torch-molecule 0.1.0__tar.gz

torch_molecule-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Haofei Yu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

torch_molecule-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: torch_molecule
+Version: 0.1.0
+Summary: Deep learning packages for molecular discovery with a simple sklearn-style interface
+Author-email: Gang Liu <gliu7@nd.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/liugangcode/torch-molecule
+Project-URL: Bug Tracker, https://github.com/liugangcode/torch-molecule
+Project-URL: Documentation, https://liugangcode.github.io/torch-molecule/
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.2.0
+Requires-Dist: torch-geometric>=2.6.1
+Requires-Dist: numpy
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: click
+Requires-Dist: huggingface_hub>=0.22.2
+Requires-Dist: joblib>=1.3.2
+Requires-Dist: networkx>=3.2.1
+Requires-Dist: PyYAML>=6.0.2
+Requires-Dist: rdkit>=2023.9.5
+Requires-Dist: scikit_learn>=1.4.1.post1
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: tqdm>=4.66.2
+Requires-Dist: optuna>=4.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://github.com/liugangcode/torch-molecule/blob/main/assets/logo.png?raw=true" alt="torch-molecule logo" width="600"/>
+</p>
+
+<p align="center">
+  <a href="https://github.com/liugangcode/torch-molecule">
+    <img src="https://img.shields.io/badge/GitHub-Repository-blue?logo=github" alt="GitHub Repository">
+  </a>
+  <a href="https://liugangcode.github.io/torch-molecule/">
+    <img src="https://img.shields.io/badge/Documentation-Online-brightgreen?logo=readthedocs" alt="Documentation">
+  </a>
+</p>
+
+<p align="center">
+  <b>Deep learning for molecular discovery with a simple sklearn-style interface</b>
+</p>
+
+---
+
+`torch-molecule` is a package under active development that facilitates molecular discovery through deep learning, featuring a user-friendly, `sklearn`-style interface. It includes model checkpoints for efficient deployment and benchmarking across a range of molecular tasks. Currently, the package focuses on three main components: **Predictive Models**, **Generative Models**, and **Representation Models**. See the [List of Supported Models](#list-of-supported-models) section for all available models.
+
+## Installation
+
+1. **Create a Conda environment**:
+   ```bash
+   conda create --name torch_molecule python=3.11.7
+   conda activate torch_molecule
+   ```
+
+2. **Install using pip (0.1.0)**:
+
+   ```bash
+   pip install torch-molecule
+   ```
+
+3. **Install from source for the latest version**:
+
+   Clone the repository:
+
+   ```bash
+   git clone https://github.com/liugangcode/torch-molecule
+   cd torch-molecule
+   ```
+
+   Install in editable mode:
+
+   ```bash
+   pip install .
+   ```
+
+### Additional Packages
+
+| Model | Required Packages |
+|-------|-------------------|
+| HFPretrainedMolecularEncoder | transformers |
+| BFGNNMolecularPredictor | torch-scatter |
+| GRINMolecularPredictor | torch-scatter |
+
+## Usage
+
+Refer to the `tests` folder for more use cases.
+
+### Python API Example
+
+The following example demonstrates how to use the `GREAMolecularPredictor` class from `torch_molecule`:
+
+More examples could be found in the folders `examples` and `tests`.
+
+```python
+from torch_molecule import GREAMolecularPredictor
+
+# Train GREA model
+grea_model = GREAMolecularPredictor(
+    num_task=num_task,
+    task_type="regression",
+    model_name="GREA_multitask",
+    evaluate_criterion='r2',
+    evaluate_higher_better=True,
+    verbose=True
+)
+
+# Fit the model
+X_train = ['C1=CC=CC=C1', 'C1=CC=CC=C1']
+y_train = [[0.5], [1.5]]
+X_val = ['C1=CC=CC=C1', 'C1=CC=CC=C1']
+y_val = [[0.5], [1.5]]
+N_trial = 10
+
+grea_model.autofit(
+    X_train=X_train.tolist(),
+    y_train=y_train,
+    X_val=X_val.tolist(),
+    y_val=y_val,
+    n_trials=N_trial,
+)
+```
+
+### Checkpoints
+
+`torch-molecule` provides checkpoint functions that can be interacted with on Hugging Face.
