analysis

Author(s):

Nuno P. Fernandes

Year:

2026

Copyright:

GNU Public License v3

Added in version 1.0.0.

This module contains functions for performing structural analysis on an ensemble of protein conformations, outputting an interactive graphical dashboard.

Example applications

Analyze an ensemble in trajectory format

The ensemblify.analysis.analyze_trajectory function can be used to create an interactive analysis graphical dashboard from a conformational ensemble in .xtc trajectory format.

For example, we can analyze an ensemble of Histatin5 (Hst5), an intrinsically disordered peptide with 24 aminoacid residues.

Assuming that the path to the required trajectory and topology files are assigned to the variables HST5_TRAJ_PATH and HST5_TOP_PATH, respectively, and that your desired trajectory ID is ‘Hst5’, you can run:

>>> import ensemblify.analysis as ea
>>> ea.analyze_trajectory(HST5_TRAJ_PATH, HST5_TOP_PATH, 'Hst5')

Available Functions

analyze_trajectory

Calculate structural data and create interactive figures for given trajectory and topology files.

calculate_analysis_data

Calculate structural data for each given pair of trajectory,topology files.

create_analysis_figures

Create interactive figures given analysis data for one or more pairs of trajectory,topology files.

calculate_ramachandran_data

Calculate a dihedral angles matrix from trajectory and topology files.

calculate_contact_matrix

Calculate a contact frequency matrix from a trajectory and topology files.

calculate_distance_matrix

Calculate an alpha carbon average distance matrix from a trajectory and topology files.

calculate_ss_assignment

Calculate a secondary structure assignment matrix from a trajectory and topology files.

calculate_ss_frequency

Calculate secondary structure assignment frequencies from a trajectory and topology files.

calculate_metrics_data

Calculate structural metrics for each frame of a trajectory.

create_ramachandran_figure

Create a ramachandran plot Figure from a calculated dihedral angles matrix.

create_contact_map_fig

Create a contact map Figure from a calculated contact matrix.

create_distance_matrix_fig

Create a distance matrix Figure from a calculated distance matrix.

create_ss_frequency_figure

Create a secondary structure frequency Figure from a secondary structure assignment frequency matrix.

create_metrics_traces

Create Plotly Box, Histogram and Scatter (KDE) traces from calculated structural metrics data to be used in the creation of a Structural Metrics Figure.

create_metrics_fig

Create a Structural Metrics Figure from previously created Box, Histogram and Scatter traces.

create_single_metrics_fig_directly

Create a Structural Metrics Figure for a single trajectory, directly from its calculated metrics data and trajectory ID.

Submodules