bayesianflow-for-chem 1.2.4__tar.gz → 2.3.1__tar.gz

{bayesianflow_for_chem-1.2.4 → bayesianflow_for_chem-2.3.1}/PKG-INFO

@@ -1,36 +1,35 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: bayesianflow_for_chem
-Version: 1.2.4
+Version: 2.3.1
 Summary: Bayesian flow network framework for Chemistry
 Home-page: https://augus1999.github.io/bayesian-flow-network-for-chemistry/
 Author: Nianze A. Tao
 Author-email: tao-nianze@hiroshima-u.ac.jp
-License: AGPL-3.0 licence
+License: AGPL-3.0-or-later
 Project-URL: Source, https://github.com/Augus1999/bayesian-flow-network-for-chemistry
 Keywords: Chemistry,CLM,ChemBFN
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU Affero General Public License v3
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: rdkit>=2023.9.6
-Requires-Dist: torch>=2.3.1
-Requires-Dist: numpy>=1.26.4
+Requires-Dist: rdkit>=2025.3.5
+Requires-Dist: torch>=2.8.0
+Requires-Dist: torchao>=0.12
+Requires-Dist: colorama>=0.4.6
+Requires-Dist: numpy>=2.3.2
+Requires-Dist: scipy>=1.16.1
 Requires-Dist: loralib>=0.1.2
-Requires-Dist: lightning>=2.2.0
-Requires-Dist: scikit-learn>=1.5.0
-Requires-Dist: typing_extensions>=4.8.0
-Provides-Extra: geo2seq
-Requires-Dist: pynauty>=2.8.8.1; extra == "geo2seq"
+Requires-Dist: lightning>=2.5.3
+Requires-Dist: scikit-learn>=1.7.1
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -39,8 +38,8 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
+Dynamic: license-file
 Dynamic: project-url
-Dynamic: provides-extra
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
@@ -52,11 +51,18 @@ Dynamic: summary
 
 This is the repository of the PyTorch implementation of ChemBFN model.
 
+### Build State
+
+[![PyPI](https://img.shields.io/pypi/v/bayesianflow-for-chem?color=ff69b4)](https://pypi.org/project/bayesianflow-for-chem/)
+![pytest](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/actions/workflows/pytest.yml/badge.svg)
+[![document](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/actions/workflows/pages/pages-build-deployment/badge.svg)](https://augus1999.github.io/bayesian-flow-network-for-chemistry/)
+
 ## Features
 
 ChemBFN provides the state-of-the-art functionalities of
 * SMILES or SELFIES-based *de novo* molecule generation
 * Protein sequence *de novo* generation
+* Template optimisation (mol2mol)
 * Classifier-free guidance conditional generation (single or multi-objective optimisation)
 * Context-guided conditional generation (inpaint)
 * Outstanding out-of-distribution chemical space sampling
@@ -68,6 +74,7 @@ in an all-in-one-model style.
 
 ## News
 
+* [09/10/2025] A web app [`chembfn_webui`](https://github.com/Augus1999/ChemBFN-WebUI) for hosting ChemBFN models is available on [PyPI](https://pypi.org/project/chembfn-webui/).
 * [30/01/2025] The package `bayesianflow_for_chem` is available on [PyPI](https://pypi.org/project/bayesianflow-for-chem/).
 * [21/01/2025] Our first paper has been accepted by [JCIM](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01792).
 * [17/12/2024] The second paper of out-of-distribution generation is available on [arxiv.org](https://arxiv.org/abs/2412.11439).
@@ -82,17 +89,17 @@ $ pip install -U bayesianflow_for_chem
 
 ## Usage
 
-You can find example scripts in [📁example](./example) folder.
+You can find example scripts in [📁example](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/tree/main/example) folder.
 
 ## Pre-trained Model
 
-You can find pretrained models in [release](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/releases) or on our [🤗Hugging Face model page](https://huggingface.co/suenoomozawa/ChemBFN).
+You can find pretrained models on our [🤗Hugging Face model page](https://huggingface.co/suenoomozawa/ChemBFN).
 
