diff-hdx 0.1.1__tar.gz → 0.1.2__tar.gz

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diff-hdx
-Version: 0.1.1
+Version: 0.1.2
 Summary: Differentiable HDX-MS prediction in JAX
 Author: George Elkins
 License: MIT
@@ -26,12 +26,12 @@ Provides-Extra: dev
 Requires-Dist: pytest>=7.0.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: ruff>=0.6.0; extra == "dev"
-Requires-Dist: mypy>=1.8.0; extra == "dev"
+Requires-Dist: mypy>=1.11.0; extra == "dev"
 Dynamic: license-file
 
 # 🧪 diff-hdx: Differentiable HDX-MS Prediction in JAX
 
-[![Tests](https://github.com/elkins/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/diff-hdx/actions/workflows/test.yml)
+[![Tests](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![JAX](https://img.shields.io/badge/backend-JAX-9cf.svg)](https://github.com/google/jax)
 
@@ -49,6 +49,14 @@ Dynamic: license-file
 
 ---
 
+## 📚 Tutorials
+
+Experience **diff-hdx** directly in your browser:
+
+- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/elkins-lab/diff-hdx/blob/main/examples/interactive_tutorials/hdx_prediction_tutorial.ipynb) **HDX-MS Prediction & Kinetics** — Learn how to simulate intrinsic rates, protection factors, and deuterium uptake curves.
+
+---
+
 ## 🏗️ Technical Architecture
 
 - **Backend:** JAX (XLA-compiled) — supports CPU, GPU, and TPU.
@@ -84,10 +92,10 @@ pip install diff-hdx
 
 diff-hdx is part of the **differentiable biophysics** ecosystem:
 
-- [diff-biophys](https://github.com/elkins/diff-biophys) — Core differentiable biophysics engine.
-- [diff-fret](https://github.com/elkins/diff-fret) — Differentiable FRET modeling.
-- [diff-epr](https://github.com/elkins/diff-epr) — Differentiable EPR/DEER simulation.
-- [synth-pdb](https://github.com/elkins/synth-pdb) — Synthetic structure generation.
+- [diff-biophys](https://github.com/elkins-lab/diff-biophys) — Core differentiable biophysics engine.
+- [diff-fret](https://github.com/elkins-lab/diff-fret) — Differentiable FRET modeling.
+- [diff-epr](https://github.com/elkins-lab/diff-epr) — Differentiable EPR/DEER simulation.
+- [synth-pdb](https://github.com/elkins-lab/synth-pdb) — Synthetic structure generation.
 
 ---
 
@@ -98,8 +106,8 @@ diff-hdx is part of the **differentiable biophysics** ecosystem:
   author  = {Elkins, George},
   title   = {diff-hdx: Differentiable HDX-MS prediction in JAX},
   year    = {2026},
-  url     = {https://github.com/elkins/diff-hdx},
-  version = {0.1.0}
+  url     = {https://github.com/elkins-lab/diff-hdx},
+  version = {0.1.2}
 }
 ```
 

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/README.md

@@ -1,6 +1,6 @@
 # 🧪 diff-hdx: Differentiable HDX-MS Prediction in JAX
 
-[![Tests](https://github.com/elkins/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/diff-hdx/actions/workflows/test.yml)
+[![Tests](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![JAX](https://img.shields.io/badge/backend-JAX-9cf.svg)](https://github.com/google/jax)
 
@@ -18,6 +18,14 @@
 
 ---
 
+## 📚 Tutorials
+
+Experience **diff-hdx** directly in your browser:
+
+- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/elkins-lab/diff-hdx/blob/main/examples/interactive_tutorials/hdx_prediction_tutorial.ipynb) **HDX-MS Prediction & Kinetics** — Learn how to simulate intrinsic rates, protection factors, and deuterium uptake curves.
+
+---
+
 ## 🏗️ Technical Architecture
 
 - **Backend:** JAX (XLA-compiled) — supports CPU, GPU, and TPU.
@@ -53,10 +61,10 @@ pip install diff-hdx
 
 diff-hdx is part of the **differentiable biophysics** ecosystem:
 
-- [diff-biophys](https://github.com/elkins/diff-biophys) — Core differentiable biophysics engine.
-- [diff-fret](https://github.com/elkins/diff-fret) — Differentiable FRET modeling.
-- [diff-epr](https://github.com/elkins/diff-epr) — Differentiable EPR/DEER simulation.
-- [synth-pdb](https://github.com/elkins/synth-pdb) — Synthetic structure generation.
+- [diff-biophys](https://github.com/elkins-lab/diff-biophys) — Core differentiable biophysics engine.
+- [diff-fret](https://github.com/elkins-lab/diff-fret) — Differentiable FRET modeling.
+- [diff-epr](https://github.com/elkins-lab/diff-epr) — Differentiable EPR/DEER simulation.
+- [synth-pdb](https://github.com/elkins-lab/synth-pdb) — Synthetic structure generation.
 
 ---
 
@@ -67,8 +75,8 @@ diff-hdx is part of the **differentiable biophysics** ecosystem:
   author  = {Elkins, George},
   title   = {diff-hdx: Differentiable HDX-MS prediction in JAX},
   year    = {2026},
-  url     = {https://github.com/elkins/diff-hdx},
-  version = {0.1.0}
+  url     = {https://github.com/elkins-lab/diff-hdx},
+  version = {0.1.2}
 }
 ```
 

