What is MolSysMT?

MolSysMT -Molecular Systems MultiToolkit - is a core molecular-system library in the MolSysSuite ecosystem. This open-source Python library offers one uniform API for building, repairing, preparing, querying, modifying, analysing and visualising molecular systems, without changing library every time the task changes.

This library was developed to provide a user-friendly interface for computational molecular biology labs, such as the UIBCDF, to use in their research.

MolSysMT does its own work. It has its own molecular model, its own HDF5-based storage format, an experimental structure-preparation pipeline with a native engine for supported templates and profiles. Select engine='MolSysMT' to add missing heavy atoms, terminal cappings or hydrogens and to solvate a system without an external engine. Its precompiled compute kernels cover distances, contacts, neighbour lists, RMSD and superposition, principal axes, PCA, dihedral angles and periodic boundary conditions. SASA, secondary-structure assignment, RMSF and interaction analyses remain experimental; see the API stability registry for symbol-level guarantees.

It is also deliberately open to the rest of the ecosystem. MolSysMT interoperates with other forms — files, libraries and in-memory objects — so a system can arrive or leave in whatever shape the rest of your workflow needs, and so you can hand work over to a specialised tool whenever that is what you want. It was never designed to replicate what MDAnalysis, MDTraj, PDBFixer, OpenMM, ParmEd, RDKit or NGLView already do well. Whenever you use methods or tools from these packages, all credit should be given to their respective authors, developers, maintainers, and contributors.

MolSysMT is an open-source project shared under the MIT license. This means that you have the right to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies without any limitations.

If you have suggestions, improvements, enhancement proposals, if you miss a functionality, or you have identified a bug or a malfunction, feel free to contribute to its development or interact with the authors and contributors by using the MolSysMT public GitHub repository.

When using MolSysMT, it is important to understand that the authors and contributors do not provide any legal warranty or assume any liability of any kind regarding its use and results.

We hope you find it useful!

Diego Prada-Gracia and Liliana M. Moreno Vargas.