Make QSAR model with PyG and pytorch2.0 #RDKit #Chemoinfo

Recently, I updated version of pytorch on my env from 1.x to 2.0. I think it’s worth to update because, original site says…. PYTORCH 2.X: FASTER, MORE PYTHONIC AND AS DYNAMIC AS EVER Today, we announce torch.compile, a feature that pushes PyTorch performance to new heights and starts the move for parts of PyTorch from C++

Make multi target predictive model for Knime #RDKit #Knime #DeepLearning

I participated my kid’s elemenary school graduation ceremony today. It was nice ceremony. …Time pasts very fast ;) In the season in Japan is very good. Beautiful cherry blossoms start to bloom. It’s good time to start anything ;-) I would like to say thank to my kid. BTW, recently chembl ver32 was released. As

Calculate atomic property with new chemoinformatics package♪ #RDKit #Jazzy

It have been long time since my last post ;) Now we are in Feburary… I hope every reader have nice start of this year. I’m enjoying my day but really busy. This is the first post of the year! Thinking the strength of hydrogen donoer and acceptor is important for drug design but difficult

Calculate similarity of popular bioisosters #RDKit #espsim #memo

It will take 3 years after changing job. Fortunately, I’m still working at early drug discovery field as chemoinformatician ;) As many drug hunter know that bioisosteric replacement is one of the major way for designing novel molecules from known biologically active molecules. Transformations from carboxylic acid to tetorazole, from amide to oxazole are major

Make pptx file from Python #chemoinformatics #memo #python-pptx

I hope all reader enjoying chemoinformatics ;)Unfortunately I’m struggling to make PPTX file in this year. So I can’t have enought time to coding. But It’s same for medicinal chemists. Because they often make presentation slide for project team, theier boss, senior etc…. They transfer SAR data from spread sheet to pptx. Sometime it seems

CLI tool for making ssslib #chemoinformatics #rdkit

As many RDKitter know that rdSubstructLibrary is one of the cool tool for conductiong substructure search. Greg Landrum introduced how to use it in his great blog post. I love the method because it works very fast for substructure searching. So I would like to make CLI tool for making substructure library database. To do

Use mmpdblib on jupyter notebook #rdkit #mmpdb #chemoinformatics

I introduced MMPDB v3 few days ago. The package is CLI tool. So user can do MMPA by typing command line. However the tool doesn’t provide API interface. I think, if we can use MMPDB on jupyter-notebook it’ll be more useful because output data can be used directly in coding process. MMPDB Cli interface is

Let’s use mmpdb v3 #memo #rdkit #chemoinformatics

Matched molecular pair (MMP) is not AI based compound design method however it’s still useful and powerful approach to do compound design. MMPDB is one of the cool package for MMP analysis. And Andrew who is developer of MMPDB preseted new version of MMPDB at RDKit UGM 2022. Version 3 is still developing state but

Embed mols2grid to web page #mols2grid #RDKit #webapp

I often use flask for my web app development because the package is light weight web framework and easy to write. BTW rendering molecules as grid image is easy in jupyter notebook by using RDKit’s Draw.MolsToGridImage function. And also recently developed package named mols2grid is really cool for rendering molecules on jupyter notebook. mols2grid generaetes

FW analysis make easily with rdkit contrib FW package #rdkit #chemoinformatics #memo

Last week I enjoyed RDKit UGM 2022. It was really great and exciting evenif I participated there from online. I hope I could participate RDKIT UGM 2023 locally ;) As you know RDKit is one of the useful OSS package for chemoinformatician. It has nice community and be developed actively. I respect the community and

Make chemoinformatics coding more easily ! #RDKit #datamol

I love RDKit because it supports lots of chemoinformatics features and it is supported top level scientific community. But for eary chemoinformacian, it’s required to learn python or C++ to write chemoinformatics code. As you know, Knime is good option for no-code chemoinformtatics. And another option for beginner is good wrapper of rdkit Recently the

Generate molecules with REINVENT and make interactive plot #RDKit #Knime #REINVENT

I introduced to use user defined condaenv in Knime. It’s really useful I think. Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo And as you know, REINVENT is the one of famous compound generation tool for drug discovery. Its community provides lots of example codes as jupyternotebook. After building some

Useful python package for QSAR related tasks of chemoinformatician #chemoinformatics #oloren-ai #RDKit

When I posted my memo about open science, @OlorenAI introduced python package named Oloren ChemEngine (OCE). I often use chemprop or interanly build system for QSAR tasks. ChemProp is the one of favorite package because it is easy to use and it includes web application flamework for users. I’ve never used OEC so I tried

Let’s enjoy open science! #memo #diary

My blogsite was started 2013, so I took almost 10 years ;) It’s amazing. I’m enjoying writing the blog and sharing my code snippet. BTW, I’m working in pharmaceutical company as a chemoinformatician. So, is it risk to write chemoinformatics related post in my blog site….? I don’t think so. As many people know that

Calculate ligand RMSD with rdkit contrib package #RDKit #memo

Today is the last day of my summer vacation…. Due to COVID-19 pandemic, I and my family didn’t go travel during the vacation however, we’ll go to national championship of dodgeball game in next sturday. It will be exciting day! BTW as you know, rdkit has lots of contrib packages. And I would like to

Useful package for ploting chemical space rapidly #chemoinformatics #memo

Visualize chemical space is important task for chemoinformatitian. And there are lots of way to represent chemical space. One of the common approach is PCA. And recently tSNE and UMAP are used. I wrote template code for plotting these data in my task but didn’t write code as a package. Today I found useful package

Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo

I think workflow tool is useful for many chemoinformatician such as Knime, Pipeline Pilot(PP) and Orange. In my knowledge, it’s difficult to use user defined conda env in PP. Of course these workflow tools provides enough components to do many tasks. But I would like to have more flexibility to build chemoinformatics pipelines. Recently I

Useful package for virtual screening #chemoinformatics #RDKit

Virtual Screening is important task of drug discovery projects. There are lots of approach for example Finger print based, substructure based and shape based screening. All approaches listed above is not only used in SBDD but also LBDD. And there are lots of apprications to do these tasks. I wrote scripts for these task and

Call RDKit from Rust with conda env ver2 #RDKit #RDKit-sys #Rust #Chemoinformatics

To use rdkit from Rust, I introduced rdkit-sys before. And fortunately recent version of rdkit-sys cleat supports rdkit-env. It’s worth to use conda-env to build rdkit-sys because user don’t need to build rdkit from source code. Following code is almost same as my previous post but I would like to share it. At first, I

Generate molecules with Link-invent #RDKit #RINVENT #chemoinformatics

General molecular generator with deep learning approach is difficult to fix substructure. But common SAR expansion by medchem is focus on specific part such as terminal part, core and linker. Linker is defined as a part which connect parts of molecules. Linker is important of drug design and is called scaffold when the linker connets