+
+```python
+from torch_molecule import GREAMolecularPredictor
+from sklearn.metrics import mean_absolute_error
+
+# Define the repository ID for Hugging Face
+repo_id = "user/repo_id"
+
+# Initialize the GREAMolecularPredictor model
+model = GREAMolecularPredictor()
+
+# Train the model using autofit
+model.autofit(
+    X_train=X.tolist(),  # List of SMILES strings for training
+    y_train=y_train,     # numpy array [n_samples, n_tasks] for training labels
+    X_val=X_val.tolist(),# List of SMILES strings for validation
+    y_val=y_val,         # numpy array [n_samples, n_tasks] for validation labels
+)
+
+# Make predictions on the test set
+output = model.predict(X_test.tolist()) # (n_sample, n_task)
+
+# Calculate the mean absolute error
+mae = mean_absolute_error(y_test, output['prediction'])
+metrics = {'MAE': mae}
+
+# Save the trained model to Hugging Face
+model.save_to_hf(
+    repo_id=repo_id,
+    task_id=f"{task_name}",
+    metrics=metrics,
+    commit_message=f"Upload GREA_{task_name} model with metrics: {metrics}",
+    private=False
+)
+
+# Load a pretrained checkpoint from Hugging Face
+model = GREAMolecularPredictor()
+model.load_from_hf(repo_id=repo_id, local_cache=f"{model_dir}/GREA_{task_name}.pt")
+
+# Set model parameters
+model.set_params(verbose=True)
+
+# Make predictions using the loaded model
+predictions = model.predict(smiles_list)
+```
+
+## List of Supported Models
+
+### Predictive Models
+
+| Model                | Reference           |
+|----------------------|---------------------|
+| GRIN                 | [Learning Repetition-Invariant Representations for Polymer Informatics. May 2025](https://arxiv.org/abs/2505.10726) |
+| BFGNN                 | [Graph neural networks extrapolate out-of-distribution for shortest paths. March 2025](https://arxiv.org/abs/2503.19173) |
+| SGIR                 | [Semi-Supervised Graph Imbalanced Regression. KDD 2023](https://dl.acm.org/doi/10.1145/3580305.3599497) |
+| GREA                | [Graph Rationalization with Environment-based Augmentations. KDD 2022](https://dl.acm.org/doi/abs/10.1145/3534678.3539347) |
+| DIR                  | [Discovering Invariant Rationales for Graph Neural Networks. ICLR 2022](https://arxiv.org/abs/2201.12872) |
+| SSR                  | [SizeShiftReg: a Regularization Method for Improving Size-Generalization in Graph Neural Networks. NeurIPS 2022](https://arxiv.org/abs/2206.07096) |
+| IRM                  | [Invariant Risk Minimization (2019)](https://arxiv.org/abs/1907.02893) |
+| RPGNN                | [Relational Pooling for Graph Representations. ICML 2019](https://arxiv.org/abs/1903.02541) |
+| GNNs                 | [Graph Convolutional Networks. ICLR 2017](https://arxiv.org/abs/1609.02907) and [Graph Isomorphism Network. ICLR 2019](https://arxiv.org/abs/1810.00826) |
+| Transformer (SMILES) | [Transformer (Attention is All You Need. NeurIPS 2017)](https://arxiv.org/abs/1706.03762) based on SMILES strings |
+| LSTM (SMILES)        | [Long short-term memory (Neural Computation 1997)](https://ieeexplore.ieee.org/abstract/document/6795963) based on SMILES strings |
+
+### Generative Models
+
+| Model      | Reference           |
+|------------|---------------------|
+| Graph DiT  | [Graph Diffusion Transformers for Multi-Conditional Molecular Generation. NeurIPS 2024](https://openreview.net/forum?id=cfrDLD1wfO) |
+| DiGress    | [DiGress: Discrete Denoising Diffusion for Graph Generation. ICLR 2023](https://openreview.net/forum?id=UaAD-Nu86WX) |
+| GDSS       | [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations. ICML 2022](https://proceedings.mlr.press/v162/jo22a/jo22a.pdf) |
+| MolGPT     | [MolGPT: Molecular Generation Using a Transformer-Decoder Model. Journal of Chemical Information and Modeling 2021](https://pubs.acs.org/doi/10.1021/acs.jcim.1c00600) |
+| JTVAE     | [Junction Tree Variational Autoencoder for Molecular Graph Generation. ICML 2018.](https://proceedings.mlr.press/v80/jin18a) |
