Changelog

All notable changes to this project will be documented in this file.

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

[Unreleased]

New nci_gadi.config configuration profile for NCI Gadi HPC cluster.
BoltzGen: support for list-valued entities[].file.path and multiple entities so all referenced files are staged as Nextflow path() inputs. Referenced config YAMLs (.yaml/.yml in entities[].file.path, eg for nanobody scaffolds) and the PDB/CIF files they reference internally are collected and staged so BoltzGen’s per-generation random selection over those configs is preserved.
Versioned documentation using mike; docs are now deployed for main (alias: latest), develop (alias: dev), and version tags.

Major project restructure shifting individual workflows into workflows/, each launched via a single main.nf entry point with the --method flag.
--method rfd for RFdiffusion binder design (previously main.nf)
--method rfd_partial for partial diffusion (previously partial.nf)
--method bindcraft for BindCraft (previously bindcraft.nf)
--method boltzgen for BoltzGen (previously boltzgen.nf)
--method boltz_pulldown for Boltz Pulldown (previously boltz_pulldown.nf)
Modules reorganised into modules/local/ with workflow-specific subdirectories (rfd/, bindcraft/, boltzgen/, common/).
Extracted common Boltz-2 refolding and scoring logic into BOLTZ_REFOLD_SCORING subworkflow (subworkflows/local/boltz_refold_scoring.nf).

BindCraft (workflows/bindcraft.nf): omitting --hotspot_res no longer fails in validateHotspotRes with Unknown method invocation 'trim' on Boolean type.
rmsd4all.py: cap worker processes to the number of pairs so single-pair comparisons (e.g. RFD3_RMSD with one design vs one refold) no longer spawn a large Pool and appear to hang; sequential path is used for one pair with progress logged.
rmsd4all.py: add --max-structural-iterations (default 100). Biotite's refinement loop uses max_iterations=inf by default and only stops when anchors stabilize; with 3di the anchor set can fail to converge (oscillate) so the loop never exits. Capping iterations fixes the hang; 0 = no limit.
rmsd4all.py: fix use of array_length (method) as if it were an attribute; use len() for atom counts.

New BoltzGen pipeline.
Refold binder designs with Boltz, with post-AF2ig filtering and RMSD analysis of predicted complex and binder monomer.
Added DOI (Zenodo) badge to README.md, added CITATION.cff.
Some parameter validation for bindcraft.nf.
Write params.json to output directory.

A plugin system for filtering designs based on calculated metrics.
--rfd_filters parameter to apply filters to RFDiffusion backbones (e.g., --rfd_filters "rg<25").
Initial filter plugin for radius of gyration (rg).
Integration of BindCraft-derived scoring of designs, as extra_scores.tsv. This adds metrics including:
Interface score, shape complementarity, dG, and dSASA.
Secondary structure percentages (helix, sheet, loop) for the binder and interface.
Unrelaxed and relaxed clash scores.
Hotspot and target RMSD.
Sequence-based metrics like extinction coefficient.
--pmpnn_omit_aas flag to exclude certain amino acids from designs (default 'CX').
--rfd_compress_trajectories flag to gzip RFDiffusion traj/*.pdb files (default true).

Filtering results are now saved to a subdirectory named after the pipeline step (in filtering/rfdiffusion/).
The score merging script (merge_scores.py) was improved to be more robust and handle an arbitrary number of score files.
Use more lightweight container for get_contigs.nf and renumber_residues.nf modules.

The gpu_device parameter is now correctly passed to the partial diffusion process, allowing proper GPU selection.

Change dl_binder_design output filenaming (include "_mpnn{n}" suffix)
Change RFDiffusion config handling when unspecified
Docs: Add APPTAINER_TMPDIR and NXF_APPTAINER_CACHEDIR advice to M3-specific docs

Initial version with RFDiffusion->ProteinMPNN->af2_initial_guess binder design and partial diffusion pipelines.