The previous couple of pages described creating a SQLite database using the Terminal https://macinchem.co.uk/2023/04/12/using-sqlite-for-exact-search/ and then running exact searches from a Jupyter notebook, python script or ChemDraw
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
A Python Script At the end of the previous page on setting up and accessing a Sqlite datasets from a Jupyter notebook there was and example of
Whilst on most occasions chemical searches involve substructure or similarity searches there are occasions when a simple exact match of a compound identifier (or list
In a recent post Pat Walters highlighted the use of molfeat in a google colab notebook https://colab.research.google.com/github/PatWalters/practicalcheminformaticstutorials/blob/main/mlmodels/QSARin8lines.ipynb. I thought I’d also mention other tools available from
I recently needed a list of all files in a particular folder, actually the folder contained sub-folders also containing files. This tedious task becomes trivial
I’m in the process of updating iBabel and one of the things I’m adding is the option to use some of the newer tools now
Codon is a high-performance Python compiler that compiles Python code to native machine code without any runtime overhead. Typical speedups over Python are on the
There have been some changes with Homebrew which have meant that a few of the scientific applications are no longer available so I’ve decided to
FPsim2 is a new tool for fast similarity search on big compound datasets (>100 million) being developed at ChEMBL. It was developed as a Python3 library
The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists