resonance-flow 0.1.0__tar.gz

resonance_flow-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 George Elkins
+
+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.

resonance_flow-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: resonance-flow
+Version: 0.1.0
+Summary: Self-correcting protein folding with differentiable NMR constraints
+Author: George Elkins
+License: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jax
+Requires-Dist: jaxlib
+Requires-Dist: flax
+Requires-Dist: optax
+Requires-Dist: jax-md
+Requires-Dist: numpy
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: mkdocs; extra == "dev"
+Requires-Dist: mkdocs-material; extra == "dev"
+Requires-Dist: mkdocstrings[python]; extra == "dev"
+Dynamic: license-file
+
+# 🧬 ResonanceFlow: Differentiable Protein Structure Prediction with NMR Self-Correction
+
+[![Tests](https://github.com/elkins/resonance-flow/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/resonance-flow/actions/workflows/test.yml)
+[![Docs](https://github.com/elkins/resonance-flow/actions/workflows/docs.yml/badge.svg)](https://github.com/elkins/resonance-flow/actions/workflows/docs.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Documentation](https://img.shields.io/badge/docs-mkdocs--material-blue.svg)](https://elkins.github.io/resonance-flow/)
+[![Python](https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12-blue.svg)](https://www.python.org/)
+[![Version](https://img.shields.io/badge/version-0.1.0--alpha-orange.svg)](https://github.com/elkins/resonance-flow/releases)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Linting: ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Type checked: mypy](https://img.shields.io/badge/type%20checked-mypy-blue.svg)](https://mypy-lang.org/)
+[![JAX](https://img.shields.io/badge/framework-JAX%20%2B%20Flax-9cf.svg)](https://jax.readthedocs.io/)
+
+**ResonanceFlow** is a JAX-native protein structure prediction framework that integrates differentiable biophysics with experimental NMR constraints. It allows models to "self-correct" by propagating gradients from physical violations (atomic clashes, bad geometry) and NMR observables (RDCs, NOE distances) back into the neural network architecture — end-to-end, with no manual refinement step.
+
+---
+
+## 🚀 Key Features
+
+- **JAX-Native Gradient Flow** — End-to-end differentiability from experimental constraints to model weights via `jax.grad`.
+- **Saupe Tensor RDC Loss** — Differentiable least-squares fitting of the alignment tensor at every forward pass (Bax & Tjandra 1997; Cornilescu et al. 1998).
+- **NOE Distance Restraints** — Flat-bottomed harmonic penalty on upper-bound violations, the primary 3D information source in protein NMR (Wüthrich 1986; Güntert et al. 1997).
+- **Biophysically Correct Geometry** — Bond length loss calibrated to the canonical Cα–Cα distance of 3.80 Å (Engh & Huber 1991).
+- **Differentiable Steric Clash** — Harmonic atom-overlap penalty with optional AMBER/CHARMM-style 1-2/1-3 bonded exclusions, powered by `jax-md`.
+- **RDC Quality Metric** — Built-in Q-factor (Cornilescu et al. 1998) for structural validation without additional tooling.
+- **PBC Support** — Periodic boundary conditions for simulation-box contexts.
+- **Transformer-to-Coords** — A pre-LN Transformer architecture that maps amino acid sequences directly to physical 3D Cα coordinates.
+
+---
+
+## 🧠 The Concept: "Self-Correction"
+
+Traditional folding models are trained on static PDB snapshots. ResonanceFlow instead teaches a model to *listen* to physical laws and NMR data during training itself:
+
+```
+  Sequence  →  [Transformer]  →  Cα Coordinates
+                                       │
+                  ┌────────────────────┼──────────────────────┐
+                  ▼                    ▼                       ▼
+           Steric Clash          Bond Length              RDC / NOE
+             Penalty               Loss                  Mismatch
+                  └────────────────────┼──────────────────────┘
+                                       │  ∇θ L_total
+                                       ▼
+                              [Optimizer Step]
+```
+
+Gradients from every constraint flow back simultaneously into the model weights — the model learns not just from data, but from physics.
