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 packageContinue reading “Develop rdkit-cli tool with typer #RDKit #chemoinformatics #typer”

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 parametarizeContinue reading “Make learning process with human in the loop #optuna #memo #python #rdkit”

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 alsoContinue reading “Optimize ML model with few line code #chemoinformatics #ML #RDKit #falcon”

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 someContinue reading “Use jupyternotebook from knime #knime #chemoinformatics #memo”

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 documentationContinue reading “Try to use recent version exmol #exmol #rdkit #chemoinformatics”

Develop new knime node with python #chemoinformatics #knime

The Golden Week is a collection of four national holidays within seven days. My kid graduated the elementary school and his favorite dodgeball team and he joined vollyball team. I quit coaching the dodgeball team at same time. So I have time for coding and drinking beer again ;) I watched knime summit about newContinue reading “Develop new knime node with python #chemoinformatics #knime”

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,Continue reading “Run RDKit task in parallel #rdkit #chemoinformatics”

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++Continue reading “Make QSAR model with PyG and pytorch2.0 #RDKit #Chemoinfo”

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 seemsContinue reading “Make pptx file from Python #chemoinformatics #memo #python-pptx”

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 doContinue reading “CLI tool for making ssslib #chemoinformatics #rdkit”

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 triedContinue reading “Useful python package for QSAR related tasks of chemoinformatician #chemoinformatics #oloren-ai #RDKit”

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 packageContinue reading “Useful package for ploting chemical space rapidly #chemoinformatics #memo”

Define a function after the request #Flask #memo #python

I love flask and django for making web app and often use Flask for web app development. Sometime the app will serve files after getting user request. In this case, static files which are generated by the app will be stored in static folder. And the folder will store lots of files. So I wouldContinue reading “Define a function after the request #Flask #memo #python”

Compare shape and electrostatic similarity of molecules #RDKit #espsim #python

There are lots of way to define molecular similarity, for example fingerprint based, descriptor based, graph based, shape based etc. etc… In the 2D world, circular fingerprint based similarity is used in many case. However, 3D based similarity approach is also useful for drug design. As you now, OpenEye provides useful software named ‘ROCS’. ROCSContinue reading “Compare shape and electrostatic similarity of molecules #RDKit #espsim #python”

Convert bit-vector to comma separated strings #memo #chemoinformatics #RDKit

Today’s post will be very short :) I had an MRI scan for my knee at the hospital today. It took almost 6 moths after my surgery. And the result was very well. So I could be able to running as same as before getting the surgery. I’m not young but I would like toContinue reading “Convert bit-vector to comma separated strings #memo #chemoinformatics #RDKit”

Self docking study workflow with vina #chemoinformatics #vina #RDKit #pdb-tools

I posted about how to run vina from python. But I split receptor and ligand with pymol GUI at previous post, Hmm…. it’s not automated process. I tried to write code for full auto self docking with vina. It will work only very limited option and case but It’ll be first step for Virtual screeningContinue reading “Self docking study workflow with vina #chemoinformatics #vina #RDKit #pdb-tools”

Run docking study from python #chemoinformatics #vina #RDKit

Docking is one of the popular approach for computer aided drug design. There are lots of applications to run docking not only commercial software but also open source. AutoDock Vina is one of the popular OSS for docking study and it was updated recently. The publication is below. https://pubs.acs.org/doi/full/10.1021/acs.jcim.1c00203 Vina has python binding and itContinue reading “Run docking study from python #chemoinformatics #vina #RDKit”

Get environment SMILES around cutting points #chemoinformatics #memo #RDKit

In this week, I’m in summer vacation but can’t go travel due to COVID19 pandemic and heavy rain. It’s really unusual summer vacation. I hope everyone stay safe. BTW, I often use R-Group decomposition and Matched molecular pairs and these method generate many fragment smiles which has [*] at attachment points. And I would likeContinue reading “Get environment SMILES around cutting points #chemoinformatics #memo #RDKit”

Embed molecular editor into Streamlit app #streamlit #chemoinformatics #RDKit

I wrote some posts about usage of combination chemoinformatics and streamlit. One was predictive model application which was used rdkit and scikit-learn. When I tweeted that, Jan Jansen (who is Great quantum chemist and I met him RDKit UGM!!!) commented me that it is useful that if molecular drawer can use in the app ;)Continue reading “Embed molecular editor into Streamlit app #streamlit #chemoinformatics #RDKit”

Useful ML tool for chemoinformatics #chemoinformatics #RDKit #Machine learning

Yesterday, I moved my main PC from Ubuntu18.04 to 20.04LTS. Now it works well. And I’m building new(clean) env for my coding. Today I would like to share useful package for machine learning named pycaret. Brief introduction of PyCaret is below. —from original site—PyCaret is an open-source, low-code machine learning library in Python that automatesContinue reading “Useful ML tool for chemoinformatics #chemoinformatics #RDKit #Machine learning”