A Molecular Systems MultiToolkit designed to simplify work with molecular models and simulations.

MolSysMT is a core molecular-system library in the MolSysSuite ecosystem. It provides the common molecular model and tools used by client components. Experimental capabilities, including native preparation and interaction analyses, follow the public API stability contract.

Install it

conda install -c uibcdf molsysmt

Use it

import molsysmt as msm

molecular_system = msm.convert('1BRS', selection='molecule_type=="protein"')

msm.info(molecular_system, element='molecule')

index	name	type	n atoms	n groups	n components	chain index	entity index	entity name
0	BARNASE	protein	864	108	1	0	0	BARNASE
1	BARNASE	protein	878	110	1	1	0	BARNASE
2	BARNASE	protein	839	108	1	2	0	BARNASE
3	BARSTAR	protein	693	87	2	3	1	BARSTAR
4	BARSTAR	protein	665	86	2	4	1	BARSTAR
5	BARSTAR	protein	699	89	1	5	1	BARSTAR

msm.view(molecular_system, selection='molecule_index==0')

Citation

Cite MolSysMT through its stable Zenodo concept DOI. For reproducible work, select the DOI of the exact version you used from the Zenodo version history.

• The paper is coming soon… [BibTeX]

• Diego Prada-Gracia & Liliana M. Moreno-Vargas. (2026). MolSysMT (Version 0.23.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.1298752 [BibTeX]