Dependency Management#

MolSysMT seamlessly interoperates with dozens of third-party libraries across the structural biology ecosystem without forcing users to install bloated monolithic environments.

Hard vs. Soft Dependencies#

Dependency status is managed centrally through DepDigest (https://www.uibcdf.org/depdigest) via molsysmt._depdigest:

  • Hard Dependencies: Core essential libraries required for basic operation (e.g. NumPy, SciPy, PyUnitWizard, ArgDigest, SMonitor).

  • Soft Dependencies: Optional feature-enabling packages (e.g. MDTraj, OpenMM, MDAnalysis, ParmEd, PyTraj, NGLView, PDBFixer, BioPython, Plotly).

Lazy Imports and Capability Enforcement#

  • Lazy Import Policy: Soft dependencies are never imported at top-level module evaluation. They are imported inside functions or methods on demand.

  • The @dep_digest Decorator: Functions requiring optional libraries use @dep_digest(library) to verify availability before execution, offering clear installation instructions if missing.

  • Capability Inspection: Users can inspect installed ecosystem capabilities dynamically via molsysmt.configure.show_all_capabilities.