refua 0.0.1__tar.gz

refua-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 Jeremy Wohlwend, Gabriele Corso, Saro Passaro
+Copyright (c) 2025 Hannes Stärk
+Copyright (c) 2026 TensorSpace, Inc.
+
+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.

refua-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: refua
+Version: 0.0.1
+Summary: Unified drug discovery ML toolkit
+License-Expression: MIT
+License-File: LICENSE
+Keywords: drug discovery,machine learning,protein design,structure prediction,generative design
+Author: JJ Ben-Joseph
+Author-email: jj@tensorspace.ai
+Requires-Python: >=3.11,<3.15
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+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 :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Provides-Extra: analysis
+Provides-Extra: cuda
+Provides-Extra: dev
+Provides-Extra: doc
+Provides-Extra: lint
+Provides-Extra: process
+Provides-Extra: test
+Provides-Extra: train
+Requires-Dist: biopython (>=1.84)
+Requires-Dist: biotite
+Requires-Dist: chembl_structure_pipeline (>=1.2.2)
+Requires-Dist: click (>=8.1.7)
+Requires-Dist: cuequivariance_ops_cu12 (>=0.5.0) ; extra == "cuda"
+Requires-Dist: cuequivariance_ops_torch_cu12 (>=0.5.0) ; extra == "cuda"
+Requires-Dist: cuequivariance_torch (>=0.5.0) ; extra == "cuda"
+Requires-Dist: dm-tree (>=0.1.8)
+Requires-Dist: einops (>=0.8.0)
+Requires-Dist: einx (>=0.3.0)
+Requires-Dist: fairscale (>=0.4.13)
+Requires-Dist: furo (>=2024.1.29) ; extra == "dev"
+Requires-Dist: furo (>=2024.1.29) ; extra == "doc"
+Requires-Dist: gemmi (>=0.6.5)
+Requires-Dist: huggingface_hub
+Requires-Dist: hydra-core (>=1.3.2)
+Requires-Dist: hydride ; extra == "analysis"
+Requires-Dist: logomaker
+Requires-Dist: logomaker ; extra == "analysis"
+Requires-Dist: mashumaro (>=3.14)
+Requires-Dist: matplotlib
+Requires-Dist: matplotlib ; extra == "analysis"
+Requires-Dist: matplotlib ; extra == "train"
+Requires-Dist: modelcif (>=1.2)
+Requires-Dist: myst-parser (>=2.0.0) ; extra == "dev"
+Requires-Dist: myst-parser (>=2.0.0) ; extra == "doc"
+Requires-Dist: numba (>=0.61.0)
+Requires-Dist: numpy (>=1.26,<2.0)
+Requires-Dist: nvidia-ml-py (>=12.535.133) ; extra == "cuda"
+Requires-Dist: p_tqdm ; extra == "process"
+Requires-Dist: pandas (>=2.2.2)
+Requires-Dist: pandas (>=2.2.2) ; extra == "analysis"
+Requires-Dist: pandas (>=2.2.2) ; extra == "dev"
+Requires-Dist: pandas (>=2.2.2) ; extra == "test"
+Requires-Dist: pandas (>=2.2.2) ; extra == "train"
+Requires-Dist: pdbeccdutils ; extra == "process"
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: pydssp
+Requires-Dist: pytest ; extra == "dev"
+Requires-Dist: pytest ; extra == "test"
+Requires-Dist: pytorch-lightning (>=2.5.0)
+Requires-Dist: pyyaml (>=6.0.2)
+Requires-Dist: rdkit (>=2024.3.2)
+Requires-Dist: redis ; extra == "dev"
+Requires-Dist: redis ; extra == "process"
+Requires-Dist: requests (>=2.32.3)
+Requires-Dist: requests ; extra == "dev"
+Requires-Dist: requests ; extra == "test"
+Requires-Dist: ruff ; extra == "dev"
+Requires-Dist: ruff ; extra == "lint"
+Requires-Dist: scikit-learn (>=1.6.1)
+Requires-Dist: scipy (>=1.13.1)
+Requires-Dist: sphinx (>=7) ; extra == "dev"
+Requires-Dist: sphinx (>=7) ; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints (>=1.25.2) ; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints (>=1.25.2) ; extra == "doc"
+Requires-Dist: torch (>=2.4.1)
+Requires-Dist: tqdm
+Requires-Dist: types-requests (>=2.32.4) ; extra == "dev"
+Requires-Dist: wandb (>=0.18.7) ; extra == "dev"
