From 26f45cb281300512367e36839c1521f50ec9e053 Mon Sep 17 00:00:00 2001 From: Maxx Tessmer Date: Mon, 7 Jul 2025 14:25:53 -0700 Subject: [PATCH 1/4] Bump python and chilife minor version --- pyproject.toml | 2 +- src/chilife/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 102e606..d63f5b7 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors=[{name = 'Maxx Tessmer', email='mhtessmer@gmail.com'}, {name = 'Stefan Stoll', email='stst@uw.edu'}] keywords=['Spin-label', 'EPR', 'DEER', 'PELDOR', 'Side-chain'] dynamic = ["version"] -requires-python = ">= 3.8,<3.13" +requires-python = ">= 3.8,<3.14" dependencies = ['numpy>=1.23.0', 'scipy>=1.6.3', 'matplotlib>=3.3.4', diff --git a/src/chilife/__init__.py b/src/chilife/__init__.py index a9c466d..45425bb 100644 --- a/src/chilife/__init__.py +++ b/src/chilife/__init__.py @@ -26,4 +26,4 @@ # SpinLabel = SpinLabel.SpinLabel # dSpinLabel = dSpinLabel.dSpinLabel -__version__ = '1.1.6' +__version__ = '1.1.7' From c9e460b4651c1c337d372ecaa38c70454fc33287 Mon Sep 17 00:00:00 2001 From: Maxx Tessmer Date: Mon, 7 Jul 2025 14:27:39 -0700 Subject: [PATCH 2/4] Fix bug in MolSysIC applying the first chain operator to all chains even when there are different operators for all frames --- src/chilife/MolSysIC.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/chilife/MolSysIC.py b/src/chilife/MolSysIC.py index 9e66960..a28ac47 100644 --- a/src/chilife/MolSysIC.py +++ b/src/chilife/MolSysIC.py @@ -813,8 +813,8 @@ def apply_chain_operators(self, idx=None, from_list=False): for i, op in zip(idx, self._chain_operators[idx]): for start, stop in self._chain_segs: current_mx, current_ori = ic_mx(*cart_coords[i, start:start+3]) - mx = self.chain_operators[start]['mx'] - ori = self.chain_operators[start]['ori'] + mx = op[start]['mx'] + ori = op[start]['ori'] m2m3 = current_mx @ mx cart_coords[i, start:stop] = (cart_coords[i, start:stop] - current_ori) @ m2m3 + ori From abcdf10fdcc9bb5d5e22eb993e3d1a690b32ffde Mon Sep 17 00:00:00 2001 From: Maxx Tessmer Date: Mon, 7 Jul 2025 14:42:17 -0700 Subject: [PATCH 3/4] Bump tolerance to fix test --- tests/test_Scoring.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_Scoring.py b/tests/test_Scoring.py index e5e8a1b..f65db6f 100644 --- a/tests/test_Scoring.py +++ b/tests/test_Scoring.py @@ -40,7 +40,7 @@ def test_efunc_dlabel(func): f = chilife.ljEnergyFunc(func) test = f(dSL) ans = np.load(f'test_data/d{func.__name__}.npy') - np.testing.assert_almost_equal(test, ans, decimal=4) + np.testing.assert_almost_equal(test, ans, decimal=3) def test_molar_gas_constant(): From ee0c10f63d7e9c78804c7ee3363493b9a5a8582f Mon Sep 17 00:00:00 2001 From: Maxx Tessmer Date: Thu, 10 Jul 2025 09:47:38 -0700 Subject: [PATCH 4/4] Add notice to README.md --- README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 2a5f0ee..1182f91 100644 --- a/README.md +++ b/README.md @@ -11,14 +11,15 @@

-| **UPDATES** | -|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| 2025.02.17 : Check out our new examples for trajectory analysis [Example_12](https://stolllab.github.io/chiLife/gallery/12-Analyzing_MD_Simulations.html) and using OpenMM for repacking [Example_13](https://stolllab.github.io/chiLife/gallery/13-OpenMM_Score_Function.html). | +| **UPDATES** | +|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| 2025.07.10 : chilife now supported for Python 3.13 | +| 2025.02.17 : Check out our new example for trajectory analysis [Example_12](https://stolllab.github.io/chiLife/gallery/12-Analyzing_MD_Simulations.html) and using OpenMM for repacking [Example_13](https://stolllab.github.io/chiLife/gallery/13-OpenMM_Score_Function.html).| | 2024.12.26 : Changes to the "energy funciton" backend. forcefield, forgive factors, etc should all be parts of the energy function now, and not parts of a rotamer library Checkout [Example_07](https://stolllab.github.io/chiLife/gallery/13-OpenMM_Score_Function.html) | -| 2024.08.15 : chiLife 1.0 released! | -| 2024.08.15 : chiLife can now be used to create arbitrary peptides with natural and NCAAs. Checkout the `make_peptide` function. | -| 2024.08.15 : chiLife can make NCAA structures from smiles. Checkout `smiles2residue`. Note: Requires RDKit to be installed. | -| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more! | +| 2024.08.15 : chiLife 1.0 released! | +| 2024.08.15 : chiLife can now be used to create arbitrary peptides with natural and NCAAs. Checkout the `make_peptide` function. | +| 2024.08.15 : chiLife can make NCAA structures from smiles. Checkout `smiles2residue`. Note: Requires RDKit to be installed. | +| chiLife now supports arbitrary backbone attachments including DNA and RNA labels and more! |