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‎docs/source/additional.rst‎

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Additional Information
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======================
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### Project Overview
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`torch-molecule` is a package under active development to support molecular discovery using deep learning. It provides a simple, `sklearn`-style interface and model checkpoints for fast deployment and benchmarking.
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Main components:
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1. **Predictive Models**
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✔ GREA, SGIR, IRM, GIN/GCN w/ virtual, DIR
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⏳ SMILES-based LSTM/Transformers and more
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2. **Generative Models**
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✔ Graph DiT, GraphGA, DiGress
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⏳ GDSS and more
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3. **Representation Models**
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✔ MoAMa, AttrMasking, ContextPred, EdgePred
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⏳ more models and pretrained checkpoints
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> **Note**: This project is in active development. Interfaces and features may change.
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### Project Structure
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```
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torch_molecule
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├── base
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├── encoder
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├── generator
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├── nn
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├── predictor
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└── utils
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```
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### Acknowledgements
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This project was adapted from [https://github.com/lwaekfjlk/python-project-template](https://github.com/lwaekfjlk/python-project-template).
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docs/source/api.rst renamed to docs/source/api/api.rst

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Encoders
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--------
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.. automodule:: torch_molecule.encoder.moama
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.. automodule:: torch_molecule.encoder.supervised
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.. (You can repeat this for other encoder modules like `attrmask`, `contextpred` if they are Python files or have `__init__.py` and docstrings inside.)
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‎docs/source/api/base.rst‎

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API Reference for Base Modules
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===============================
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This section documents base classes in `torch_molecule.base`.
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Base Modules
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------------
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.. automodule:: torch_molecule.base
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:members:
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:undoc-members:
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:show-inheritance:
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.. automodule:: torch_molecule.base.encoder
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.. automodule:: torch_molecule.base.generator
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.. automodule:: torch_molecule.base.predictor
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‎docs/source/api/encoder.rst‎

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API Reference for Encoders
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===========================
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This section documents contain the encoder (representation learning) models in `torch_molecule.encoder`.
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Encoders
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--------
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.. automodule:: torch_molecule.encoder.constant
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.. automodule:: torch_molecule.encoder.attrmask
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.. automodule:: torch_molecule.encoder.contextpred
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.. automodule:: torch_molecule.encoder.edgepred
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.. automodule:: torch_molecule.encoder.moama
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.. automodule:: torch_molecule.encoder.supervised
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‎docs/source/api/generator.rst‎

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API Reference for Generators
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=============================
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This section documents contain the generation models in `torch_molecule.generator`.
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Generators
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----------
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.. (If `digress`, `graph_dit`, etc., are packages with docstrings, add them.)
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.. automodule:: torch_molecule.generator.digress
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.. automodule:: torch_molecule.generator.graph_dit
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.. automodule:: torch_molecule.generator.graphga
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‎docs/source/api/index.rst‎

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API Reference
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=============
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This section documents the main modules and classes in `torch_molecule`.
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.. toctree::
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:maxdepth: 2
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:caption: API Contents:
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predictor
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generator
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encoder
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utils
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nn
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base

‎docs/source/api/nn.rst‎

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API Reference for Neural Network Components
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============================================
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This section documents the neural network components in `torch_molecule.nn`.
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Neural Network Components
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-------------------------
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.. automodule:: torch_molecule.nn.attention
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.. automodule:: torch_molecule.nn.embedder
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.. automodule:: torch_molecule.nn.gnn
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.. automodule:: torch_molecule.nn.mlp
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‎docs/source/api/predictor.rst‎

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API Reference for Predictors
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=============================
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This section documents contain the predictor models in `torch_molecule.predictor`.
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Predictors
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----------
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.. (Add predictors here as needed. You might write summaries and link submodules.)
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.. automodule:: torch_molecule.predictor.gnn
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.. automodule:: torch_molecule.predictor.dir
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.. automodule:: torch_molecule.predictor.grea
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.. automodule:: torch_molecule.predictor.sgir
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.. automodule:: torch_molecule.predictor.irm
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.. automodule:: torch_molecule.predictor.lstm
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.. automodule:: torch_molecule.predictor.rpgnn
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.. automodule:: torch_molecule.predictor.ssr
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‎docs/source/api/utils.rst‎

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API Reference for Utilities
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===========================
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This section documents the utility functions in `torch_molecule.utils`.
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Utilities
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---------
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.. automodule:: torch_molecule.utils.checker
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.. automodule:: torch_molecule.utils.format
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.. automodule:: torch_molecule.utils.search
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Base Modules
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------------
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.. automodule:: torch_molecule.base
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.. automodule:: torch_molecule.base.encoder
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.. automodule:: torch_molecule.base.generator
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.. automodule:: torch_molecule.base.predictor
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