MolSysSuite

MolSysSuite is an integrated open-source collection of computational biophysics software packages developed at UIBCDF. Designed to cover structural molecular modeling, trajectory manipulation, 3D visualization, AI-assisted workflows, topological analysis, pharmacophore identification, elastic network dynamics, and database query management, MolSysSuite provides a unified ecosystem for molecular simulations and structural bioinformatics.

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MolSysMT

MolSysMT is the foundational molecular systems, topology, and trajectory kernel of the suite. It provides a form-agnostic bridge across third-party Python structural biology libraries (MDTraj, OpenMM, MDAnalysis, ParmEd, PyTraj, BioPython, OpenFF, RDKit, NetworkX), zero-copy array operations, a declarative selection engine, and unit-safe data manipulation.

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MolSysViewer

MolSysViewer is the native 3D WebGL visualization widget of the suite. Engineered for interactive Jupyter Notebook, JupyterLab, and web application environments, it enables high-performance 3D rendering, custom molecular representations, shape overlays, dynamic selections, and synchronized session state management.

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MolSys-AI

(Under development)

MolSys-AI is the AI-assisted agentic assistant and workflow automation package of the suite. It enables natural language query interpretation, automated simulation protocol assembly, intelligent trajectory diagnostics, and agent-driven biophysical analysis.

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TopoMT

(Under development)

TopoMT is the topological analysis and molecular connectivity package of the suite. It provides covalent graph representations, contact network calculations, secondary structure topology assignment, and structural graph invariants.

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PharmacophoreMT

(Under development)

PharmacophoreMT is the 3D pharmacophore modeling package of the suite. It enables spatial feature extraction, ligand interaction field mapping, pharmacophoric query construction, and high-throughput virtual screening matching.

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ElastNetMT

(Under development)

ElastNetMT is the elastic network modeling and normal mode analysis package of the suite. It implements Anisotropic Network Models (ANM), Gaussian Network Models (GNM), coarse-grained vibrational dynamics, and conformational flexibility predictions.

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Sabueso

(Under development)

Sabueso is the biological database query and metadata parser agent of the suite. It automates information retrieval, sequence-structure mapping, entity identification, and metadata synchronization across major structural repositories (PDB, UniProt, AlphaFold DB).

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Infrastructure and Developer Tooling

MolSysSuite relies on a dedicated suite of core software engineering and governance libraries developed to ensure strict numerical safety, lazy loading, boundary validation, and testing integrity across all suite packages.

PyUnitWizard

PyUnitWizard standardizes physical unit handling, dimensional consistency checks, and Fast-Track unit bypass across Python scientific packages. It ensures seamless inter-conversion between unit libraries (Pint, OpenMM units, PyUnitWizard native quantities) and zero-overhead numerical extraction for high-performance array operations.

ArgDigest

ArgDigest provides a declarative public boundary validation framework for Python packages. By decorating public API functions with @digest, ArgDigest validates argument contracts, sanitizes input types, handles default values, and enables explicit trusted delegation without boilerplate validation logic inside internal methods.

DepDigest

DepDigest is the centralized dependency management infrastructure for MolSysSuite. It manages soft dependency registration, lazy loading, and runtime package availability inspection, ensuring that optional third-party packages are never imported at top-level load time.

SMonitor

SMonitor is an execution monitoring, structured diagnostics, and warning catalog system. It provides catalog-driven warning protocols, diagnostic tracing, and execution monitoring to maintain operational transparency and error reporting across suite packages.

Pytest-Receptor

Pytest-Receptor provides testing infrastructure, fixtures, and deterministic verification frameworks tailored for receptor-aware computational biophysics workflows and structural modeling test suites.