+
+---
+
+## 🛠️ Installation
+
+```bash
+pip install resonance-flow
+```
+
+For development (includes linting, type-checking, testing, and docs):
+
+```bash
+git clone https://github.com/elkins/resonance-flow.git
+cd resonance-flow
+pip install -e ".[dev]"
+```
+
+**Requirements:** Python 3.10+, JAX ≥ 0.4, Flax, Optax, jax-md, NumPy.
+
+---
+
+## 🧪 Quick Start
+
+### Run the self-correction demo
+
+```python
+from resonance_flow.train import main
+
+state = main(num_steps=100)
+# Step   0 | Total Loss: 12.3421 | Steric: 0.0012 | Bond: 1.2034 | RDC: 0.0087
+# Step  10 | Total Loss:  4.1823 | ...
+# Step 100 | Total Loss:  0.0031 | ...
+```
+
+### Use individual loss functions
+
+```python
+import jax.numpy as jnp
+from resonance_flow import (
+    get_steric_clash_loss,
+    get_bond_length_loss,
+    rdc_loss,
+    rdc_q_factor,
+    noe_upper_bound_loss,
+    estimate_nh_proxy_vectors,
+)
+
+# ── Steric clash (AMBER-style 1-2 bonded exclusion) ──────────────────────────
+clash_fn   = get_steric_clash_loss(exclude_bonded_range=1)
+positions  = jnp.array([[0.0, 0.0, 0.0], [4.0, 0.0, 0.0]])
+atom_radii = jnp.array([1.5, 1.5])
+clash_fn(positions, atom_radii)          # → 0.0  (no overlap)
+
+# ── Bond length (Cα–Cα virtual bond, Engh & Huber 1991) ─────────────────────
+bond_fn  = get_bond_length_loss()        # default target = 3.8 Å
+ca_chain = jnp.array([[0.0,0.0,0.0],[3.8,0.0,0.0],[7.6,0.0,0.0]])
+bond_fn(ca_chain)                        # → ~0.0
+
+# ── RDC loss (Saupe tensor fitting) ─────────────────────────────────────────
+nh_vecs      = jnp.array([[1.,0.,0.],[0.,1.,0.],[0.,0.,1.],
+                           [0.7,0.7,0.],[0.7,0.,0.7],[0.,0.7,0.7]])
+measured_rdc = jnp.array([10., -5., 2., 0., 4., 8.])
+rdc_loss(nh_vecs, measured_rdc)          # → scalar MSE
+
+# ── RDC Q-factor (structure quality; Q ≤ 0.20 = high quality) ───────────────
+rdc_q_factor(nh_vecs, measured_rdc)      # → 0 – 1 (lower is better)
+
+# ── N-H proxy vectors from Cα coordinates (Cα-only models) ──────────────────
+ca_coords = jax.random.normal(jax.random.PRNGKey(0), (10, 3))
+nh_proxy  = estimate_nh_proxy_vectors(ca_coords)   # → (8, 3) unit vectors
+
+# ── NOE upper-bound distance restraints (Wüthrich 1986) ─────────────────────
+noe_pairs    = jnp.array([[0, 2], [1, 3]])
+upper_bounds = jnp.array([5.0, 4.5])
+noe_upper_bound_loss(positions, noe_pairs[:1], upper_bounds[:1])  # → 0.0
+```
+
+---
+
+## 🔬 Scientific Basis
+
+All loss functions and validation metrics are grounded in published, peer-reviewed NMR methodology:
+
+| Loss / Metric | Scientific Basis |
+|---|---|
+| RDC loss — Saupe tensor | Bax & Tjandra, *J. Biomol. NMR* 1997; Cornilescu et al., *JACS* 1998 |
+| RDC Q-factor | Cornilescu et al., *JACS* 1998; Clore & Garrett, *JACS* 1999 |
+| NOE distance restraints | Wüthrich, *NMR of Proteins and Nucleic Acids* 1986; Güntert et al., *J. Mol. Biol.* 1997 |
+| Cα–Cα bond distance (3.8 Å) | Engh & Huber, *Acta Crystallogr. A* 1991 |
+| N-H proxy vectors | Zweckstetter & Bax, *JACS* 2000 |
+| Bonded exclusion (1-2/1-3) | Cornell et al. (AMBER), *JACS* 1995; MacKerell et al. (CHARMM), *J. Phys. Chem. B* 1998 |
+| d_max = 21 700 Hz | Ottiger & Bax, *JACS* 1998 |
+
+---
+
+## 🧬 Architecture
+
+```
+TransformerCoordinatePredictor
+├── Embedding         (vocab_size=21, d_model=128)
+├── Positional Embed  (learned, max_len=512)
+├── N × Pre-LN Block
+│   ├── LayerNorm → MultiHeadSelfAttention → Residual
+│   └── LayerNorm → FFN (4× expand, GELU) → Residual
+└── LayerNorm → Linear(3)   # → (batch, seq_len, 3) Cα coordinates
+```
+
+The pre-LN (LayerNorm before attention) layout avoids gradient
+explosion and follows the convention recommended by Xiong et al. 2020.
