Examples

Here you can find worked-out example scripts that demonstrate how to use MDSA-tools for clustering, visualization, and analysis of molecular dynamics data.

Circos Example

Circos example visualization
MDcircos (PCA-weighted contacts)

Data Generation Example

Data generation workflow
Data generation (H-bond matrices)

Importer Example

Import from cpptraj
cpptraj (series) → residue×residue H-bond matrices

Contourplots

Example systems
Contours on PCA/UMAP embeddings

Cohesion (RMSD) Analysis

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Cohesion over time (sliding & shrinking windows)

Clustering and Dim-Red Examples

Example of clustering analysis
Feature matrix & exploratory clustering

Hbond Replicate Maps

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Replicate maps (discrete H-bond labels)

UMAP embedding visualization example

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UMAP embeddings (per-frame labelling)