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Update python version dependency to include Python 3.13 #197

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Merged
mtessmer merged 4 commits into from
Jul 10, 2025
Merged

Update python version dependency to include Python 3.13 #197

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26f45cb
Bump python and chilife minor version
mtessmer Jul 7, 2025
c9e460b
Fix bug in MolSysIC applying the first chain operator to all chains e…
mtessmer Jul 7, 2025
abcdf10
Bump tolerance to fix test
mtessmer Jul 7, 2025
ee0c10f
Add notice to README.md
mtessmer Jul 10, 2025
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15 changes: 8 additions & 7 deletions README.md
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Expand Up @@ -11,14 +11,15 @@
</p>


| **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! |



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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -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',
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4 changes: 2 additions & 2 deletions src/chilife/MolSysIC.py
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion src/chilife/__init__.py
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Expand Up @@ -26,4 +26,4 @@
# SpinLabel = SpinLabel.SpinLabel
# dSpinLabel = dSpinLabel.dSpinLabel

__version__ = '1.1.6'
__version__ = '1.1.7'
2 changes: 1 addition & 1 deletion tests/test_Scoring.py
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Expand Up @@ -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():
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