Generate fragment fingerprint using RDKit

I often use MorganFP( ECFP or FCFP like ) for machine learning. But for the chemist, I think it’s difficult to understand. On the other hand, fragment based fingerprint is easy to understand. There are lots of report about fragment based fingerprint for QSAR. Fortunately, RDKit already implemented the method to generate FragmentFingerprint. ;-) ItContinue reading “Generate fragment fingerprint using RDKit”

calculate exit vector distance of each molecule

Some days ago, I participated a seminar about drug discovery. All presentations were nice, and I interested in one of unique method to representation chemical space, named “exit vector plot”. ref is following Following Ramachandran: exit vector plots (EVP) as a tool to navigate chemical space covered by 3D bifunctional scaffolds. The case of cycloalkanesContinue reading “calculate exit vector distance of each molecule”

Seed up of array calculation.

My colleague in CADD team told me that to calculate massive data in python, his recommendation is numpy. And he showed me very nice code. ( Nice stuff. ) Numpy is the fundamental package for scientific computing with Python. It can handle data as vector, array. That means native python handles Ns list data withContinue reading “Seed up of array calculation.”