Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.
Project description
ClopHfit
This package provides a command line interface for fitting pH titration or binding assay data for macromolecules, such as fluorescence spectra. With this tool, users can easily analyze their data and obtain accurate fitting results.
- Version: "0.6.0"
Installation
You can get the library directly from PyPI:
pip install clophfit
or with pipx:
pipx install clophfit
Usage
You can check out the documentation on https://darosio.github.io/ClopHfit for up to date usage information and examples.
CLI
ClopHfit provides several command line interface tools for fitting and processing data.
prtecan
Extract and fit titrations from a list of Tecan files collected at various pH or chloride concentrations:
clop prtecan list.pH -k ph --scheme ../scheme.txt --dil additions.pH --norm
--out prova2 --Klim 6.8,8.4 --sel 7.6,20
Use the --no-weight option to reproduce an older pr.tecan version.
eq1
Predict chloride dissociation constant K_d at a given pH:
clop eq1 --help
prenspire
Parser for EnSpire (PerkinElmer) file:
clop prenspire file.csv -out folder
Destination folder (default: "./Meas") will contain for each Measurement:
- a table (csv) in wide tabular form e.g. <lambda, A01, ..., H12>;
- corresponding graphical (png) representation of spectra from all wells.
Python
ClopHfit can be imported and used as a Python package. The following modules are available:
clophfit.prenspire - parser for EnSpire (PerkinElmer) files
clophfit.prtecan - perform fitting of pH titration or binding assay data
clophfit.binding - perform fitting of macromolecule binding assay data
To use clophfit in your python:
from clophfit import prenspire, prtecan, binding
Features
- Plate Reader data Parser.
- Perform non-linear least square fitting.
- Extract and fit pH and chloride titrations of GFP libraries.
- For 2 labelblocks (e.g. 400, 485 nm) fit data separately and globally.
- Estimate uncertainty using bootstrap.
- Subtract buffer for each titration point.
- Report controls e.g. S202N, E2 and V224Q.
- Correct for dilution of titration additions.
- Plot data when fitting fails and save txt file anyway.
License
We use a shared copyright model that enables all contributors to maintain the copyright on their contributions.
All code is licensed under the terms of the revised BSD license.
Contributing
If you are interested in contributing to the project, please read our contributing and development environment guides, which outline the guidelines and conventions that we follow for contributing code, documentation, and other resources.
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