+
+---
+
+## 🤝 Contributing
+
+Contributions are welcome! Please open an issue or pull request. The project follows:
+
+- **Formatting + Linting:** `ruff` / `ruff format`
+- **Type checking:** `mypy`
+- **Testing:** `pytest` with coverage
+
+```bash
+# Run the full quality pipeline before submitting a PR
+ruff check resonance_flow tests
+ruff format resonance_flow tests
+mypy resonance_flow tests
+pytest --cov=resonance_flow tests
+```
+
+---
+
+## 📚 Documentation
+
+Full theory, API reference, and examples at **[elkins.github.io/resonance-flow](https://elkins.github.io/resonance-flow/)**.
+
+---
+
+## ⚖️ License
+
+MIT © George Elkins
+
+---
+
+## 🔗 Related Projects
+
+ResonanceFlow is the most complete end-to-end model in this ecosystem, depending on:
+
+- [diff-biophys](https://github.com/elkins/diff-biophys) — Differentiable RDC, NOE, bond-length, and clash kernels
+- [synth-nmr](https://github.com/elkins/synth-nmr) — NMR parameter libraries (chemical shifts, Karplus, RDC)
+- [synth-pdb](https://github.com/elkins/synth-pdb) — Protein structure data generation
+- [TorsionTuner](https://github.com/elkins/TorsionTuner) — Single-structure refinement using similar torsion-space kinematics
+- [diff-ensemble](https://github.com/elkins/diff-ensemble) — Ensemble counterpart for IDPs
+
+---
+
+## 📖 Citation
+
+```bibtex
+@software{resonance_flow,
+  author  = {Elkins, George},
+  title   = {ResonanceFlow: Differentiable protein structure prediction with NMR self-correction},
+  year    = {2024},
+  url     = {https://github.com/elkins/resonance-flow},
+  version = {0.1.0}
+}
+```

resonance_flow-0.1.0/README.md

@@ -0,0 +1,213 @@
+# 🧬 ResonanceFlow: Differentiable Protein Structure Prediction with NMR Self-Correction
+
+[![Tests](https://github.com/elkins/resonance-flow/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/resonance-flow/actions/workflows/test.yml)
+[![Docs](https://github.com/elkins/resonance-flow/actions/workflows/docs.yml/badge.svg)](https://github.com/elkins/resonance-flow/actions/workflows/docs.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Documentation](https://img.shields.io/badge/docs-mkdocs--material-blue.svg)](https://elkins.github.io/resonance-flow/)
+[![Python](https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12-blue.svg)](https://www.python.org/)
+[![Version](https://img.shields.io/badge/version-0.1.0--alpha-orange.svg)](https://github.com/elkins/resonance-flow/releases)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Linting: ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Type checked: mypy](https://img.shields.io/badge/type%20checked-mypy-blue.svg)](https://mypy-lang.org/)
+[![JAX](https://img.shields.io/badge/framework-JAX%20%2B%20Flax-9cf.svg)](https://jax.readthedocs.io/)
+
+**ResonanceFlow** is a JAX-native protein structure prediction framework that integrates differentiable biophysics with experimental NMR constraints. It allows models to "self-correct" by propagating gradients from physical violations (atomic clashes, bad geometry) and NMR observables (RDCs, NOE distances) back into the neural network architecture — end-to-end, with no manual refinement step.
