Data Analysis

Data Analysis#

This section describes how to analyze MD simulation results and calculate photophysical properties related to FRET using the FAMP pipeline.

All analysis functions are encapsulated in the DataAnalysis class.

Initialization#

To begin analysis, initialize the DataAnalysis class with the following attributes:

  • working_dir: Path to the output directory for analysis results

  • path_sim_results: Path to the directory containing MD output files (.gro, .tpr, .xtc). These file names must match the simulation_name used in the parameters.

  • analysis_parameter: Dictionary with simulation and dye information (see parameter section)

  • macv_label_pars: Dictionary with dye parameters for mACV calculation (see parameter section)

md_analysis = famp.data_analysis.DataAnalysis(
    working_dir="/home/user/famp_project",
    path_sim_results="/home/user/famp_project/simulation1",
    analysis_parameter=analysis_paras,
    macv_label_pars=dye_acv_parameter
)

Step 1: Set Up the Analysis Environment#

Creates the required directory structure and initializes input files.

md_analysis.make_data_analysis_results_dirs()

Step 2: Calculate FRET Parameters from Explicit Dye Trajectories#

This step extracts the inter-dye distances and orientation factors (κ²) from MD trajectories from explicit dyes.

md_analysis.generate_r_kappa_from_dyes()

Output: rkappa.dat file in the directory analysis/explicit_dyes/

Step 3: Calculate FRET Parameters from mACV Model#

If no explicit dye simulation is available, this step calculates FRET observables using the multiple accessible contact volume (mACV) model.

md_analysis.generate_r_kappa_from_macv()

Output: rkappa.dat file in analysis/MACV/ and additional summary data in macv.pkl

Step 4: Simulate FRET Distributions#

Using the rkappa.dat files, FRET distributions and anisotropy decay curves can be simulated with FRETraj.

Example#

import fretraj as ft

macv_bursts = ft.burst.Experiment(
    path="analysis/MACV/",
    parameter=burst_parameter,
    compute_anisotropy=False,
    units="nm"
)

For explicit dye data:

dye_bursts = ft.burst.Experiment(
    path="analysis/explicit_dyes/",
    parameter=burst_parameter,
    compute_anisotropy=True,
    units="nm"
)

Description of the burst_paramter can be found here

Output Overview#

The results of the analysis include:

  • rkappa.dat: Inter-dye distance and κ² over time

  • macv.pkl: Serialized FRET trajectory from mACV

  • dye_bursts.FRETefficiencies: Simulated FRET efficiencies

  • dye_bursts.anisotropy: Anisotropy decay (donor and acceptor channels)

These results can be visualized or directly compared to experimental FRET data.

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