README.md

Bindfit datakit

Bindfit is a binding constant fitting tool designed to work with classical supramolecular titration data obtained from NMR, UV, Fluorescence and other methods.

• 🗒️ Datakit documentation
• 💻 Bindfit Python library GitHub

Example usage

dk reset                                   # Clear any previous outputs
dk init                                    # Initialise the default run
dk load data ./data/nmr11.csv              # Load input data
dk set model "nmr1to1"                     # Set fit model
dk set method "nelder-mead"                # Set fit method
dk set inputParams.k.init 314              # Set initial parameter guess
dk run                                     # Run algorithm
dk show outputParams                       # View optimised parameters
dk show summary                            # View fit summary
dk view fitGraphMatplotlib                 # View fit graph

Development

Requirements

• Docker
• Python (to run CLI)
• open-datakit/cli
• open-datakit/containers

Set up pre-commit hooks

Set up included Flake (flake.nix) with direnv (.envrc) to automatically load development environment.

Install/run pre-commit hooks:

pre-commit install
pre-commit run --all-files

Build execution container

Build base execution container:

# Navigate to python-run-base repository
./build.sh

Build bindfit-datakit container:

# Navigate back to bindfit-datakit repository
cd containers
./build.sh

Install CLI

python -m venv .venv
source .venv/bin/activate
pip install -e /PATH/TO/CLI

dk  # Check CLI is installed

See Usage for command reference.