Useful experimental method for removing solvent #memo #organic_synthesis

There are many kinds of solvents are used in organic synthesis. Such as THF, Et2O, EtOAc, DCM, DMF, DMSO and water etc. etc…. Most of solvent can be easily removed by using rotary evaporator. When I was bench chemist, I like the solvent which has low boiling point. Because it is easy to remove. TheContinue reading “Useful experimental method for removing solvent #memo #organic_synthesis”

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Embed interactive plot in jupyter notebook with panel #chemoinformatics #RDKit #memo #panel

As you know Jupyter notebook is very useful tool for data scientist. It can analyze scientific data with nice view. And there are lots of packages for data visualization. And I often use matplotlib and seaborn for my task. However few days ago, I found an interesting package named Panel which is high level appContinue reading “Embed interactive plot in jupyter notebook with panel #chemoinformatics #RDKit #memo #panel”

Example code of DGL for chemoinformatics task #DGL #chemoinformatics #RDKit #memo

There are many publications about graph based approach for chemoinformatics area. I can’t cover all of them but still have interest these area. I think pytorch_geometric (PyG) and deep graph library (DGL) are very attractive and useful package for chemoinformaticians. I wrote some posts about DGL and PyG. Recent DGL is more chemoinformatics friendly soContinue reading “Example code of DGL for chemoinformatics task #DGL #chemoinformatics #RDKit #memo”

Use pytorch for QSAR model building more simply like scikit-learn #pytorch #chemoinformatics #RDKit

I often use pytorch for deep learning framework. I like pytorch because it is very flexible and many recent articles are used it for their implementation. But to build model and train the model, I need to define training method. So it seems nice if I can train pytorch model just calling fit like scikit-learnContinue reading “Use pytorch for QSAR model building more simply like scikit-learn #pytorch #chemoinformatics #RDKit”

Make molecule mesh data #RDKit #chemoinformatics #meshlab

I have an interest to predictive model build with 3D compound information. Pytorch3d and open3d seems attractive package for me. However, to use the package, I need to convert molecular information to 3D data such as pointcloud etc. At first I tried it to use openbabel because recent version of openbabel can convert molecule fromContinue reading “Make molecule mesh data #RDKit #chemoinformatics #meshlab”

Use RDKit from NIM language #RDKit #Nim #memo

Recently I bought a book which title is ‘Nim in Action’ and started to learn NIM language. I never touched language like a nim-lang which is required compile to run the code. I had interest about nim-lang because, many documents say NIM is speedy and efficient, and grammar seems like python. And also, rdkit bindingContinue reading “Use RDKit from NIM language #RDKit #Nim #memo”