Molecular Systems MultiToolkit to make the work with molecular models and simulations easy.

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')

/home/diego/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/nglview/__init__.py:12: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

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', viewer='NGLView')

Citation

Citing the Zenodo DOI of MolSysMT in addition to the scientific paper is a way to ensure that others can reproduce your results, as they will know exactly which version of the software you used.

PaperSoftware

Coming soon…

BibTeX