Latent semantic analysis with python

Yesterday, I learned about gensim. Gensim is a free python library for topic modeling. The library seems easy to use and is implemented lots of method like doc2vec, word2vec…. At first, I tried basic tutorial for doc2vec and similarity queries. Code is following. Almost is same as official site. https://radimrehurek.com/gensim/tut3.html In this tutorial, I foundContinue reading “Latent semantic analysis with python”

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Calculate USRCAT with RDKit #RDKit

Some years ago, I posted blog about USRCAT. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505738/ USRCAT is shape based method like ROCS. And it works very fast. The code was freely available but to use the code, user need to install it. But as you know, new version of RDKit implements this function! That is good news isn’t it. I triedContinue reading “Calculate USRCAT with RDKit #RDKit”

Draw high quality molecular image in RDKit #rdkit

Recently, I want to draw high quality image molecule using RDKit. Older version of RDKit png image is not enough for me. I found the solution in RDKit discuss. The discussion recommended to install cairocffi. I installed cairocffi via conda. But… Result is not enough for me. ( this case is my Mac environment. LinuxContinue reading “Draw high quality molecular image in RDKit #rdkit”