+Requires-Dist: wandb (>=0.18.7) ; extra == "train"
+Project-URL: Homepage, https://tensorspace.ai/
+Project-URL: Repository, https://github.com/tensorspace-ai/refua
+Description-Content-Type: text/markdown
+
+# Refua
+
+Refua is a general drug discovery ML toolkit that brings together structure prediction, affinity modeling, and generative design in one package. It unifies the Boltz inference stack with the BoltzGen design pipeline so you can move from target definition to candidate generation using a shared, programmatic API.
+
+## Why use Refua?
+
+- **Fluent Python API:** Build specs, run predictions, and post-process results with a readable, composable
+  API—no need to stitch together CLI calls, YAML, or intermediate files.
+- **No per-call model reload:** Keep a predictor/model instance alive and run many inferences in a loop
+  without paying initialization and checkpoint-loading cost each time.
+- **All-in-memory workflows:** Prepare inputs, run inference, and perform analysis entirely in memory
+  (e.g., passing objects/arrays between steps) without writing temporary files to disk.
+- **Improved build:** We are able to support more up to date dependencies. Over time we expect to widen this support.
+
+## Quickstart
+
+Install:
+
+```bash
+pip install refua
+```
+
+Install with NVIDIA GPU support:
+
+```bash
+pip install "refua[cuda]"
+```
+
+Boltz-2 API:
+
+```python
+from pathlib import Path
+
+from refua import Boltz2
+
+model = Boltz2()
+
+complex_spec = (
+    model.fold_complex()
+    .protein("A", "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ")
+    .ligand("L", "CCO")
+)
+
+Path("complex.bcif").write_bytes(complex_spec.to_bcif())
+affinity = complex_spec.get_affinity()
+print(affinity.ic50, affinity.binding_probability)
+```
+
+BoltzGen API:
+
+```python
+from refua import BoltzGen
+
+gen = BoltzGen()
+design = (
+    gen.design("simple_design")
+    .protein("A", "12")
+    .total_length(8, 20)
+)
+
+features = design.to_features()
+print(sorted(features.keys())[:6])
+```
+
+BoltzGen defaults to the bundled molecule library in the Hugging Face cache. Set `BOLTZGEN_MOLDIR` or pass `mol_dir` to override.
+
+CLI entrypoints are still available:
+
+```bash
+boltz --help
+boltzgen --help
+```
+
+## Documentation
+
+- Boltz docs live in `docs/boltz`.
+- BoltzGen docs live in `docs/boltzgen`.
+- API reference source lives in `docs/api` (build with `sphinx-build -b html docs/api docs/api/_build/html`).
+
+## Examples
+
+- `examples/antibody_design.py` shows a minimal BoltzGen antibody design spec.
+- `examples/protein_ligand_affinity.py` shows a Boltz protein-ligand affinity spec.
+- `examples/boltz2_kras_mrtx1133.py` folds KRAS G12D with the MRTX-1133 inhibitor and prints affinity.
+- `examples/boltzgen_peptide_binder.py` shows a BoltzGen peptide binder spec with optional cyclic peptides.
+- `examples/boltz_constraints.py` shows a Boltz complex with pocket/contact constraints and an optional MSA.
+- `examples/boltz_multichain_msa.py` shows multi-chain MSAs with cross-chain constraints.
+- `examples/boltzgen_template_insertions.py` shows template structure groups and design insertions.
+- `examples/boltz_multi_pocket_complex.py` shows multi-ligand pocket constraints with contacts.
+- `examples/boltzgen_template_masks.py` shows template masks with design/not-design ranges and structure groups.
+
+## Notes
+
+This repository consolidates the two stacks into a single build and dependency set. If you need the legacy standalone documentation, it has been preserved under `docs/`.
+

