├── LICENSE ├── README.md ├── Species Name Cross-reference Table.csv ├── __init__.py ├── config.yaml ├── data ├── .ipynb_checkpoints │ └── datasets-checkpoint.py ├── __pycache__ │ ├── datasets.cpython-38.pyc │ └── ms_io.cpython-38.pyc └── datasets.py ├── denovo ├── .ipynb_checkpoints │ ├── dataloaders-checkpoint.py │ ├── evaluate-checkpoint.py │ ├── model-checkpoint.py │ └── model_runner-checkpoint.py ├── __pycache__ │ ├── dataloaders.cpython-38.pyc │ ├── evaluate.cpython-38.pyc │ ├── model.cpython-38.pyc │ └── model_runner.cpython-38.pyc ├── dataloaders.py ├── evaluate.py ├── model.py └── model_runner.py ├── depthcharge ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── masses.cpython-38.pyc │ ├── utils.cpython-38.pyc │ └── version.cpython-38.pyc ├── components │ ├── .ipynb_checkpoints │ │ └── transformers-checkpoint.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── encoders.cpython-38.pyc │ │ ├── feedforward.cpython-38.pyc │ │ ├── mixins.cpython-38.pyc │ │ └── transformers.cpython-38.pyc │ ├── encoders.py │ ├── feedforward.py │ ├── mixins.py │ └── transformers.py ├── data │ ├── .ipynb_checkpoints │ │ ├── hdf5-checkpoint.py │ │ ├── loaders-checkpoint.py │ │ ├── parsers-checkpoint.py │ │ └── preprocessing-checkpoint.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── datasets.cpython-38.pyc │ │ ├── hdf5.cpython-38.pyc │ │ ├── loaders.cpython-38.pyc │ │ ├── parsers.cpython-38.pyc │ │ └── preprocessing.cpython-38.pyc │ ├── datasets.py │ ├── hdf5.py │ ├── loaders.py │ ├── parsers.py │ └── preprocessing.py ├── masses.py ├── models │ ├── __init__.py │ ├── __pycache__ │ │ └── __init__.cpython-38.pyc │ └── denovo │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ └── model.cpython-38.pyc │ │ └── model.py ├── similarity.py ├── utils.py └── version.py ├── main.py ├── main_env.yaml ├── merge-config.yaml ├── run_in_docker ├── docker-env.md └── docker-env │ ├── run0.png │ 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