+| GraphGA    | [A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules. Journal of Chemical Information and Computer Sciences 2004](https://pubs.acs.org/doi/10.1021/ci034290p) |
+| LSTM (SMILES)        | [Long short-term memory (Neural Computation 1997)](https://ieeexplore.ieee.org/abstract/document/6795963) based on SMILES strings |
+
+### Representation Models
+
+| Model        | Reference           |
+|--------------|---------------------|
+| MoAMa        | [Motif-aware Attribute Masking for Molecular Graph Pre-training. LoG 2024](https://arxiv.org/abs/2309.04589) |
+| GraphMAE        | [GraphMAE: Self-Supervised Masked Graph Autoencoders. KDD 2022](https://arxiv.org/abs/2205.10803) |
+| AttrMasking  | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| ContextPred  | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| EdgePred     | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| InfoGraph    | [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization. ICLR 2020](https://arxiv.org/abs/1908.01000) |
+| Supervised   | Supervised pretraining |
+| Pretrained   | More than ten pretrained models from [Hugging Face](https://huggingface.co) |
+
+## Project Structure
+
+See the structure of `torch_molecule` with the command `tree -L 2 torch_molecule -I '__pycache__|*.pyc|*.pyo|.git|old*'`
+
+## Plan
+
+1. **Predictive Models**: Done: GREA, SGIR, IRM, GIN/GCN w/ virtual, DIR. SMILES-based LSTM/Transformers. TODO more
+2. **Generative Models**: Done: Graph DiT, GraphGA, DiGress, GDS, MolGPT TODO: more
+3. **Representation Models**: Done: MoAMa, AttrMasking, ContextPred, EdgePred. Many pretrained models from HF. TODO: checkpoints, more 
+
+> **Note**: This project is in active development, and features may change.
+
+## Acknowledgements
+
+The project template was adapted from [https://github.com/lwaekfjlk/python-project-template](https://github.com/lwaekfjlk/python-project-template). We thank the authors for their contribution to the open-source community.

torch_molecule-0.1.0/README.md

@@ -0,0 +1,204 @@
+<p align="center">
+  <img src="https://github.com/liugangcode/torch-molecule/blob/main/assets/logo.png?raw=true" alt="torch-molecule logo" width="600"/>
+</p>
+
+<p align="center">
+  <a href="https://github.com/liugangcode/torch-molecule">
+    <img src="https://img.shields.io/badge/GitHub-Repository-blue?logo=github" alt="GitHub Repository">
+  </a>
+  <a href="https://liugangcode.github.io/torch-molecule/">
+    <img src="https://img.shields.io/badge/Documentation-Online-brightgreen?logo=readthedocs" alt="Documentation">
+  </a>
+</p>
+
+<p align="center">
+  <b>Deep learning for molecular discovery with a simple sklearn-style interface</b>
+</p>
+
+---
+
+`torch-molecule` is a package under active development that facilitates molecular discovery through deep learning, featuring a user-friendly, `sklearn`-style interface. It includes model checkpoints for efficient deployment and benchmarking across a range of molecular tasks. Currently, the package focuses on three main components: **Predictive Models**, **Generative Models**, and **Representation Models**. See the [List of Supported Models](#list-of-supported-models) section for all available models.
+
+## Installation
+
+1. **Create a Conda environment**:
+   ```bash
+   conda create --name torch_molecule python=3.11.7
+   conda activate torch_molecule
+   ```
+
+2. **Install using pip (0.1.0)**:
+
+   ```bash
+   pip install torch-molecule
+   ```
+
+3. **Install from source for the latest version**:
+
+   Clone the repository:
+
+   ```bash
+   git clone https://github.com/liugangcode/torch-molecule
+   cd torch-molecule
+   ```
+
+   Install in editable mode:
+
+   ```bash
+   pip install .
+   ```
+
+### Additional Packages
+
+| Model | Required Packages |
+|-------|-------------------|
+| HFPretrainedMolecularEncoder | transformers |
+| BFGNNMolecularPredictor | torch-scatter |
+| GRINMolecularPredictor | torch-scatter |
+
+## Usage
+
+Refer to the `tests` folder for more use cases.
