# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# Apple crap
.DS_Store

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
bioconda_recipe/
publish.sh
*.tgz
artifacts/publication_figures/

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
pytest-output*.txt
.venv_colab/
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/
random_linear_peptide_*.pdb
random_linear_peptide_*.pqr
custom_peptide_*.pdb
custom_peptide_*.nef
custom_peptide_*.fasta
test_*.pdb
test.pdb
out.pdb
reproduce_*.py
fix_*.py
decoys/
decoy_test/
bmr6457.json
1d3z_mr.str
1D3Z.pdb
1UBQ.pdb
sfti1.pdb
tmp/
benchmarks/bench_results.csv

# Large binary artifacts
*.mrc
*.npz

# Runtime benchmark outputs (generated by scripts/experimental_benchmark.py)
artifacts/benchmarks/*.pdf
artifacts/benchmarks/*.json
artifacts/benchmarks/*_clean.pdb

# Runtime-downloaded PDB files (fetched by BMRBAPI.download_pdb)
examples/*.pdb

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# IDEs such as Pycharm
.idea

# Sphinx documentation
docs/_build/
paper/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# celery
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyderworkspace

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# Scratch directory
scratch

# Machine Learning Models
*.pt
*.joblib
*.h5
*.onnx

# AI crap
.gemini/
_version.py
