.gitignore

homework
inference_out_dir_not_specified
.plotly_cache
.DS_store
renew.sh
tmux_renew.sh
images
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so
.so3_*

# 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/
.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

# pyenv
.python-version

# celery beat schedule file
celerybeat-schedule

# 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/
local_config_inference2.yml
.vscode/


*.zip

.idea/


#################### Project specific
.p.npy
.score.npy
# this ignores everything in data except for the file
!/data
/data/*
!/data/splits
!/data/protein_ligand_example_csv.csv
!/data/testset_csv.csv
!/data/INDEX_general_PL_data.2020
test_run

cache
wandb
logs

# temporary files
.openbabel_cache
temp/
bsub*
stderr*
stdout*
!/workdir
/workdir/*
!/workdir/paper_confidence_model
!/workdir/paper_score_model
runs2
results
# this excludes everything in the runs directory except for that specific run
!/runs
/runs/*
!/runs/rigid_redocking
!/runs/flexible_self_docking
local_config.yml
local_config_inference.yml
local_config_confidence.yml
temp1.py
temp5.py
temp3.py
temp4.py
temp5.py
temp6.py
temp7.py

# additional
base-key-pair.pem
n-virginia-keys.pem