+
+### Python API Example
+
+The following example demonstrates how to use the `GREAMolecularPredictor` class from `torch_molecule`:
+
+More examples could be found in the folders `examples` and `tests`.
+
+```python
+from torch_molecule import GREAMolecularPredictor
+
+# Train GREA model
+grea_model = GREAMolecularPredictor(
+    num_task=num_task,
+    task_type="regression",
+    model_name="GREA_multitask",
+    evaluate_criterion='r2',
+    evaluate_higher_better=True,
+    verbose=True
+)
+
+# Fit the model
+X_train = ['C1=CC=CC=C1', 'C1=CC=CC=C1']
+y_train = [[0.5], [1.5]]
+X_val = ['C1=CC=CC=C1', 'C1=CC=CC=C1']
+y_val = [[0.5], [1.5]]
+N_trial = 10
+
+grea_model.autofit(
+    X_train=X_train.tolist(),
+    y_train=y_train,
+    X_val=X_val.tolist(),
+    y_val=y_val,
+    n_trials=N_trial,
+)
+```
+
+### Checkpoints
+
+`torch-molecule` provides checkpoint functions that can be interacted with on Hugging Face.
+
+```python
+from torch_molecule import GREAMolecularPredictor
+from sklearn.metrics import mean_absolute_error
+
+# Define the repository ID for Hugging Face
+repo_id = "user/repo_id"
+
+# Initialize the GREAMolecularPredictor model
+model = GREAMolecularPredictor()
+
+# Train the model using autofit
+model.autofit(
+    X_train=X.tolist(),  # List of SMILES strings for training
+    y_train=y_train,     # numpy array [n_samples, n_tasks] for training labels
+    X_val=X_val.tolist(),# List of SMILES strings for validation
+    y_val=y_val,         # numpy array [n_samples, n_tasks] for validation labels
+)
+
+# Make predictions on the test set
+output = model.predict(X_test.tolist()) # (n_sample, n_task)
+
+# Calculate the mean absolute error
+mae = mean_absolute_error(y_test, output['prediction'])
+metrics = {'MAE': mae}
+
+# Save the trained model to Hugging Face
+model.save_to_hf(
+    repo_id=repo_id,
+    task_id=f"{task_name}",
+    metrics=metrics,
+    commit_message=f"Upload GREA_{task_name} model with metrics: {metrics}",
+    private=False
+)
+
+# Load a pretrained checkpoint from Hugging Face
+model = GREAMolecularPredictor()
+model.load_from_hf(repo_id=repo_id, local_cache=f"{model_dir}/GREA_{task_name}.pt")
+
+# Set model parameters
+model.set_params(verbose=True)
+
+# Make predictions using the loaded model
+predictions = model.predict(smiles_list)
+```
+
+## List of Supported Models
+
+### Predictive Models
+
+| Model                | Reference           |
+|----------------------|---------------------|
+| GRIN                 | [Learning Repetition-Invariant Representations for Polymer Informatics. May 2025](https://arxiv.org/abs/2505.10726) |
+| BFGNN                 | [Graph neural networks extrapolate out-of-distribution for shortest paths. March 2025](https://arxiv.org/abs/2503.19173) |
+| SGIR                 | [Semi-Supervised Graph Imbalanced Regression. KDD 2023](https://dl.acm.org/doi/10.1145/3580305.3599497) |
+| GREA                | [Graph Rationalization with Environment-based Augmentations. KDD 2022](https://dl.acm.org/doi/abs/10.1145/3534678.3539347) |
+| DIR                  | [Discovering Invariant Rationales for Graph Neural Networks. ICLR 2022](https://arxiv.org/abs/2201.12872) |
+| SSR                  | [SizeShiftReg: a Regularization Method for Improving Size-Generalization in Graph Neural Networks. NeurIPS 2022](https://arxiv.org/abs/2206.07096) |
+| IRM                  | [Invariant Risk Minimization (2019)](https://arxiv.org/abs/1907.02893) |
