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Category: Hints and Tutorials

Tutorials, Hints, Tips and Tricks

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Some new ways to speed RDKit calls up using multiple threads

11 February 202411 February 2024 chris

Another tutorial from Greg Landrum, focussing on how to take advantage of modern multithreaded CPUs. https://greglandrum.github.io/rdkit-blog/posts/2024-02-11-more-multithreading.html Looking at Generating fingerprints, Molecular standardization, Conformer generation, RMSD

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Downloading ligands from the PDB

24 January 202424 January 2024 chris

A previous post described Getting Ligand ID for multiple PDB files, using the PDBe API (https://www.ebi.ac.uk/pdbe/pdbe-services). The result is a csv file containing the ligand

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Another PDB tools Jupyter Notebook

22 January 202422 January 2024 chris

The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)

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Hints and Tutorials Jupyter Notebook

Getting Ligand ID for multiple PDB files

21 January 202422 January 2024 chris

The Protein Data Bank (https://www.rcsb.org) is an invaluable repository of 3D biomolecular structures. As of writing the database contains 214,791 structures (X-ray, Cryo-EM and NMR)

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Hints and Tutorials Macinchem Blog Science Apps

Chemprop: A Machine Learning Package for Chemical Property Prediction

28 December 202329 December 2023 chris

I know a few folks have been using this, good to see this publication DOI. Chemprop implements the D-MPNN architecture and offers simple, easy, and

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Hints and Tutorials Jupyter Notebook Macinchem Blog

Scikit-Mol – Easy Embedding of RDKit into Scikit-Learn

20 December 202320 December 2023 chris

Scikit-Mol originated during an RDKit hackathon and has gradually evolved into a tool that I looks extremely useful. Scikit-Mol is related to Scikit-learn and molecules,

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Hints and Tutorials Macinchem Blog

RDKit MolsMatrixToGridImage

6 December 202312 November 2024 chris

If you need to display molecules and associated data in a grid then Jeremy Monat’s MolsMatrixToGridImage is exactly what you need. To underline just how

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Hints and Tutorials Macinchem Blog

An interesting Cheminformatics blog

22 November 202322 November 2023 chris

Just stumbled across this blog on cheminformatics, machine learning (ML) and data science projects in drug discovery. Lots of useful code! Data in Life https://jhylin.github.io/Data_in_life_blog/

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Hints and Tutorials Uncategorised

Psi4 on Apple Silicon

17 November 202317 November 2023 chris

A couple of folks have asked about the availability of Psi4 on Apple Silicon From Wikipedia Psi is an ab initio computational chemistry package originally written by the research

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Applescript Hints and Tutorials Macinchem Blog

Applescripts updated

29 October 202329 October 2023 chris

I’ve started adding a selection of useful applescripts, code can be copied from page or script downloaded. https://macinchem.org/category/applescript/ Applescript Description Print Clipboard This AppleScript prints

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