Develop rdkit-cli tool with typer #RDKit #chemoinformatics #typer

Recently I’m learning not only coding but also no-code tool such as knime. It’s important to chatch up wide range of informatics IMHO…. BTW, as you know rdkit has lots of useful tools. And there are many useful packages which depend on RDKit. It’s because rdkit is growing very rapidly. Today I learned useful package

Make learning process with human in the loop #optuna #memo #python #rdkit

Many chemofinromaticians have checked Greg’s great blog post which describes how to draw draw molecules in various way. https://greglandrum.github.io/rdkit-blog/posts/2023-05-26-drawing-options-explained.html Rendering molecule doesn’t directly contribute drug design but it’s really importnt for us because medicinal chemists have their own preferences for drawing moleucles such as font size, highlight color etc, etc. It’s too difficult to parametarize

Optimize ML model with few line code #chemoinformatics #ML #RDKit #falcon

Machine learning is democratizing, and there are many great libraries available in Python such as scikit-lean pycaret. Recenlty we can build ML model without writing lots of code. Today I found new package named ‘falcon‘ which can build optimized model few lines. One of the famous package for AutoML is auto-scikitlearn, the package is also

Use jupyternotebook from knime #knime #chemoinformatics #memo

Recently I posted an example to build custom knime node with python. It was a nice experience for me. And I’m still reading knime documentation. Today I tried to use jupyter notebook from knime. There is a good example to do that with workflow and dataset.https://docs.knime.com/latest/python_installation_guide/index.html#jupyter-notebooks The example described avobe reads dataset and do some

Try to use recent version exmol #exmol #rdkit #chemoinformatics

Previously I wrote blog post about ‘exmol’ which is useful package for ML related task. Examol is developed by Andrew White. I installed it almost 2 years ago and Didn’t check the update, recently I found new verson of exmol is released and new versoin have new functions. Following code is bollowed from original documentation

Visualize MMP data with OSS webapp! #chemoinformatics #rdkit #mmpdb

Matched molecular pairs (MMPs) are old but still useful approach for not only retrospective analysis but also forward compound design. As many chemoinformatitians know that mmpdb is the one of famous MMP CLI tool. I like tha package because it’s easy to make own MMP db. However mmpdb doesn’t have visualization tool for chemists. So

Run RDKit task in parallel #rdkit #chemoinformatics

Recently we can get huge amout of molecules and can use it for drug discovery tasks. It’s really good news however, we need computational resources more and more… When I wrote code for chemoinformatics task with python, ‘for loop’ approach is often used. But it is straight way, it’s not so efficient. Long time ago,

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++

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

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

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

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

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

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