January 2017 – Is life worth living?

encode and decode SMILES strings.

Today was very cold. ;-( But, my kids play at a park long time! @_@ I want to go snow board with my family… BTW, recently I am interested in recurrent neural network. There are a lot of report about deep learning using smiles strings as input. To use smiles strings as input, it needsContinue reading “encode and decode SMILES strings.”

Convert function in RDKit

It become large data file when large amount of molecules are saved as SDF format. So I often convert to SMILES from SDF. I use MolToSmiles function to do that. But, new version of RDKit has convenient method to convert file format. Here is sample snippet. Now I got out.csv file. Check the file. 🎵🎵

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”

Try Grumpy.

Somedays ago, I read a news from google. Google developed “Grumpy”, it is an experimental runtime for Go. https://opensource.googleblog.com/2017/01/grumpy-go-running-python.html Grumpy translates python code into Go programs. I do not have knowledge about Golang, but it seems interesting. So, I used grumpy. Grumpy can get from github. https://github.com/google/grumpy If user want to use grumpy, install isContinue reading “Try Grumpy.”

Get bit information with RDKit

RDKit is updated constantly not only function but also document. Today I read “Getting started with python” and found interesting code. http://www.rdkit.org/docs/GettingStartedInPython.html Now I can get bit information as smiles strings. Sample code is following. FindAtomEnvironmentOfRadiusN finds the bonds within a certain radius of an atom in a molecule. PathToSubmol returns molecule around environment. TestContinue reading “Get bit information with RDKit”

Replace comma in double quotation marks using python Regex.

Happy new year ! May the year of 2017 bring all readers a lot of happiness and smiles. First topic of the year is regular expression. ;-) I want to replace comma only in double quotation marks of a CSV files. Maybe I can do it using regular expression. But, how to do it ?Continue reading “Replace comma in double quotation marks using python Regex.”