kinalite 0.0.5

A simple package for VTNA analysis of chemical reactions

Kinalite - Simple VTNA

Kinalite is a Python package that provides a simple API for running Variable Time Normalization Analysis on chemical data.

Requirements

Python 3.6+

Installation

Kinalite can be installed with pip:

$ pip install kinalite

Usage

To use kinalite you will need to provide two DataFrames with experiment data to compare. Kinalite will then use VTNA to find a best order for the first experiment.

Reading data

The first step is using the Pandas package to convert your experiment data into DataFrames:

import pandas as pd

# supply an absolute or relative path to CSV files
experiment_a_data = pd.read_csv('./data/experiment_a.csv')
experiment_b_data = pd.read_csv('./data/experiment_b.csv')

These CSV files need to have a single header row and time in the first columns. All values, including Time, are numbers. For example:

Time	C	A	B	D	cat
0	0	1	1	0	0.01
5	5.45911E-05	0.997274	0.997328	0.00267175	0.00994541
10	5.45909E-05	0.994555	0.99461	0.0053903	0.00994541
15	5.45907E-05	0.991844	0.991899	0.00810143	0.00994541
20	5.45906E-05	0.98914	0.989195	0.0108052	0.00994541

Running VTNA

Next you can use your converted data to create an Experiment and run VTNA. You must also provide the column indexes for the substrate and product, starting at 0 (Time is column index 0):

import pandas as pd
from kinalite.experiment import Experiment

# supply an absolute or relative path to CSV files
experiment_a_data = pd.read_csv('./data/experiment_a.csv')
experiment_b_data = pd.read_csv('./data/experiment_b.csv')

# create an experiment and supply the column indexes for the substrate and product
experiment = Experiment('A', [experiment_a_data, experiment_b_data], substrate_index=2, product_index=4)
# run VTNA and print out the best order
result = experiment.calculate_best_result()
print('Order in A: ', result.order)

Plotting data

Kinalite provides some plotting methods to help visualize the results of running VTNA:

from kinalite.plots import plot_experiment_results

plot_experiment_results(experiment)

Example Script

There is also an example script with a comparison of multiple sets of data: kinalite_example/main.py