+
+---
+
+## 🚀 Key Features
+
+- **JAX-Native Gradient Flow** — End-to-end differentiability from experimental constraints to model weights via `jax.grad`.
+- **Saupe Tensor RDC Loss** — Differentiable least-squares fitting of the alignment tensor at every forward pass (Bax & Tjandra 1997; Cornilescu et al. 1998).
+- **NOE Distance Restraints** — Flat-bottomed harmonic penalty on upper-bound violations, the primary 3D information source in protein NMR (Wüthrich 1986; Güntert et al. 1997).
+- **Biophysically Correct Geometry** — Bond length loss calibrated to the canonical Cα–Cα distance of 3.80 Å (Engh & Huber 1991).
+- **Differentiable Steric Clash** — Harmonic atom-overlap penalty with optional AMBER/CHARMM-style 1-2/1-3 bonded exclusions, powered by `jax-md`.
+- **RDC Quality Metric** — Built-in Q-factor (Cornilescu et al. 1998) for structural validation without additional tooling.
+- **PBC Support** — Periodic boundary conditions for simulation-box contexts.
+- **Transformer-to-Coords** — A pre-LN Transformer architecture that maps amino acid sequences directly to physical 3D Cα coordinates.
+
+---
+
+## 🧠 The Concept: "Self-Correction"
+
+Traditional folding models are trained on static PDB snapshots. ResonanceFlow instead teaches a model to *listen* to physical laws and NMR data during training itself:
+
+```
+  Sequence  →  [Transformer]  →  Cα Coordinates
+                                       │
+                  ┌────────────────────┼──────────────────────┐
+                  ▼                    ▼                       ▼
+           Steric Clash          Bond Length              RDC / NOE
+             Penalty               Loss                  Mismatch
+                  └────────────────────┼──────────────────────┘
+                                       │  ∇θ L_total
+                                       ▼
+                              [Optimizer Step]
+```
+
+Gradients from every constraint flow back simultaneously into the model weights — the model learns not just from data, but from physics.
+
+---
+
+## 🛠️ Installation
+
+```bash
+pip install resonance-flow
+```
+
+For development (includes linting, type-checking, testing, and docs):
+
+```bash
+git clone https://github.com/elkins/resonance-flow.git
+cd resonance-flow
+pip install -e ".[dev]"
+```
+
+**Requirements:** Python 3.10+, JAX ≥ 0.4, Flax, Optax, jax-md, NumPy.
+
+---
+
+## 🧪 Quick Start
+
+### Run the self-correction demo
+
+```python
+from resonance_flow.train import main
+
+state = main(num_steps=100)
+# Step   0 | Total Loss: 12.3421 | Steric: 0.0012 | Bond: 1.2034 | RDC: 0.0087
+# Step  10 | Total Loss:  4.1823 | ...
+# Step 100 | Total Loss:  0.0031 | ...
+```
+
+### Use individual loss functions
+
+```python
+import jax.numpy as jnp
+from resonance_flow import (
+    get_steric_clash_loss,
+    get_bond_length_loss,
+    rdc_loss,
+    rdc_q_factor,
+    noe_upper_bound_loss,
+    estimate_nh_proxy_vectors,
+)
+
+# ── Steric clash (AMBER-style 1-2 bonded exclusion) ──────────────────────────
+clash_fn   = get_steric_clash_loss(exclude_bonded_range=1)
+positions  = jnp.array([[0.0, 0.0, 0.0], [4.0, 0.0, 0.0]])
+atom_radii = jnp.array([1.5, 1.5])
+clash_fn(positions, atom_radii)          # → 0.0  (no overlap)
+
+# ── Bond length (Cα–Cα virtual bond, Engh & Huber 1991) ─────────────────────
+bond_fn  = get_bond_length_loss()        # default target = 3.8 Å
+ca_chain = jnp.array([[0.0,0.0,0.0],[3.8,0.0,0.0],[7.6,0.0,0.0]])
+bond_fn(ca_chain)                        # → ~0.0
+
+# ── RDC loss (Saupe tensor fitting) ─────────────────────────────────────────
+nh_vecs      = jnp.array([[1.,0.,0.],[0.,1.,0.],[0.,0.,1.],
+                           [0.7,0.7,0.],[0.7,0.,0.7],[0.,0.7,0.7]])
+measured_rdc = jnp.array([10., -5., 2., 0., 4., 8.])
