Navigating the Documentation#

The MolSysMT documentation is organized into complementary sections designed to support users at every stage of their workflow — whether you need a 5-minute quickstart or a deep conceptual understanding.

Quickstart Guide#

If you want an immediate hands-on feeling for MolSysMT, skip directly to the interactive Quickstart tutorial in the Showcase section:

Quickstart Guide
Load a system, inspect basic topological attributes, perform simple selections, and run basic transformations in minutes.

Foundations#

If you are starting a new research project or want to understand the architectural philosophy and data models behind MolSysMT, explore the 8 sections of Foundations step by step:

Entrance: Mission statement, installation, and documentation roadmap.
Molecular System: The internal representation model, structural axes, and attributes.
Native World: Working natively with molsysmt.MolSys, molsysmt.Topology, and molsysmt.Structures.
Language: Mastering the selection syntax, query semantics, and form conversions.
Performance: Parallel execution, Rust kernels, and memory efficiency for large trajectories.
Governance: Standards, data invariants, and error-handling principles.
Support: Supported forms, tier stability guarantees, and diagnostic logging.
Ecosystem: Integration with the broader MolSysSuite stack and third-party ecosystems.

Tools#

When you need to look up function signatures, tutorials, or usage examples for specific tools, consult the Tools section:

Basic: Core operations (get, set, select, convert, build, view, compare).
Build: Structure preparation, missing heavy atoms, cappings, protonation at pH, and solvation.
Structure: RMSD, distances, SASA, radius of gyration, superposition, and dihedrals.
Topology: Bond matrices, covalent paths, sequence extractions, and secondary structure.
Elements: Selection and manipulation by atom, group, component, molecule, or chain.
Third Party: Specialized bridges to OpenMM, MDAnalysis, MDTraj, ParmEd, RDKit, and NGLView.

Cookbook#

If you want to see how multiple tools combine to solve complete scientific tasks, consult the Cookbook. Here you will find practical recipes for multi-step system preparation, solvation pipelines, trajectory alignment, structural fluctuation analysis, and converting complex multi-file trajectories into clean native H5MSM files.

Master Course#

If you want a systematic, step-by-step training curriculum from beginner to advanced mastery, explore The Four Paths of the MolSysMT Master. This comprehensive 156-notebook course covers foundational theory, hands-on tutorials, applied case studies in biophysics and drug design, and advanced software engineering paths.

Showcase#

If you are interested in exploring complex integrations and interactive visualization workflows, browse the Showcase. It features end-to-end demonstration notebooks showing seamless interoperation with OpenMM simulations, MDAnalysis trajectory processing, RDKit chemoinformatics, and 3D web rendering via MolSysViewer and NGLView.

API Documentation#

When you need exact low-level technical specifications, docstring signatures, module internal structures, or developer API details for any function or form adapter, consult the technical API Documentation.

Documentation Formats & Interactivity

Throughout the documentation, you will encounter two complementary page formats:

Conceptual Guides (.md): Narrative MyST Markdown pages explaining architectural principles, design choices, and conceptual frameworks without requiring code execution.
Interactive Notebooks (.ipynb): Executable Jupyter Notebooks with live Python code cells, structured outputs, and 3D web visualizations that you can download and execute in your local Python environment.