ChEMBL provides multitask prediction model from its github repo. And shared useful blog post.https://chembl.blogspot.com/2019/05/multi-task-neural-network-on-chembl.html By using the code, we can get predicted target list from given molecules. And the prediction can run python, C++, JS and Knime! ChEMBL team provides not only source code but also predicted results when we search compound in ChEMBL DB.Continue reading “ChEMBL multitask prediction with python requrests #memo #chembl #cheminfo”
Tag Archives: python
Useful package for filtering molecules of python #RDKit #Python #memo
I wrote blog post of how to use Lilly filter from REINVENT4. In the post, I build lilly filter from source code. After posted, Hadrien introduced me a package for using lilly filter which can call from python. Thanks! The package is provided from datamol-io’s reposidory named medchem. I had intreste the package so I installedContinue reading “Useful package for filtering molecules of python #RDKit #Python #memo”
Run virtual screening with only python! #chemoinformatics #SBDD
If you have protein-ligand co- crystal structure at the early stage of drug discovery, SBDD based approach is useful I think. As many readers know that there are lots of useful commercial packages to conduct SBDD. But also there are useful packages at Open science area. One of the famous and useful OSS for SBDDContinue reading “Run virtual screening with only python! #chemoinformatics #SBDD”
Regist new molecules with lwreg from web app #RDKit #lwreg #cheminformatics
Now there is RDKit based chemical cartridge for sqlite3 and posgresql. So it’s useful for developping cheminfo web app with these databases. By using these databases with web app, we need to defne the schema of databases at first. Also many cheminformaticians handle lots of molecules. So it’s useful to register their idea or handledContinue reading “Regist new molecules with lwreg from web app #RDKit #lwreg #cheminformatics”
Visualize result of molshap #RDKit #chemoinformatics #memo
Finding the best combination of substituents is very important task for compound optimization. Recently there are lots of methods to predict the combination. By using Deep learning or other complex methods are difficult understand for chemists. So I like Free Wilson analysis, because it’s simple but easy to understand because FW analysis uses liner regression.Continue reading “Visualize result of molshap #RDKit #chemoinformatics #memo”
Update Scikitlearn and visualize chemical space with rdkit #RDKit #Chemoinformatics #Scikitlearn
As most of readers know that new version of scikitlearn is released ;) There are lots of improvements are implemented. And you can see the details in original documenation.https://scikit-learn.org/stable/whats_new/v1.3.html One of interesting news is that scikit-learn v13 has implemented HDBSCAN. The origainal article is following link. And it implemented indpendend package of python.Article: https://link.springer.com/chapter/10.1007/978-3-642-37456-2_14Package: https://github.com/scikit-learn-contrib/hdbscanContinue reading “Update Scikitlearn and visualize chemical space with rdkit #RDKit #Chemoinformatics #Scikitlearn”
Some updates of rdkit_cli #RDKit #chemoinformatics #typer
I enjoyed a user group meeting last week I could have lots of useful discussion there thanks for all presenters and perticipants ;) BTW, I’m still enjoying to make RDKit based CLI tool and I added some routine task to the code. Of course some function is already impremented other tool such as openbabel etc.Continue reading “Some updates of rdkit_cli #RDKit #chemoinformatics #typer”
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”
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