.gitignore

# Editors
**/.vscode/
.idea/
Pipfile
# Vagrant
.vagrant/

# Mac/OSX
.DS_Store

# Windows
Thumbs.db

_build/
# Source for the following rules: https://raw.githubusercontent.com/github/gitignore/master/Python.gitignore
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# 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

# 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
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

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

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
cluster_venv/
ENV/
env.bak/
venv.bak/
env_310/
pyenv3.10/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

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

# All benchmark results
benchmark_data/all_uniprots/clustering_results/swarm_plots/*
benchmark_data/all_uniprots/clustering_results/dendrograms/*
benchmark_data/all_uniprots/clustering_results/*
benchmark_data/all_uniprots/ca_distances/*
benchmark_data/all_uniprots/distance_differences/all_conformers/*
benchmark_data/all_uniprots/distance_difference_maps/*
benchmark_data/updated_mmcifs/*
benchmark_data/alphafold_mmcifs/*

# Exceptions to keep folders getting committed
!benchmark_data/all_uniprots/clustering_results/swarm_plots/.gitkeep
!benchmark_data/all_uniprots/clustering_results/dendrograms/.gitkeep
!benchmark_data/all_uniprots/clustering_results/.gitkeep
!benchmark_data/all_uniprots/ca_distances/.gitkeep
!benchmark_data/all_uniprots/distance_differences/all_conformers/.gitkeep
!benchmark_data/all_uniprots/distance_difference_maps/.gitkeep
!benchmark_data/updated_mmcifs/.gitkeep
!benchmark_data/alphafold_mmcifs/.gitkeep

# Example outputs -- P15291
benchmark_data/examples/P15291/P15291_distance_differences/*
benchmark_data/examples/P15291/P15291_distance_difference_maps/*
benchmark_data/examples/P15291/P15291_ca_distances/*
benchmark_data/examples/P15291/P15291_cluster_results/*
benchmark_data/examples/P15291/P15291_alphafold/*

!benchmark_data/examples/P15291/P15291_distance_differences/.gitkeep
!benchmark_data/examples/P15291/P15291_distance_difference_maps/.gitkeep
!benchmark_data/examples/P15291/P15291_ca_distances/.gitkeep
!benchmark_data/examples/P15291/P15291_cluster_results/.gitkeep
!benchmark_data/examples/P15291/P15291_alphafold/.gitkeep

# Example outputs -- O34926
benchmark_data/examples/O34926/O34926_distance_differences/*
benchmark_data/examples/O34926/O34926_distance_difference_maps/*
benchmark_data/examples/O34926/O34926_ca_distances/*
benchmark_data/examples/O34926/O34926_cluster_results/*
benchmark_data/examples/O34926/O34926_path_alphafold/*

!benchmark_data/examples/O34926/O34926_distance_differences/.gitkeep
!benchmark_data/examples/O34926/O34926_distance_difference_maps/.gitkeep
!benchmark_data/examples/O34926/O34926_ca_distances/.gitkeep
!benchmark_data/examples/O34926/O34926_cluster_results/.gitkeep
!benchmark_data/examples/O34926/O34926_path_alphafold/.gitkeep

# Outputs from unit tests
tests/test_output/*
tests/test_output/downloads/*
tests/test_output/distance_difference_maps/*
tests/test_output/distance_differences/*
tests/test_output/ca_distances/*
tests/test_output/cluster_results/*
tests/test_output/renaming/*
tests/test_output/figures/*

!tests/test_output/downloads/.gitkeep
!tests/test_output/distance_difference_maps/.gitkeep
!tests/test_output/distance_differences/.gitkeep
!tests/test_output/ca_distances/.gitkeep
!tests/test_output/cluster_results/.gitkeep
!tests/test_output/renaming/.gitkeep
!tests/test_output/figures/.gitkeep


TODO