+rdc_loss(nh_vecs, measured_rdc)          # → scalar MSE
+
+# ── RDC Q-factor (structure quality; Q ≤ 0.20 = high quality) ───────────────
+rdc_q_factor(nh_vecs, measured_rdc)      # → 0 – 1 (lower is better)
+
+# ── N-H proxy vectors from Cα coordinates (Cα-only models) ──────────────────
+ca_coords = jax.random.normal(jax.random.PRNGKey(0), (10, 3))
+nh_proxy  = estimate_nh_proxy_vectors(ca_coords)   # → (8, 3) unit vectors
+
+# ── NOE upper-bound distance restraints (Wüthrich 1986) ─────────────────────
+noe_pairs    = jnp.array([[0, 2], [1, 3]])
+upper_bounds = jnp.array([5.0, 4.5])
+noe_upper_bound_loss(positions, noe_pairs[:1], upper_bounds[:1])  # → 0.0
+```
+
+---
+
+## 🔬 Scientific Basis
+
+All loss functions and validation metrics are grounded in published, peer-reviewed NMR methodology:
+
+| Loss / Metric | Scientific Basis |
+|---|---|
+| RDC loss — Saupe tensor | Bax & Tjandra, *J. Biomol. NMR* 1997; Cornilescu et al., *JACS* 1998 |
+| RDC Q-factor | Cornilescu et al., *JACS* 1998; Clore & Garrett, *JACS* 1999 |
+| NOE distance restraints | Wüthrich, *NMR of Proteins and Nucleic Acids* 1986; Güntert et al., *J. Mol. Biol.* 1997 |
+| Cα–Cα bond distance (3.8 Å) | Engh & Huber, *Acta Crystallogr. A* 1991 |
+| N-H proxy vectors | Zweckstetter & Bax, *JACS* 2000 |
+| Bonded exclusion (1-2/1-3) | Cornell et al. (AMBER), *JACS* 1995; MacKerell et al. (CHARMM), *J. Phys. Chem. B* 1998 |
+| d_max = 21 700 Hz | Ottiger & Bax, *JACS* 1998 |
+
+---
+
+## 🧬 Architecture
+
+```
+TransformerCoordinatePredictor
+├── Embedding         (vocab_size=21, d_model=128)
+├── Positional Embed  (learned, max_len=512)
+├── N × Pre-LN Block
+│   ├── LayerNorm → MultiHeadSelfAttention → Residual
+│   └── LayerNorm → FFN (4× expand, GELU) → Residual
+└── LayerNorm → Linear(3)   # → (batch, seq_len, 3) Cα coordinates
+```
+
+The pre-LN (LayerNorm before attention) layout avoids gradient
+explosion and follows the convention recommended by Xiong et al. 2020.
+
+---
+
+## 🤝 Contributing
+
+Contributions are welcome! Please open an issue or pull request. The project follows:
+
+- **Formatting + Linting:** `ruff` / `ruff format`
+- **Type checking:** `mypy`
+- **Testing:** `pytest` with coverage
+
+```bash
+# Run the full quality pipeline before submitting a PR
+ruff check resonance_flow tests
+ruff format resonance_flow tests
+mypy resonance_flow tests
+pytest --cov=resonance_flow tests
+```
+
+---
+
+## 📚 Documentation
+
+Full theory, API reference, and examples at **[elkins.github.io/resonance-flow](https://elkins.github.io/resonance-flow/)**.
