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.gitignore
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# 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/
pip-wheel-metadata/
share/python-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
*.py,cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal
# 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
# 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
# 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/
.DS_Store
# Checkpoints (too heavy to upload them all)
checkpoints/agnostic_all_modes/seed_13/
checkpoints/agnostic_all_modes/seed_23/
checkpoints/agnostic_all_modes/seed_398/
checkpoints/agnostic_all_modes/seed_447/
checkpoints/contact_maps/seed_13/
checkpoints/contact_maps/seed_23/
checkpoints/contact_maps/seed_398/
checkpoints/contact_maps/seed_447/
checkpoints/contact_maps/seed_917/
checkpoints/full_ags_all_modes/seed_13/
checkpoints/full_ags_all_modes/seed_23/
checkpoints/full_ags_all_modes/seed_398/
checkpoints/full_ags_all_modes/seed_447/
checkpoints/full_ags_all_modes/seed_917/
checkpoints/full_ags_n_modes/250_modes/
checkpoints/full_ags_n_modes/50_modes/
checkpoints/full_ags_n_modes/30_modes/
checkpoints/full_ags_n_modes/15_modes/
checkpoints/full_ags_n_modes/100_modes/learnt_filter_epochs_434_modes_100_pool_2_filters_4_size_4.npy
checkpoints/full_ags_n_modes/100_modes/learnt_filter_epochs_577_modes_100_pool_1_filters_4_size_4.npy
checkpoints/full_ags_n_modes/100_modes/learnt_filter_epochs_599_modes_100_pool_1_filters_4_size_4.npy
checkpoints/full_ags_n_modes/100_modes/learnt_filter_epochs_608_modes_100_pool_1_filters_4_size_4.npy
checkpoints/full_ags_n_modes/100_modes/learnt_filter_epochs_1073_modes_100_pool_1_filters_4_size_4.npy
checkpoints/full_ags_n_modes/100_modes/model_epochs_434_modes_100_pool_2_filters_4_size_4.pt
checkpoints/full_ags_n_modes/100_modes/model_epochs_577_modes_100_pool_1_filters_4_size_4.pt
checkpoints/full_ags_n_modes/100_modes/model_epochs_599_modes_100_pool_1_filters_4_size_4.pt
checkpoints/full_ags_n_modes/100_modes/model_epochs_608_modes_100_pool_1_filters_4_size_4.pt
checkpoints/full_ags_n_modes/100_modes/model_epochs_794_modes_100_pool_2_filters_4_size_4.pt
checkpoints/full_ags_n_modes/100_modes/model_epochs_1073_modes_100_pool_1_filters_4_size_4.pt
checkpoints/full_ags_all_modes/model_epochs_1000_modes_all_pool_1_filters_4_size_4.pt
checkpoints/full_ags_all_modes/learnt_filter_epochs_1000_modes_all_pool_1_filters_4_size_4.npy
# Data not used
data/contact_maps_explorer/
data/contact_maps_with_antigen_explorer/
notebooks/biological_properties/
# Part of the data (too heavy)
data/dccm_maps_agnostic_15
data/dccm_maps_agnostic_30
data/dccm_maps_full_ags_15
data/dccm_maps_full_ags_30
data/dccm_maps_full_ags_50
data/dccm_maps_full_ags_250
data/cov_maps_full_ags_all
# Raw notebooks
notebooks/explainability_raw.ipynb
# Scripts
scripts/measure_all_distances.py
# Under construction
scripts/evaluation.py
scripts/training.py