# Rust build artifacts
/target/
**/*.rs.bk

# IDE and editors
.idea/
.vscode/
*.swp
*.swo
*~

# OS files
.DS_Store
Thumbs.db

# AI stuff
.claude/
.copilot/
.cursor/
.aider*
.continue/
.windsurf/
.ai/
.ai-cache/
*.ai.md
*-ai-context.txt

# Common AI tool caches
.ai-cache
.llm-cache
.gpt-cache

# Anthropic Claude specific
.claude-history
claude-context.json

# GitHub Copilot
.copilot-chat-history

# AI-generated temporary files
ai-scratch/
ai-temp/

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
#   For a library or package, you might want to ignore these files since the code is
#   intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# poetry
#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

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

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

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

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
.idea/

# VScode
.vscode/

# Project-related stuff
.coverage
benchmark/*/
example/dev
tests/test_data/setup.toml
tests/dummy_f
tests/test_data/clustering/*.contacts

# Third-party stuff
src/haddock-tools
src/pdb-tools
src/ProFit_V3.3
src/fcc
src/dcomplex_single_file
best_by_dockq.pdb
best_by_score.pdb
native_reference.pdb
top_opls_aam.inp
SUMMARY.md
calibration/.Rhistory

# Downloaded data
benchmark5.5.tgz
benchmark5.5/
data/

# Results
results/
benchmark/complexes.txt
paper/jats