+
+---
+
+## ⚖️ License
+
+MIT © George Elkins
+
+---
+
+## 🔗 Related Projects
+
+ResonanceFlow is the most complete end-to-end model in this ecosystem, depending on:
+
+- [diff-biophys](https://github.com/elkins/diff-biophys) — Differentiable RDC, NOE, bond-length, and clash kernels
+- [synth-nmr](https://github.com/elkins/synth-nmr) — NMR parameter libraries (chemical shifts, Karplus, RDC)
+- [synth-pdb](https://github.com/elkins/synth-pdb) — Protein structure data generation
+- [TorsionTuner](https://github.com/elkins/TorsionTuner) — Single-structure refinement using similar torsion-space kinematics
+- [diff-ensemble](https://github.com/elkins/diff-ensemble) — Ensemble counterpart for IDPs
+
+---
+
+## 📖 Citation
+
+```bibtex
+@software{resonance_flow,
+  author  = {Elkins, George},
+  title   = {ResonanceFlow: Differentiable protein structure prediction with NMR self-correction},
+  year    = {2024},
+  url     = {https://github.com/elkins/resonance-flow},
+  version = {0.1.0}
+}
+```

resonance_flow-0.1.0/pyproject.toml

@@ -0,0 +1,130 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "resonance-flow"
+version = "0.1.0"
+description = "Self-correcting protein folding with differentiable NMR constraints"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [{name = "George Elkins"}]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "jax",
+    "jaxlib",
+    "flax",
+    "optax",
+    "jax-md",
+    "numpy",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "ruff",
+    "black",
+    "mypy",
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings[python]",
+]
+
+[tool.setuptools.packages.find]
+include = ["resonance_flow*"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+pythonpath = ["."]
+python_files = ["test_*.py"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py310"
+
+[tool.black]
+line-length = 100
+target-version = ['py310']
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
+[tool.ruff.lint]
+select = [
+    "E",   # pycodestyle errors
+    "W",   # pycodestyle warnings
+    "F",   # pyflakes
+    "I",   # isort
+    "N",   # pep8-naming
+    "UP",  # pyupgrade
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+]
+ignore = [
+    "E501",  # line length handled by formatter
+    "N806",  # uppercase variables in functions (scientific constants: Da, R, S2)
+    "N803",  # uppercase arguments (common in biophysics)
+    "N802",  # uppercase function names (physics convention)
+    "B017",  # asserting on Exception (acceptable in generic error tests)
+    "B904",  # raise from (not yet fixed project-wide)
+]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]  # re-exports are intentional
+"tests/*" = ["N", "B"]   # naming/bugbear not enforced in tests
+
+[tool.ruff.lint.isort]
+known-first-party = ["resonance_flow"]
+
+[tool.mypy]
+python_version = "3.10"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+check_untyped_defs = true
+strict_equality = true
+exclude = ["build/", "dist/", "scratch/", "site/"]
+
+[[tool.mypy.overrides]]
+module = ["tests.*", "scripts.*", "examples.*"]
+disallow_untyped_defs = false
+
+[[tool.mypy.overrides]]
+module = [
+    "jax.*",
+    "jaxlib.*",
+    "flax.*",
+    "optax.*",
+    "jax_md.*",
+    "numpy.*",
+]
+ignore_missing_imports = true
+
+# ── Coverage ──────────────────────────────────────────────────────────────────
+[tool.coverage.run]
+source = ["."]
+omit = ["*/tests/*", "*/test_*.py"]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
+]

resonance_flow-0.1.0/resonance_flow/__init__.py

@@ -0,0 +1,11 @@
+from resonance_flow.losses import estimate_nh_proxy_vectors as estimate_nh_proxy_vectors
+from resonance_flow.losses import get_bond_length_loss as get_bond_length_loss
+from resonance_flow.losses import get_steric_clash_loss as get_steric_clash_loss
+from resonance_flow.losses import noe_upper_bound_loss as noe_upper_bound_loss
+from resonance_flow.losses import rdc_loss as rdc_loss
+from resonance_flow.losses import rdc_q_factor as rdc_q_factor
+from resonance_flow.model import (
+    TransformerCoordinatePredictor as TransformerCoordinatePredictor,
+)
+
+__version__ = "0.1.0"