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‎.gitignore‎

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# tests
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tests/**/*.png
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test_model.*
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# Distribution / packaging
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.Python

‎README.md‎

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More detailed and comprehensive documentation in [DeepMol readthedocs](https://deepmol.readthedocs.io/en/latest/).
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### Google colabs to run AutoML
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- [Binary and multiclass classification](https://colab.research.google.com/drive/1wtiwuuhfWKVo40ywgweWUMavKL0zdwJK?usp=sharing)
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- [Regression](https://colab.research.google.com/drive/1vE-Q01orImdD4qFTo20MAT4E4kP2hsYF?usp=sharing)
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- [Multi-task/multi-label](https://colab.research.google.com/drive/18z2vN6zLNSVJ3qgskKZTYxA_t9UNS1b8?usp=sharing)
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### Table of contents:
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- [Requirements](#requirements)
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- [Installation](#installation)
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- [Pip](#pip)
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- [Manually](#manually)
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- [Docker](#docker)
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- [Disclaimer](#disclaimer)
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- [Getting Started](#getting-started)
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- [Load dataset from csv](#load-a-dataset-from-a-csv)
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- [Load dataset from sdf](#load-a-dataset-from-a-sdf)
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- [License](#licensing)
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## Installation
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### Pip
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pip install deepmol[all]
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```
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or in MacOS:
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```bash
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pip install "deepmol[all]"
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```
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Extra modules:
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```bash
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pip install deepmol[deep-learning]
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```
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or in MacOS:
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```bash
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pip install "deepmol[preprocessing]"
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pip install "deepmol[machine-learning]"
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pip install "deepmol[deep-learning]"
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```
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Also, you should install mol2vec and its dependencies:
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```bash
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docker pull biosystemsum/deepmol
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```
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### Disclaimer
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If you’d like to use the GPU, make sure to install the versions of TensorFlow and DGL that match the CUDA drivers for your hardware.
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Do not install JAX, it will result dependency conflicts.
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Loading tensorflow models will be problematic for MacOS users due to a known tensorflow issue [46](https://github.com/keras-team/tf-keras/issues/46).
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## Getting Started
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## Citing DeepMol
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Correia, J., Capela, J., & Rocha, M. (2024). DeepMol: An Automated Machine and Deep Learning Framework for Computational Chemistry. [https://doi.org/10.1186/s13321-024-00937-7](https://doi.org/10.1186/s13321-024-00937-7)
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Correia, J., Capela, J. & Rocha, M. Deepmol: an automated machine and deep learning framework for computational chemistry. J Cheminform 16, 136 (2024). [https://doi.org/10.1186/s13321-024-00937-7](https://doi.org/10.1186/s13321-024-00937-7)
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### Publications using DeepMol
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‎README_pypi.md‎

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More detailed and comprehensive documentation in [DeepMol readthedocs](https://deepmol.readthedocs.io/en/latest/).
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### Google colabs to run AutoML
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- [Binary and multiclass classification](https://colab.research.google.com/drive/1wtiwuuhfWKVo40ywgweWUMavKL0zdwJK?usp=sharing)
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- [Regression](https://colab.research.google.com/drive/1vE-Q01orImdD4qFTo20MAT4E4kP2hsYF?usp=sharing)
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- [Multi-task/multi-label](https://colab.research.google.com/drive/18z2vN6zLNSVJ3qgskKZTYxA_t9UNS1b8?usp=sharing)
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## Installation
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### Pip
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pip install deepmol[all]
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```
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or in MacOS:
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```bash
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pip install "deepmol[all]"
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```
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Extra modules:
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```bash
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pip install deepmol[deep-learning]
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```
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or in MacOS:
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```bash
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pip install "deepmol[preprocessing]"
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pip install "deepmol[machine-learning]"
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pip install "deepmol[deep-learning]"
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```
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Also, you should install mol2vec and its dependencies:
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```bash
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docker pull biosystemsum/deepmol
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```
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### Disclaimer
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If you’d like to use the GPU, make sure to install the versions of TensorFlow and DGL that match the CUDA drivers for your hardware.
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Do not install JAX, it will result dependency conflicts.
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Loading tensorflow models will be problematic for MacOS users due to a known tensorflow issue [46](https://github.com/keras-team/tf-keras/issues/46).
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## Getting Started
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‎docs/conf.py‎

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sys.path.insert(0, os.path.abspath('../src/'))
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project = 'deepmol'
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copyright = '2023, João Correia and João Capela'
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copyright = '2024, João Correia and João Capela'
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author = 'João Correia and João Capela'
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release = '1.0.0'
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‎docs/deepmol.compound_featurization.md‎

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# deepmol.compound_featurization package
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## Subpackages
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```{toctree}
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:maxdepth: 4
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deepmol.compound_featurization.nc_mfp
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deepmol.compound_featurization.neural_npfp
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```
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## Submodules
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## deepmol.compound_featurization.base_featurizer module
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:show-inheritance:
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```
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## deepmol.compound_featurization.mhfp module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.mhfp
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.mixed_descriptors module
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```{eval-rst}
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp_generator module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp_generator
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.neural_npfp_generator module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.neural_npfp_generator
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.np_classifier_fp module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.np_classifier_fp
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:members:
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:undoc-members:
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:show-inheritance:
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```
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‎docs/deepmol.compound_featurization.nc_mfp.md‎

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# deepmol.compound_featurization.nc_mfp package
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## Submodules
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## deepmol.compound_featurization.nc_mfp.Fingerprint_representation_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.Fingerprint_representation_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.Fragment_identifying_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.Fragment_identifying_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.Fragment_list_generation_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.Fragment_list_generation_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.Preprocessing_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.Preprocessing_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.SFCP_assigning_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.SFCP_assigning_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.Scaffold_matching_step module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.Scaffold_matching_step
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.generate_database module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.generate_database
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.nc_mfp.identify_smarts_fragmets module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.nc_mfp.identify_smarts_fragmets
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## Module contents
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.. automodule:: deepmol.compound_featurization.nc_mfp
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:members:
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:undoc-members:
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:show-inheritance:
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```

‎docs/deepmol.compound_featurization.neural_npfp.md‎

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# deepmol.compound_featurization.neural_npfp package
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## Submodules
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## deepmol.compound_featurization.neural_npfp.model module
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```{eval-rst}
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.. automodule:: deepmol.compound_featurization.neural_npfp.model
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.compound_featurization.neural_npfp.utils module
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.. automodule:: deepmol.compound_featurization.neural_npfp.utils
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## Module contents
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:undoc-members:
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:show-inheritance:
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```

‎docs/deepmol.encoders.md‎

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# deepmol.encoders package
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## Submodules
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## deepmol.encoders.label_encoder module
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```{eval-rst}
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.. automodule:: deepmol.encoders.label_encoder
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## deepmol.encoders.label_one_hot_encoder module
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```{eval-rst}
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.. automodule:: deepmol.encoders.label_one_hot_encoder
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:members:
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:undoc-members:
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:show-inheritance:
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```
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## Module contents
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:undoc-members:
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:show-inheritance:
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```

‎docs/deepmol.md‎

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deepmol.base
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deepmol.encoders
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deepmol.feature_importance
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‎docs/deepmol.pipeline.md‎

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## deepmol.pipeline.ensemble module
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```{eval-rst}
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.. automodule:: deepmol.pipeline.ensemble
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:members:
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:undoc-members:
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:show-inheritance:
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```
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```{eval-rst}

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