+| RPGNN                | [Relational Pooling for Graph Representations. ICML 2019](https://arxiv.org/abs/1903.02541) |
+| GNNs                 | [Graph Convolutional Networks. ICLR 2017](https://arxiv.org/abs/1609.02907) and [Graph Isomorphism Network. ICLR 2019](https://arxiv.org/abs/1810.00826) |
+| Transformer (SMILES) | [Transformer (Attention is All You Need. NeurIPS 2017)](https://arxiv.org/abs/1706.03762) based on SMILES strings |
+| LSTM (SMILES)        | [Long short-term memory (Neural Computation 1997)](https://ieeexplore.ieee.org/abstract/document/6795963) based on SMILES strings |
+
+### Generative Models
+
+| Model      | Reference           |
+|------------|---------------------|
+| Graph DiT  | [Graph Diffusion Transformers for Multi-Conditional Molecular Generation. NeurIPS 2024](https://openreview.net/forum?id=cfrDLD1wfO) |
+| DiGress    | [DiGress: Discrete Denoising Diffusion for Graph Generation. ICLR 2023](https://openreview.net/forum?id=UaAD-Nu86WX) |
+| GDSS       | [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations. ICML 2022](https://proceedings.mlr.press/v162/jo22a/jo22a.pdf) |
+| MolGPT     | [MolGPT: Molecular Generation Using a Transformer-Decoder Model. Journal of Chemical Information and Modeling 2021](https://pubs.acs.org/doi/10.1021/acs.jcim.1c00600) |
+| JTVAE     | [Junction Tree Variational Autoencoder for Molecular Graph Generation. ICML 2018.](https://proceedings.mlr.press/v80/jin18a) |
+| GraphGA    | [A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules. Journal of Chemical Information and Computer Sciences 2004](https://pubs.acs.org/doi/10.1021/ci034290p) |
+| LSTM (SMILES)        | [Long short-term memory (Neural Computation 1997)](https://ieeexplore.ieee.org/abstract/document/6795963) based on SMILES strings |
+
+### Representation Models
+
+| Model        | Reference           |
+|--------------|---------------------|
+| MoAMa        | [Motif-aware Attribute Masking for Molecular Graph Pre-training. LoG 2024](https://arxiv.org/abs/2309.04589) |
+| GraphMAE        | [GraphMAE: Self-Supervised Masked Graph Autoencoders. KDD 2022](https://arxiv.org/abs/2205.10803) |
+| AttrMasking  | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| ContextPred  | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| EdgePred     | [Strategies for Pre-training Graph Neural Networks. ICLR 2020](https://arxiv.org/abs/1905.12265) |
+| InfoGraph    | [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization. ICLR 2020](https://arxiv.org/abs/1908.01000) |
+| Supervised   | Supervised pretraining |
+| Pretrained   | More than ten pretrained models from [Hugging Face](https://huggingface.co) |
+
+## Project Structure
+
+See the structure of `torch_molecule` with the command `tree -L 2 torch_molecule -I '__pycache__|*.pyc|*.pyo|.git|old*'`
+
+## Plan
+
+1. **Predictive Models**: Done: GREA, SGIR, IRM, GIN/GCN w/ virtual, DIR. SMILES-based LSTM/Transformers. TODO more
+2. **Generative Models**: Done: Graph DiT, GraphGA, DiGress, GDS, MolGPT TODO: more
+3. **Representation Models**: Done: MoAMa, AttrMasking, ContextPred, EdgePred. Many pretrained models from HF. TODO: checkpoints, more 
+
+> **Note**: This project is in active development, and features may change.
+
+## Acknowledgements
+
+The project template was adapted from [https://github.com/lwaekfjlk/python-project-template](https://github.com/lwaekfjlk/python-project-template). We thank the authors for their contribution to the open-source community.

