Similarity”

MMP using predict

I’m still thinking about how to use mmp data in our lab. Inspired following nice presentation, I challenged to make predictive model from MMPA. One of ipython notebook about rdkit. link And another is Greg’s nice presentation about reaction finger print . link2 To make predictive model from mmps, I think, I need to convertContinue reading “MMP using predict”

calculate fingerprint

I’m interested in chemoinformatics and machine learning and a fun of RDKit. (But I’m still …..) Calculate molecular fingerprint is a very important process to build QSAR model. I some time use RDKit-Morgan Fingerprint (like scitegic ECFP4). Chemfp is a good tool to calculate many type of fingerprint . It can generate and search fingerprintContinue reading “calculate fingerprint”

access CHEMBL DB with python

CHEMBL is a one of big public database. It has lots of useful data. If you are good at python, pychembldb will be good tool. I like the python package. And I found another package chembl “chembl_web_client”. The package can install using pip. Yah, it easy. OK Let’s get data from python ! For exampleContinue reading “access CHEMBL DB with python”

Deep learning with python.

I’m interested in machine-learning. And python is good tool to do that for me. Deep learning is one of the hot topic in these area. There are some library for deep learning in python, “Theano”, “Pylearn2”. But, these packages are difficult for me ;-( . So, I used nolearn to do deep-learning Nolearn is easyContinue reading “Deep learning with python.”

Make biplot using ggplot.

Principal Component Analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into set of values of linearly un correlated variables. (from wiki) R can preform PCA very simple command “prcomp”. The result can visualise using biplot function. ggplot2 is a plotting system forContinue reading “Make biplot using ggplot.”

Try to subshape alignment

Molecular shape based alignment is useful for VS, scaffold hopping, etc. ROCS is very popular tool to do it. But there are some another tools. I found nice reference on web, and tried to do subshape alignment using RDKit. My try was failed because it took very long time ;-(. This is snippet.. ” IContinue reading “Try to subshape alignment”

Make graph with python

Visualization of data is very important. Some years ago, I was interested in cytoscape to visualize molecular network (a.k.a. similarity, MMP, etc.). But it was difficult to integrate python script. Today, I found cool python library “d3py”. It can get from github ;-). “” This library can make any graphs easy like ggplot, vincent andContinue reading “Make graph with python”