Project Roadmap

March 23, 2026 ยท View on GitHub

Completed (v1.0.0)

  • Topology Module Reorganization: Consolidated api/ and core/ into unified topology/ module
  • Simulation Module: New simulation/ package with config, base, md, remd modules
  • CLI Module: New cli/ package with unified entry points
  • Utils Reorganization: Snake_case naming, cleaned up deprecated files
  • Data Cleanup: Removed deprecated scripts, organized templates
  • Analysis Reorganization: Moved REMD scripts, converted notebooks to Python
  • Vermouth 0.14.0+ Compatibility: Updated for latest Martinize2
  • MDTraj Integration: Replace DSSP with MDTraj for secondary structure
  • Type Annotations: Full type hints using Python 3.12+ syntax
  • MIT License: Added open-source license
  • Testing Framework: Comprehensive test suite with pytest (137 tests)
  • Checkpoint Support: Save/resume simulations
  • Constraint Tolerance: Configurable in .inp files
  • Anisotropic Position Restraints: x,y,z restraint support
  • PDB Validation: Input structure compatibility checking with detailed error reporting
  • New Contact Types: Contacts6_12, Contacts10_12
  • Parameter Searching: Automated parameter optimization via FESAnalyzer.parameter_sweep()
  • Tutorial update: Update tutorials for new CLI
  • Contacts Generation: The contacts are different between different versions
  • Analysis Module: Comprehensive analysis tools including dRMS analysis, MBAR free energy calculation, REMD exchange ratio, and trajectory extraction
  • Multi-EXP System Support: Fixed global parameters bug (beta, C1, C2) by hardcoding values into energy expressions
  • Command-line Fix: Correct handling of dash-prefixed parameters in -other_params (e.g., "-nt")

In Progress / Planned