Developer Guide

• 2026-09-17: Cluster (n-mer) extraction for MLFF data
• 2026-09-18: Reproducibility, motif selection, many frames
• extract_clusters_step
• Installation
• Contributing
• Usage

Code layout

extract_clusters_step/cluster_sampling.py

The algorithm, free of any SEAMM dependency: molecule_neighbour_graph, grow_connected, unwrap_shifts, classify_motif, bond_index_pairs, extract_nmers and cluster_summary. Unit tested directly in tests/test_cluster_sampling.py (pure numpy) and tests/test_extract_nmers.py (on a synthetic periodic water box).

extract_clusters_step/extract_clusters.py

The seamm.Node: parses the parameters, calls extract_nmers once per requested size sharing one seen set, writes clusters.csv and prints the motif × bin summary.

extract_clusters_step/tk_extract_clusters.py

The dialog; reset_dialog shows only the stratification controls that apply to the chosen scheme.

extract_clusters_step/data/properties.csv

Registers the #ExtractClusters#scan properties with molsystem at import.