refua-0.0.1/README.md

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+# Refua
+
+Refua is a general drug discovery ML toolkit that brings together structure prediction, affinity modeling, and generative design in one package. It unifies the Boltz inference stack with the BoltzGen design pipeline so you can move from target definition to candidate generation using a shared, programmatic API.
+
+## Why use Refua?
+
+- **Fluent Python API:** Build specs, run predictions, and post-process results with a readable, composable
+  API—no need to stitch together CLI calls, YAML, or intermediate files.
+- **No per-call model reload:** Keep a predictor/model instance alive and run many inferences in a loop
+  without paying initialization and checkpoint-loading cost each time.
+- **All-in-memory workflows:** Prepare inputs, run inference, and perform analysis entirely in memory
+  (e.g., passing objects/arrays between steps) without writing temporary files to disk.
+- **Improved build:** We are able to support more up to date dependencies. Over time we expect to widen this support.
+
+## Quickstart
+
+Install:
+
+```bash
+pip install refua
+```
+
+Install with NVIDIA GPU support:
+
+```bash
+pip install "refua[cuda]"
+```
+
+Boltz-2 API:
+
+```python
+from pathlib import Path
+
+from refua import Boltz2
+
+model = Boltz2()
+
+complex_spec = (
+    model.fold_complex()
+    .protein("A", "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ")
+    .ligand("L", "CCO")
+)
+
+Path("complex.bcif").write_bytes(complex_spec.to_bcif())
+affinity = complex_spec.get_affinity()
+print(affinity.ic50, affinity.binding_probability)
+```
+
+BoltzGen API:
+
+```python
+from refua import BoltzGen
+
+gen = BoltzGen()
+design = (
+    gen.design("simple_design")
+    .protein("A", "12")
+    .total_length(8, 20)
+)
+
+features = design.to_features()
+print(sorted(features.keys())[:6])
+```
+
+BoltzGen defaults to the bundled molecule library in the Hugging Face cache. Set `BOLTZGEN_MOLDIR` or pass `mol_dir` to override.
+
+CLI entrypoints are still available:
+
+```bash
+boltz --help
+boltzgen --help
+```
+
+## Documentation
+
+- Boltz docs live in `docs/boltz`.
+- BoltzGen docs live in `docs/boltzgen`.
+- API reference source lives in `docs/api` (build with `sphinx-build -b html docs/api docs/api/_build/html`).
+
+## Examples
+
+- `examples/antibody_design.py` shows a minimal BoltzGen antibody design spec.
+- `examples/protein_ligand_affinity.py` shows a Boltz protein-ligand affinity spec.
+- `examples/boltz2_kras_mrtx1133.py` folds KRAS G12D with the MRTX-1133 inhibitor and prints affinity.
+- `examples/boltzgen_peptide_binder.py` shows a BoltzGen peptide binder spec with optional cyclic peptides.
+- `examples/boltz_constraints.py` shows a Boltz complex with pocket/contact constraints and an optional MSA.
+- `examples/boltz_multichain_msa.py` shows multi-chain MSAs with cross-chain constraints.
+- `examples/boltzgen_template_insertions.py` shows template structure groups and design insertions.
+- `examples/boltz_multi_pocket_complex.py` shows multi-ligand pocket constraints with contacts.
+- `examples/boltzgen_template_masks.py` shows template masks with design/not-design ranges and structure groups.
+
+## Notes
+
+This repository consolidates the two stacks into a single build and dependency set. If you need the legacy standalone documentation, it has been preserved under `docs/`.

