.gitignore

*.nc
.pdb
*.gro
*.out
*.top
*.itp
workdir
.ipynb_checkpoints
__pycache__
*.xml
.ipynb

scratch_homework*
checkpoints
tmp
pocket_gen
inference_out_dir_not_specified
.plotly_cache
.DS_store
renew.sh
tmux_renew.sh
# 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/




# Jupyter Notebook
.ipynb_checkpoints

# pyenv
.python-version


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


# mkdocs documentation
/site

# mypy
.mypy_cache/
local_config_inference2.yml
.vscode/


*.zip
Ala2TSF300.npy
.idea/


#################### Project specific
.p.npy
.score.npy
# this ignores everything in data except for the file
!/data
!/data/aldp.sdf
!/data/MCMC.pdb
!/data/TG.pdb
!/data/MC.pdb
!/data/EY.pdb
!/data/DF.pdb
!/data/RT.pdb
!/data/2fc2_HEM_HBI_HAR_NO.mol2
!/data/2fc2_HEM_HBI_HAR_NO.pdb
!/data/2fc2_unit1_protein.pdb
!/data/2fc2_unit1_protein.cif
!/data/bpti.pdb
!/data/inference_csv_example.csv
!/data/1uao.pdb
/data/*
!/data/aldp.pdb
!/data/splits
!/data/protein_ligand_example_csv.csv
!/data/testset_csv.csv
!/data/INDEX_general_PL_data.2020
!/data/not_git_ignored/
!/data/not_git_ignored/*
test_run

Untitled.ipynb
cache
wandb
logs

# temporary files
.openbabel_cache
temp/
stderr*
stdout*
results
# this excludes everything in the runs directory except for that specific run
!/runs
/runs/*