Delayed-reactant-labeling

Delayed Reactant Labeling (DRL) is a method which allows kinetic information to be extracted from experiments on a mass spectrometer. By coupling the mass spectrometer to a TIMS unit, also different diastereomers can be modeled.

This module can:

1. extract the rate equations of a chemical system from the reaction steps,

2. model the rate equations using a Radau ODE solver, to ensure accuracy and efficiency of the model,

3. use the Nelder-Mead algorithm with adapted parameters to find an optimal solution in a highly dimensional space,

4. perform multiple analyses of a system from different starting positions and,

5. visualize the model in different ways.

To get started check out the Getting started section for further information.

Contents

• Getting started
• Predict
  • DRL
    • predict_concentration()
    • predict_concentration_Euler()
    • calculate_step()
    • calculate_jac()
  • example
• Optimize
  • RateConstantOptimizerTemplate
    • create_prediction()
    • calculate_curves()
    • calculate_errors()
    • weigh_errors()
    • calculate_total_error()
    • optimize()
    • optimize_multiple()
    • load_optimized_model()
  • OptimizedModel
  • OptimizedMultipleModels
    • get_model()
  • Example
• Visualize
  • VisualizeModel
    • save_image()
    • plot_optimization_progress()
    • plot_grouped_by()
    • plot_path_in_pca()
    • plot_enantiomer_ratio()
    • plot_rate_over_time()
    • plot_rate_sensitivity()
    • plot_error_all_runs()
    • plot_ratio_all_runs()
    • plot_x_all_runs()
    • plot_biplot_all_runs()
• Extensive example
  • Experimental data
  • Defining the error metric
  • Utilizing normal kinetics
  • Defining the model
  • Optimizing the model
  • Visualize
    • Model progression
    • Model output
    • Heat maps
    • Error curves
    • Multiple guesses
• Implementation details
  • Rate equations
  • Estimating the Jacobian
  • Explict Euler formula