refua-0.0.1/pyproject.toml

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+[build-system]
+requires = ["poetry-core>=1.9.0"]
+build-backend = "poetry.core.masonry.api"
+
+[project]
+name = "refua"
+version = "0.0.1"
+requires-python = ">=3.11,<3.15"
+description = "Unified drug discovery ML toolkit"
+readme = "README.md"
+license = "MIT"
+authors = [{name = "JJ Ben-Joseph", email = "jj@tensorspace.ai"}]
+keywords = [
+    "drug discovery",
+    "machine learning",
+    "protein design",
+    "structure prediction",
+    "generative design",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "torch>=2.4.1",
+    "numpy>=1.26,<2.0",
+    "hydra-core>=1.3.2",
+    "pytorch-lightning>=2.5.0",
+    "rdkit>=2024.3.2",
+    "dm-tree>=0.1.8",
+    "requests>=2.32.3",
+    "einops>=0.8.0",
+    "einx>=0.3.0",
+    "fairscale>=0.4.13",
+    "mashumaro>=3.14",
+    "modelcif>=1.2",
+    "click>=8.1.7",
+    "pyyaml>=6.0.2",
+    "biopython>=1.84",
+    "scipy>=1.13.1",
+    "numba>=0.61.0",
+    "gemmi>=0.6.5",
+    "scikit-learn>=1.6.1",
+    "chembl_structure_pipeline>=1.2.2",
+    "biotite",
+    "pydssp",
+    "huggingface_hub",
+    "pandas>=2.2.2",
+    "matplotlib",
+    "logomaker",
+    "tqdm",
+]
+
+[project.urls]
+Homepage = "https://tensorspace.ai/"
+Repository = "https://github.com/tensorspace-ai/refua"
+
+[project.scripts]
+boltz = "refua.boltz.main:cli"
+boltzgen = "refua.boltzgen.cli.boltzgen:main"
+
+[project.optional-dependencies]
+lint = ["ruff"]
+test = ["pytest", "requests", "pandas>=2.2.2"]
+doc = [
+    "sphinx>=7",
+    "furo>=2024.1.29",
+    "myst-parser>=2.0.0",
+    "sphinx-autodoc-typehints>=1.25.2",
+]
+cuda = [
+    "cuequivariance_ops_cu12>=0.5.0",
+    "cuequivariance_ops_torch_cu12>=0.5.0",
+    "cuequivariance_torch>=0.5.0",
+    "nvidia-ml-py>=12.535.133",
+]
+analysis = [
+    "pandas>=2.2.2",
+    "matplotlib",
+    "logomaker",
+    "hydride",
+]
+train = [
+    "wandb>=0.18.7",
+    "pandas>=2.2.2",
+    "matplotlib",
+]
+process = [
+    "pdbeccdutils",
+    "p_tqdm",
+    "redis",
+]
+dev = [
+    "ruff",
+    "pre-commit",
+    "pytest",
+    "requests",
+    "types-requests>=2.32.4",
+    "pandas>=2.2.2",
+    "redis",
+    "wandb>=0.18.7",
+    "sphinx>=7",
+    "furo>=2024.1.29",
+    "myst-parser>=2.0.0",
+    "sphinx-autodoc-typehints>=1.25.2",
+]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+refua.boltzgen = ["resources/**/*"]
+
+[tool.ruff]
+src = ["src"]
+extend-exclude = ["conf.py"]
+target-version = "py311"
+lint.select = ["ALL"]
+lint.ignore = [
+    "COM812",  # Conflicts with the formatter
+    "ISC001",  # Conflicts with the formatter
+    "RET504",  # Unnecessary assignment to `x` before `return` statement
+    "S101",    # Use of `assert` detected
+    "D100",    # Missing docstring in public module
+    "D104",    # Missing docstring in public package
+    "PT001",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
+    "PT023",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
+    "FBT001",
+    "FBT002",
+    "PLR0913", # Too many arguments to init (> 5)
+    "TRY003",  # Exception messages
+    "EM101",   # Exception messages
+    "FA102",   # typing
+    "T201",    # Print statements
+]
+
+[tool.ruff.lint.per-file-ignores]
+"**/__init__.py" = [
+    "F401", # Imported but unused
+    "F403", # Wildcard imports
+]
+"docs/**" = [
+    "INP001", # Requires __init__.py but folder is not a package.
+]
+"scripts/**" = [
+    "INP001", # Requires __init__.py but folder is not a package.
+]
+"tests/**" = [
+    "S101", # Use of `assert` detected
+    "D103", # Missing docstring in public function
+]
+
+[tool.ruff.lint.pyupgrade]
+# Preserve types, even if a file imports `from __future__ import annotations`
+keep-runtime-typing = true
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.pytest.ini_options]
+markers = [
+    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
+    "regression",
+]
+pythonpath = ["src"]
+
+[tool.mypy]
+# Functions need to be annotated
+disallow_untyped_defs = true
+warn_unused_ignores = true
+exclude = ["configs/", "build/", "dist/", "docs/", "tests/"]

refua-0.0.1/src/refua/__init__.py

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+from importlib.metadata import PackageNotFoundError, version
+
+from refua.api import download_assets
+from refua.boltz.api import Boltz2
+from refua.boltzgen.api import BoltzGen
+
+try:  # noqa: SIM105
+    __version__ = version("refua")
+except PackageNotFoundError:
+    # package is not installed
+    pass
+
+__all__ = ["Boltz2", "BoltzGen", "download_assets"]