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Merged
mtessmer merged 8 commits into from
Feb 17, 2025
Merged

New Examples: Trajectory analysis and OpenMM Energy function #183

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aaf3aad
Remove logging info, remove energy_func from input_kwargs to allow se…
mtessmer Feb 14, 2025
c7c0c39
Bump version
mtessmer Feb 14, 2025
df6549d
Update test
mtessmer Feb 15, 2025
640f7dc
Refactor mutate. Clean up repack code. Fix broken test
mtessmer Feb 15, 2025
168bfc2
Add 2 new examples
mtessmer Feb 17, 2025
bfe1aa3
Update docs to include new examples
mtessmer Feb 17, 2025
a061d1e
Add new examples to readme updates
mtessmer Feb 17, 2025
3999af4
Alter test to be more specific
mtessmer Feb 17, 2025
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15 changes: 8 additions & 7 deletions README.md
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</p>


| **UPDATES** |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 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/07-Custom_Energy_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! |
| **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/07-Custom_Energy_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! |



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2 changes: 2 additions & 0 deletions docs/source/examples.rst
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gallery/09-Bifunctional_Labels.nblink
gallery/10-Nucleic_acid_labels.nblink
gallery/11-Arbitrary_molecular_labels.nblink
gallery/12-Analyzing_MD_Simulations.nblink
gallery/13-OpenMM_Score_Function.nblink
3 changes: 3 additions & 0 deletions docs/source/gallery/12-Analyzing_MD_Simulations.nblink
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{
"path": "../../../examples/12 - Analyzing MD simulations/12 - Analyzing MD Simulations.ipynb"
}
3 changes: 3 additions & 0 deletions docs/source/gallery/13-OpenMM_Score_Function.nblink
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{
"path": "../../../examples/13 - OpenMM score function/13 - OpenMM Score Function.ipynb"
}
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139 changes: 139 additions & 0 deletions examples/12 - Analyzing MD simulations/12 - Analyzing MD Simulations.ipynb
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