https://github.com/opendatastudio/bindfit-datakit
Bindfit datakit for opendata.studio
https://github.com/opendatastudio/bindfit-datakit
datakit opendatastudio
Last synced: about 1 year ago
JSON representation
Bindfit datakit for opendata.studio
- Host: GitHub
- URL: https://github.com/opendatastudio/bindfit-datakit
- Owner: opendatastudio
- Created: 2023-05-19T02:18:19.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-23T01:24:57.000Z (over 1 year ago)
- Last Synced: 2025-03-27T21:52:11.986Z (over 1 year ago)
- Topics: datakit, opendatastudio
- Language: Python
- Homepage: https://docs.opendata.studio
- Size: 261 KB
- Stars: 1
- Watchers: 2
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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](https://docs.opendata.studio/)
* 💻 [Bindfit Python library GitHub](https://github.com/opendatastudio/bindfit)
## 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)
* [opendatastudio/cli](https://github.com/opendatastudio/cli)
* [opendatastudio/containers](https://github.com/opendatastudio/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](#usage) for command reference.