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/diff_hdx/kernels.py

@@ -65,6 +65,9 @@ def intrinsic_rates(
     """
     n = len(sequence)  # noqa: F841 -- kept for readability; not used in vectorised ops
 
+    if not sequence:
+        return jnp.zeros(0)
+
     # Encode sequence as integer indices (unknown residues → Ala)
     seq_idx = [_AA_IDX.get(aa, _ALA_IDX) for aa in sequence]
 
@@ -104,7 +107,15 @@ def intrinsic_rates(
     kb = kb_ref_t * 10.0 ** (left_corr[:, 2] + right_corr[:, 3])  # bl + br
     kw = kw_ref_t * 10.0 ** (left_corr[:, 2] + right_corr[:, 3])  # same as kb
 
-    return jnp.asarray(ka * h_plus + kb * oh_minus + kw)  # explicit Array, satisfies mypy
+    rates = ka * h_plus + kb * oh_minus + kw
+
+    # Proline has no amide proton, so its intrinsic rate is physically 0.0.
+    # Note: we use 0.0 here as the rate; downstream tools should handle this
+    # appropriately if a sentinel value or NaN is preferred instead.
+    pro_idx = _AA_IDX.get("P", -1)
+    pro_mask = jnp.where(jnp.array(seq_idx) == pro_idx, 0.0, 1.0)
+
+    return jnp.asarray(rates * pro_mask)  # explicit Array, satisfies mypy
 
 
 def sasa_approx(

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/diff_hdx.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diff-hdx
-Version: 0.1.1
+Version: 0.1.2
 Summary: Differentiable HDX-MS prediction in JAX
 Author: George Elkins
 License: MIT
@@ -26,12 +26,12 @@ Provides-Extra: dev
 Requires-Dist: pytest>=7.0.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: ruff>=0.6.0; extra == "dev"
-Requires-Dist: mypy>=1.8.0; extra == "dev"
+Requires-Dist: mypy>=1.11.0; extra == "dev"
 Dynamic: license-file
 
 # 🧪 diff-hdx: Differentiable HDX-MS Prediction in JAX
 
-[![Tests](https://github.com/elkins/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins/diff-hdx/actions/workflows/test.yml)
+[![Tests](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml/badge.svg)](https://github.com/elkins-lab/diff-hdx/actions/workflows/test.yml)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![JAX](https://img.shields.io/badge/backend-JAX-9cf.svg)](https://github.com/google/jax)
 
@@ -49,6 +49,14 @@ Dynamic: license-file
 
 ---
 
+## 📚 Tutorials
+
+Experience **diff-hdx** directly in your browser:
+
+- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/elkins-lab/diff-hdx/blob/main/examples/interactive_tutorials/hdx_prediction_tutorial.ipynb) **HDX-MS Prediction & Kinetics** — Learn how to simulate intrinsic rates, protection factors, and deuterium uptake curves.
+
+---
+
 ## 🏗️ Technical Architecture
 
 - **Backend:** JAX (XLA-compiled) — supports CPU, GPU, and TPU.
@@ -84,10 +92,10 @@ pip install diff-hdx
 
 diff-hdx is part of the **differentiable biophysics** ecosystem:
 
-- [diff-biophys](https://github.com/elkins/diff-biophys) — Core differentiable biophysics engine.
-- [diff-fret](https://github.com/elkins/diff-fret) — Differentiable FRET modeling.
-- [diff-epr](https://github.com/elkins/diff-epr) — Differentiable EPR/DEER simulation.
-- [synth-pdb](https://github.com/elkins/synth-pdb) — Synthetic structure generation.
+- [diff-biophys](https://github.com/elkins-lab/diff-biophys) — Core differentiable biophysics engine.
+- [diff-fret](https://github.com/elkins-lab/diff-fret) — Differentiable FRET modeling.
+- [diff-epr](https://github.com/elkins-lab/diff-epr) — Differentiable EPR/DEER simulation.
+- [synth-pdb](https://github.com/elkins-lab/synth-pdb) — Synthetic structure generation.
 
