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ChemLink v1.0.0 — Initial stable release

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@PipeJF9 PipeJF9 released this 22 May 23:37
· 138 commits to main since this release
v1.0.0
51c9dd9

ChemLink v1.0.0

First stable release of ChemLink, a modular orchestration platform for computational chemistry on HPC clusters.

Features

  • Docking pipeline — end-to-end automation: active site detection (fpocket), receptor/ligand preparation (MGLTools + AutoGrid4), GPU-accelerated docking (AutoDock-GPU), and results analysis
  • Molecular dynamics pipeline — full GROMACS 2025.4 workflow supporting six biological system types from topology preparation to trajectory analysis
  • Single-node mode — parallel ligand processing with configurable worker count (up to 24 workers tested)
  • Multi-node mode — distributed docking via SLURM Job Arrays across GPU nodes
  • Unified CLI — chemlink docking and chemlink dynamics commands with chemlink doctor for environment verification
  • Reproducibility — timestamped run directories, stats.json per campaign, versioned Conda environments (bio, mgl_legacy)
  • Monitoring — Prometheus + Grafana integration for real-time resource tracking
  • Docker support — containerized execution for isolated environments
  • Test dataset — ready-to-run inputs: receptors (1HSG, 6LU7, 3PTB from RCSB PDB) and ligands (Indinavir, Nirmatrelvir, Benzamidine, Ibuprofen, Aspirin, Caffeine from PubChem)

Validated performance (1 000 ligands)

Mode Duration Throughput
Single-node Opt (24 workers) 54 min 18.5 lig/min
Single-node Min (1 worker) 335 min 3.0 lig/min
Multi-node (3 GPUs, SLURM) 31.6 min 31.6 lig/min

Speedup vs single-node: up to 2.2× with 3 GPUs.

Installation

# Base installation (Python layer + Conda environments)
curl -fsSL https://raw.githubusercontent.com/PipeJF9/chemlink/main/install.sh | bash

# Full installation (includes fpocket, AutoGrid4, AutoDock-GPU, GROMACS 2025.4)
curl -fsSL https://raw.githubusercontent.com/PipeJF9/chemlink/main/install.sh | bash -s -- --full

Quick test

chemlink doctor
chemlink docking --receptor data/test/receptors/1hsg.pdb --ligands data/test/ligands/indinavir.sdf --output data/output/test
Assets 2
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