mdforge v0.2.1

Maintenance + feature release.

New

• Ramachandran analysis — φ/ψ before-vs-after MD, ensemble density, favoured-region fractions.
• Richer H-bond outputs — per-pair occupancy CSV, donor/acceptor table, top-occupancy figure, and effective H-bond lifetime from the autocorrelation.
• Author ORCID added to citation metadata.

Brings the toolkit to 25 built-in analyses. Archived to Zenodo under concept DOI 10.5281/zenodo.21265946.

🤖 Generated with Claude Code

mdforge v0.2.0

First tagged release of mdforge — a reusable, extensible, reproducible framework for analysing GROMACS molecular dynamics simulations of arbitrary biomolecular systems.

Highlights

• Point-at-a-directory: recursive file discovery + validation.
• Automatic system detection (protein / ligand / DNA / RNA / membrane / ions / multi-chain) and auto-selection of applicable analyses (--plan explains why).
• 24 built-in analyses: RMSD, RMSF, Rg, SASA, structural descriptors, native contacts (Q), contact maps, DSSP, RIN, PCA + free-energy landscape, DCCM, clustering, COM, H-bonds, salt bridges, energies, convergence (RMSIP/block-avg), statistics, ProLIF, MM/PBSA workflow, and system-specific interface / ligand / nucleic modules — plus an example plugin.
• Plugin architecture and YAML config workflows.
• Reproducibility manifest (library versions, git commit, input fingerprints, seeds, params, runtimes).
• Publication output: 300-dpi PNG + vector PDF; Markdown / HTML / PDF reports.
• Scales via frame streaming + cached solute-only trajectory (100 GB+).
• Packaging (mdforge CLI), unit tests, Dockerfile, GitHub Actions CI.

Install

pip install -e ".[all]"
mdforge analyze --input /path/to/gromacs_sim --output results/

🤖 Generated with Claude Code