 ## Dataset Handling
 
-We provide a Python class [`CSVData`](./bayesianflow_for_chem/data.py) to handle data stored in CSV or similar format containing headers to identify the entities. The following is a quickstart.
+We provide a Python class [`CSVData`](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/blob/main/bayesianflow_for_chem/data.py#L153) to handle data stored in CSV or similar format containing headers to identify the entities. The following is a quickstart.
 
-1. Download your dataset file (e.g., ESOL form [MoleculeNet](https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/delaney-processed.csv)) and split the file:
+1. Download your dataset file (e.g., ESOL from [MoleculeNet](https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/delaney-processed.csv)) and split the file:
 ```python
 >>> from bayesianflow_for_chem.tool import split_data
 

{bayesianflow_for_chem-1.2.4 → bayesianflow_for_chem-2.3.1}/README.md

@@ -5,11 +5,18 @@
 
 This is the repository of the PyTorch implementation of ChemBFN model.
 
+### Build State
+
+[![PyPI](https://img.shields.io/pypi/v/bayesianflow-for-chem?color=ff69b4)](https://pypi.org/project/bayesianflow-for-chem/)
+![pytest](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/actions/workflows/pytest.yml/badge.svg)
+[![document](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/actions/workflows/pages/pages-build-deployment/badge.svg)](https://augus1999.github.io/bayesian-flow-network-for-chemistry/)
+
 ## Features
 
 ChemBFN provides the state-of-the-art functionalities of
 * SMILES or SELFIES-based *de novo* molecule generation
 * Protein sequence *de novo* generation
+* Template optimisation (mol2mol)
 * Classifier-free guidance conditional generation (single or multi-objective optimisation)
 * Context-guided conditional generation (inpaint)
 * Outstanding out-of-distribution chemical space sampling
@@ -21,6 +28,7 @@ in an all-in-one-model style.
 
 ## News
 
+* [09/10/2025] A web app [`chembfn_webui`](https://github.com/Augus1999/ChemBFN-WebUI) for hosting ChemBFN models is available on [PyPI](https://pypi.org/project/chembfn-webui/).
 * [30/01/2025] The package `bayesianflow_for_chem` is available on [PyPI](https://pypi.org/project/bayesianflow-for-chem/).
 * [21/01/2025] Our first paper has been accepted by [JCIM](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01792).
 * [17/12/2024] The second paper of out-of-distribution generation is available on [arxiv.org](https://arxiv.org/abs/2412.11439).
@@ -39,13 +47,13 @@ You can find example scripts in [📁example](./example) folder.
 
 ## Pre-trained Model
 
-You can find pretrained models in [release](https://github.com/Augus1999/bayesian-flow-network-for-chemistry/releases) or on our [🤗Hugging Face model page](https://huggingface.co/suenoomozawa/ChemBFN).
+You can find pretrained models on our [🤗Hugging Face model page](https://huggingface.co/suenoomozawa/ChemBFN).
 
 ## Dataset Handling
 
 We provide a Python class [`CSVData`](./bayesianflow_for_chem/data.py) to handle data stored in CSV or similar format containing headers to identify the entities. The following is a quickstart.
 
-1. Download your dataset file (e.g., ESOL form [MoleculeNet](https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/delaney-processed.csv)) and split the file:
+1. Download your dataset file (e.g., ESOL from [MoleculeNet](https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/delaney-processed.csv)) and split the file:
 ```python
 >>> from bayesianflow_for_chem.tool import split_data
 

bayesianflow_for_chem-2.3.1/bayesianflow_for_chem/__init__.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+# Author: Nianze A. Tao (Omozawa Sueno)
+"""
+ChemBFN package.
+"""
+from . import data, tool, train, scorer, spectra
+from .model import ChemBFN, MLP, EnsembleChemBFN
+
+__all__ = [
+    "data",
+    "tool",
+    "train",
+    "scorer",
+    "spectra",
+    "ChemBFN",
+    "MLP",
+    "EnsembleChemBFN",
+]
+__version__ = "2.3.1"
+__author__ = "Nianze A. Tao (Omozawa Sueno)"
+
+
+def main() -> None:
+    """
+    CLI main function.
+
+    :return:
+    :rtype: None
+    """
+    import colorama
+    from bayesianflow_for_chem.cli import main_script
+
+    colorama.just_fix_windows_console()
+    main_script(__version__)
+    colorama.deinit()