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Changelog

All notable changes to PRISM will be documented here.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.2.0] - 2024-10-25

Added

  • PMF Module: Complete umbrella sampling and WHAM analysis workflow
  • Automated SMD generation
  • Umbrella window setup and execution
  • WHAM analysis with bootstrap error estimation
  • Binding free energy calculations
  • Batch Processing: High-throughput virtual screening support
  • Parallel system building
  • Batch trajectory processing
  • Multi-system analysis and comparison
  • Interactive Visualization: HTML-based contact analysis
  • 2D/3D interactive contact maps
  • Drag-and-drop interface
  • High-resolution image export
  • Trajectory Processing: PBC artifact correction
  • DCD to XTC conversion
  • Automatic centering and wrapping
  • Batch processing support
  • Force Field Support: Added MMFF, MATCH, and Hybrid options
  • Configuration System: YAML-based configuration files
  • Template export functionality
  • Parameter validation
  • Configuration inheritance

Changed

  • Improved Protein Preparation: Enhanced metal ion handling
  • Smart mode for selective metal retention
  • Distance-based filtering
  • Better artifact removal
  • Enhanced Error Messages: More informative error reporting
  • Updated Documentation: Comprehensive tutorials and examples
  • Performance: Optimized ligand parameterization speed

Fixed

  • Issue with OPLS-AA force field generation
  • Box size calculation for large systems
  • Ion concentration accuracy
  • Trajectory analysis memory usage

[1.1.0] - 2024-08-15

Added

  • Analysis Module: Comprehensive trajectory analysis tools
  • RMSD/RMSF calculations
  • Contact frequency analysis
  • Hydrogen bond detection
  • SASA calculations
  • Multiple Force Fields: Support for additional ligand force fields
  • OpenFF (Open Force Field)
  • OPLS-AA (via LigParGen)
  • CGenFF (CHARMM)
  • Command-Line Interface: Full CLI for all operations
  • Progress Indicators: Real-time build progress display

Changed

  • Refactored builder architecture for modularity
  • Improved GROMACS version detection
  • Enhanced water model selection

Fixed

  • GAFF2 parameter generation edge cases
  • Solvation box shape issues
  • MDP file generation for CHARMM force fields

[1.0.0] - 2024-06-01

Added

  • Initial Release: Core system building functionality
  • Protein-ligand system construction
  • GAFF/GAFF2 force field support
  • AMBER protein force fields
  • Automated solvation and neutralization
  • MDP file generation
  • GROMACS integration
  • Documentation: User guide and API reference
  • Examples: Basic tutorials and examples

[0.9.0] - 2024-04-15 (Beta)

Added

  • Beta testing version
  • Core PRISMBuilder class
  • Basic force field generation
  • Protein cleaning utilities

Known Issues

  • Limited force field options
  • No analysis tools
  • Documentation incomplete

Planned Features

[1.3.0] - Planned Q1 2025

  • MM/PBSA Module: Binding energy calculations
  • Mutation Analysis: Automated mutation scanning
  • Enhanced Visualization: Advanced 3D visualization
  • Machine Learning Integration: ML-based predictions
  • Cloud Computing: AWS/GCP integration

[2.0.0] - Planned Q3 2025

  • Multi-Ligand Support: Handle multiple ligands
  • Membrane Proteins: Automated membrane system building
  • Alchemical Free Energy: FEP/TI support
  • Enhanced PMF: Multiple reaction coordinates
  • Web Interface: Browser-based interface

Version History Summary

Version Release Date Major Features
1.2.0 2024-10-25 PMF, Batch Processing, Visualization
1.1.0 2024-08-15 Analysis Tools, More Force Fields
1.0.0 2024-06-01 Initial Release
0.9.0 2024-04-15 Beta Version

Upgrade Guide

From 1.1.0 to 1.2.0

Breaking Changes: None

New Features: 

# New PMF functionality
import prism
results = prism.run_pmf_workflow("md_dir", "pmf_output")

# New batch processing
prism.batch_process_trajectories(trajectories, "output", "topology.tpr")

# New visualization
prism.visualize_trajectory("traj.xtc", "system.gro", "ligand.sdf")

Deprecated: Nothing deprecated

From 1.0.0 to 1.1.0

Breaking Changes: None

New Features: 

# Analysis module
analyzer = prism.analyze_trajectory("system.gro", "traj.xtc")

# Additional force fields
system = prism.system(
    "protein.pdb", "ligand.sdf",
    ligand_forcefield="openff"  # New option
)

Migration Notes

Configuration Files

1.2.0 introduces YAML configuration files. Old command-line arguments still work:

# Old style (still works)
system = prism.system("protein.pdb", "ligand.mol2",
                      forcefield="amber99sb",
                      water_model="tip3p")

# New style (recommended)
system = prism.system("protein.pdb", "ligand.mol2",
                      config="my_config.yaml")

Analysis

The analysis module API is stable but new functions are added:

# 1.1.0
analyzer.calc_rmsd()
analyzer.calc_contacts()

# 1.2.0 (added)
analyzer.calc_dihedral()
analyzer.calc_clustering()

Reporting Issues

Found a bug or regression?

  1. Check if it's already reported: GitHub Issues
  2. Search discussions: GitHub Discussions
  3. Create new issue with:
  4. PRISM version (prism.get_version())
  5. Python version
  6. Operating system
  7. Minimal example to reproduce

Contributing

For contributions, please open an issue or pull request on GitHub.

Full Changelog: github.com/AIB001/PRISM/blob/main/CHANGELOG.md

Last Updated: October 25, 2024