# =============================================================================
# Python
# =============================================================================
__pycache__/
*.py[cod]
*$py.class
*.so
*.egg
*.egg-info/
.eggs/
MANIFEST
pip-wheel-metadata/
dist/
build/
benchmark/
benchmark2/

# =============================================================================
# Virtual environments
# =============================================================================
.env
.venv
env/
venv/
ENV/
myenv/

# =============================================================================
# Testing & coverage
# =============================================================================
.pytest_cache/
.tox/
.coverage
.coverage.*
coverage.xml
htmlcov/

# =============================================================================
# Type checking & linting
# =============================================================================
.mypy_cache/
.pytype/
.ruff_cache/

# =============================================================================
# Pre-commit
# =============================================================================
.pre-commit-cache/

# =============================================================================
# IDEs & editors
# =============================================================================
.vscode/
.idea/
*.swp
*.swo
*~

# =============================================================================
# OS
# =============================================================================
.DS_Store
Thumbs.db
Thumbs.db:encryptable
desktop.ini

# =============================================================================
# Project-specific: temporary / work directories
# =============================================================================
try/
demo/

# =============================================================================
# Project-specific: generated docking outputs
# =============================================================================

# Prepared PDBQT files (generated from PDB/SDF/MOL2 inputs)
*.pdbqt

# AutoDock result files
*.dlg

# Docking output PDB files
*_out.pdb

# Per-run log files
*_log.txt

# Vina split SDF output
*_ligand_*.sdf

# Docking results aggregate
docking_results.csv

# Completed-combinations tracker (np_dock)
*_completed.txt

# Output folder created by np_dock
out/

# =============================================================================
# Project-specific: generated mutation outputs
# =============================================================================

# Cleaned PDB files
*_clean.pdb

# Generated mutation CSV files
*_mutations.csv
*_mutations_all.csv
*_ddG.csv
*_ddG_sorted.csv
*_double_ddg.csv
*_double_ddg_sorted.csv
*_triple_ddg.csv
*_triple_ddg_sorted.csv

# Mutant PDB folder (generate_mutants output)
mutation_*/

# Mutant paths text file
*_mutants.txt

# Timestamped backups created by backup()
backups/