 ---
 
@@ -98,8 +106,8 @@ diff-hdx is part of the **differentiable biophysics** ecosystem:
   author  = {Elkins, George},
   title   = {diff-hdx: Differentiable HDX-MS prediction in JAX},
   year    = {2026},
-  url     = {https://github.com/elkins/diff-hdx},
-  version = {0.1.0}
+  url     = {https://github.com/elkins-lab/diff-hdx},
+  version = {0.1.2}
 }
 ```
 

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/diff_hdx.egg-info/requires.txt

@@ -7,4 +7,4 @@ biotite
 pytest>=7.0.0
 pytest-cov>=4.0.0
 ruff>=0.6.0
-mypy>=1.8.0
+mypy>=1.11.0

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "diff-hdx"
-version = "0.1.1"
+version = "0.1.2"
 description = "Differentiable HDX-MS prediction in JAX"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -37,7 +37,7 @@ dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
     "ruff>=0.6.0",
-    "mypy>=1.8.0",
+    "mypy>=1.11.0",
 ]
 
 [tool.setuptools.packages.find]
@@ -56,7 +56,6 @@ select = ["E", "F", "I", "N", "UP", "B"]
 ignore = ["E501", "N806", "N803", "N802"]
 
 [tool.mypy]
-python_version = "3.10"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true

{diff_hdx-0.1.1 → diff_hdx-0.1.2}/tests/test_kernels.py

@@ -155,7 +155,8 @@ def test_intrinsic_rates_jit_compatible() -> None:
     # Should compile and run without error
     rates = jit_rates("ACDEFGHIKLMNPQRSTVWY", ph=7.0, temperature=293.15)
     assert rates.shape == (20,)
-    assert jnp.all(rates > 0)
+    assert jnp.all(rates >= 0)
+    assert jnp.sum(rates == 0) == 1  # The Proline residue should be exactly 0
 
 
 def test_intrinsic_rates_temperature_dependence() -> None:
@@ -194,3 +195,74 @@ def test_h_bond_energy_far_acceptor() -> None:
     assert count_far[0] < 0.01, (
         f"H-bond count must be ~0 for acceptor far outside cutoff, got {count_far[0]:.6f}"
     )
+
+
+def test_intrinsic_rates_proline() -> None:
+    """
+    Verify that Proline (P) has an intrinsic rate of 0.0 since it lacks an amide proton.
+    """
+    rates = intrinsic_rates("APA", ph=7.0, temperature=293.15)
+    # The middle residue is Proline, should be exactly 0
+    assert rates[1] == 0.0
+    assert rates[0] > 0.0
+    assert rates[2] > 0.0
+
+
+def test_intrinsic_rates_empty_sequence() -> None:
+    """
+    Verify that an empty sequence correctly returns an empty array.
+    """
+    rates = intrinsic_rates("", ph=7.0, temperature=293.15)
+    assert rates.shape == (0,)
+
+
+def test_intrinsic_rates_ph_dependence() -> None:
+    """
+    Verify the V-shape of HDX rates across pH (minimal around pH 2.5 - 3.0).
+    """
+    rate_ph3 = intrinsic_rates("AAAA", ph=3.0, temperature=293.15)
+    rate_ph7 = intrinsic_rates("AAAA", ph=7.0, temperature=293.15)
+    rate_ph1 = intrinsic_rates("AAAA", ph=1.0, temperature=293.15)
+
+    # Rate at pH 3 should be a minimum compared to pH 1 (acid-catalyzed) and pH 7 (base-catalyzed)
+    assert jnp.all(rate_ph3 < rate_ph7)
+    assert jnp.all(rate_ph3 < rate_ph1)
+
+
+def test_protection_factors_beta_scaling() -> None:
+    """
+    Verify that beta_c and beta_asa correctly scale the H-bond and SASA burial terms.
+    """
+    coords = jnp.array([[0.0, 0.0, 0.0]])
+    h_bonds = jnp.array([2.0])
+
+    # None active (ln(PF) = 0 -> PF = 1.0)
+    pf_none = protection_factors(coords, h_bonds, beta_c=0.0, beta_asa=0.0)
+    assert jnp.allclose(pf_none, 1.0)
+
+    # Only H-bond active
+    pf_hb_only = protection_factors(coords, h_bonds, beta_c=1.0, beta_asa=0.0)
+    assert pf_hb_only[0] > 1.0
+
+    # Only SASA active - use two atoms to create some burial (SASA < 1.0)
+    coords_two = jnp.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
+    h_bonds_two = jnp.array([0.0, 0.0])
+    pf_sasa_only_two = protection_factors(coords_two, h_bonds_two, beta_c=0.0, beta_asa=1.0)
+    assert pf_sasa_only_two[0] > 1.0  # Partially buried, so 1-SASA > 0 => PF > 1
+
+
+def test_h_bond_energy_cutoff() -> None:
+    """
+    Verify that overriding the cutoff parameter successfully rejects acceptors
+    that would otherwise be included.
+    """
+    donors = jnp.array([[0.0, 0.0, 0.0]])
+    acceptors = jnp.array([[2.0, 0.0, 0.0]])  # At 2.0 A
+
+    # With default cutoff 3.5, it should be heavily counted (sigmoid(3) approx 0.95+)
+    count_default = h_bond_energy(donors, acceptors)
+    assert count_default[0] > 0.9
+
+    # With strict cutoff 1.0, it should be mostly rejected (sigmoid(-2) approx 0.11)
+    count_strict = h_bond_energy(donors, acceptors, cutoff=1.0)
+    assert count_strict[0] < 0.2