SEAMM Extract Clusters Plug-in¶
A SEAMM plug-in for extracting molecular clusters (trimers, tetramers, … larger n-mers) from a condensed-phase, typically periodic, configuration as unwrapped, non-periodic structures – e.g. many-body training data and diagnostics for machine-learned force fields.
Free software: BSD-3-Clause
Documentation: https://molssi-seamm.github.io/extract_clusters_step/index.html
Features¶
Clusters are connected subgraphs of a molecular contact graph (molecules are in contact if their contact atoms are within a cutoff, minimum image), so chains, rings and stars all occur – not just the most compact cluster.
Any cluster size, and several sizes per frame (e.g.
3, 4).Works on many frames in one step – all configurations of a system holding a trajectory, or any standard SEAMM structure selection – so no loop is needed and the clusters land in one system.
Stratification so the set is flat in a spread coordinate (radius of gyration or largest centroid separation), with bin edges from equal quantiles of a pilot sample or given explicitly; optional balancing over the contact-graph motif.
Clusters are unwrapped across the periodic boundary, centred, non-periodic, with molecules and bonds intact.
Provenance on every configuration: unique names
<frame>_<seed>_<m1-m2-...>and#ExtractClusters#scanproperties (size, spread, motif, contacts, source molecules) that survive SDF/extxyz export; aclusters.csvsummary per step.Works on any cell (orthorhombic fast path via a periodic KD-tree; exact minimum image otherwise) and on non-periodic sources.
Acknowledgements¶
This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.
Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award ACI-1547580
Development Team¶
Paul Saxe <psaxe@molssi.org> (Lead)
Why don’t you join the team? Become a contributor!