Metadata-Version: 2.4
Name: qubodock
Version: 0.1.1
Summary: QUBO docking tools (build J, solve, align, rmsd, apply R,t).
Author: Pei-Kun Yang
License: MIT License
Project-URL: Homepage, https://github.com/peikunyang/02_QUBO_Dock
Project-URL: Documentation, https://peikunyang.github.io/02_QUBO_Dock
Project-URL: Source, https://github.com/peikunyang/02_QUBO_Dock
Project-URL: Issues, https://github.com/peikunyang/02_QUBO_Dock/issues
Keywords: QUBO,docking,PyTorch,computational-chemistry
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.20
Provides-Extra: gpu
Requires-Dist: torch>=2.2.0; extra == "gpu"

# qubodock 0.5.6

Silent CLIs for QUBO docking pipeline.

## Commands
- `qubodock-buildj protein.pdb [options]` → write `j.txt` and `grid_points.txt`
- `qubodock-solve j.txt [options]` → write `solution_bits.txt` (+ optional `active_points.txt`) and `<out>.time.txt`
- `qubodock-align ligand.pdb active_points.txt protein.pdb [options]` → write `placements.txt` and `<placements-out>.time.txt`
- `qubodock-rmsd placements.txt ligand_model.pdb ligand_exp.pdb [options]` → write `placements_rmsd.txt` (sorted ascending by default)
- `qubodock-applyrt ligand_model.pdb placements(_rmsd).txt --pose-index K --out pose_K.pdb` → write transformed ligand

All tools are **silent (no stdout)**; errors only go to stderr.

See `--help` on each command for full list of options and defaults.