torch_molecule-0.1.0/pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "torch_molecule"
+version = "0.1.0"
+description = "Deep learning packages for molecular discovery with a simple sklearn-style interface"
+authors = [{name = "Gang Liu", email = "gliu7@nd.edu"}]
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "MIT"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "torch>=2.2.0",
+    "torch-geometric>=2.6.1",
+    "numpy",
+    "pandas>=2.2.3",
+    "click",
+    "huggingface_hub>=0.22.2",
+    "joblib>=1.3.2",
+    "networkx>=3.2.1",
+    "PyYAML>=6.0.2",
+    "rdkit>=2023.9.5",
+    "scikit_learn>=1.4.1.post1",
+    "scipy>=1.14.1",
+    "tqdm>=4.66.2",
+    "optuna>=4.0.0",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/liugangcode/torch-molecule"
+"Bug Tracker" = "https://github.com/liugangcode/torch-molecule"
+"Documentation" = "https://liugangcode.github.io/torch-molecule/"
+
+[tool.setuptools.packages.find]
+include = ["torch_molecule*"]
+exclude = [
+    "private*", 
+    "tests*", 
+    "old_*.py", 
+    "**/old_*.py"
+]
+
+[tool.setuptools.package-data]
+"torch_molecule" = ["**/*.yaml", "**/*.json"]
+
+[tool.setuptools]
+zip-safe = false
+
+[tool.pytest.ini_options]
+addopts = "--verbose"
+testpaths = ["tests"]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "black",
+    "isort",
+    "flake8",
+]
+
+[tool.black]
+line-length = 100
+target-version = ['py38']
+
+[tool.isort]
+profile = "black"
+line_length = 100

torch_molecule-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

torch_molecule-0.1.0/torch_molecule/__init__.py

@@ -0,0 +1,70 @@
+__version__ = "0.1.0"
+
+"""
+predictor module
+"""
+from .predictor.grea import GREAMolecularPredictor
+from .predictor.gnn import GNNMolecularPredictor
+from .predictor.sgir import SGIRMolecularPredictor
+from .predictor.irm import IRMMolecularPredictor
+from .predictor.ssr import SSRMolecularPredictor
+from .predictor.dir import DIRMolecularPredictor
+from .predictor.rpgnn import RPGNNMolecularPredictor
+from .predictor.bfgnn import BFGNNMolecularPredictor
+from .predictor.grin import GRINMolecularPredictor
+from .predictor.lstm import LSTMMolecularPredictor
+from .predictor.smiles_transformer import SMILESTransformerMolecularPredictor
+"""
+encoder module
+"""
+from .encoder.attrmask import AttrMaskMolecularEncoder
+from .encoder.moama import MoamaMolecularEncoder
+from .encoder.graphmae import GraphMAEMolecularEncoder
+from .encoder.supervised import SupervisedMolecularEncoder
+from .encoder.contextpred import ContextPredMolecularEncoder
+from .encoder.edgepred import EdgePredMolecularEncoder
+from .encoder.infograph import InfoGraphMolecularEncoder
+from .encoder.pretrained import HFPretrainedMolecularEncoder
+"""
+generator module
+"""
+from .generator.graph_dit import GraphDITMolecularGenerator
+from .generator.digress import DigressMolecularGenerator
+from .generator.gdss import GDSSMolecularGenerator
+from .generator.graph_ga import GraphGAMolecularGenerator
+from .generator.jtvae import JTVAEMolecularGenerator
+from .generator.lstm import LSTMMolecularGenerator
+from .generator.molgpt import MolGPTMolecularGenerator
+
+__all__ = [
+    # 'BaseMolecularPredictor',
+    # predictors
+    'SGIRMolecularPredictor',
+    'GREAMolecularPredictor',
+    'GNNMolecularPredictor',
+    'IRMMolecularPredictor',
+    'SSRMolecularPredictor',
+    'DIRMolecularPredictor',
+    'RPGNNMolecularPredictor',
+    'BFGNNMolecularPredictor',
+    'GRINMolecularPredictor',
+    'LSTMMolecularPredictor',
+    'SMILESTransformerMolecularPredictor',
+    # encoders
+    'SupervisedMolecularEncoder',
+    'AttrMaskMolecularEncoder',
+    'MoamaMolecularEncoder',
+    'GraphMAEMolecularEncoder',
+    'ContextPredMolecularEncoder',
+    'EdgePredMolecularEncoder',
+    'InfoGraphMolecularEncoder',
+    'HFPretrainedMolecularEncoder',
+    # generators
+    'GraphDITMolecularGenerator',
+    'DigressMolecularGenerator',
+    'GDSSMolecularGenerator',
+    'GraphGAMolecularGenerator',
+    'JTVAEMolecularGenerator',
+    'MolGPTMolecularGenerator',
+    'LSTMMolecularGenerator',
+]

torch_molecule-0.1.0/torch_molecule/base/__init__.py

@@ -0,0 +1,8 @@
+from .predictor import BaseMolecularPredictor
+from .encoder import BaseMolecularEncoder
+from .generator import BaseMolecularGenerator
+__all__ = [
+    "BaseMolecularPredictor",
+    "BaseMolecularEncoder",
+    "BaseMolecularGenerator",
+]