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Add simulation extraction and viewing notebook #226

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0562cfb
add trajectory notebook
jthorton Sep 5, 2025
2169fe2
add info on extracting end states, use mdtraj to image the molecules
jthorton Sep 22, 2025
c8d5ea6
Update simulation_visualisation/simulation_visualisation.ipynb
jthorton Oct 8, 2025
3c77455
Merge branch 'main' into traj-view
jthorton Oct 8, 2025
1251354
Merge branch 'main' into traj-view
jthorton Oct 22, 2025
9342a9c
Merge branch 'main' into traj-view
atravitz Dec 11, 2025
9980155
Merge branch 'main' into traj-view
IAlibay Dec 11, 2025
ef80ed0
apply feedback, add pngs for nglview sections
jthorton Jan 6, 2026
21d55f8
add septop end-state selection info
jthorton Jan 6, 2026
584b1bb
Merge branch 'main' into traj-view
hannahbaumann Jun 2, 2026
671d19e
Update env to install openfe_analysis from main
hannahbaumann Jun 2, 2026
a9c0f51
Updates to reflect changes in openfe_analysis API
hannahbaumann Jun 2, 2026
0a6bf07
Add rendered images
hannahbaumann Jun 2, 2026
9448ed1
Use smaller dataset
hannahbaumann Jun 2, 2026
e934315
Increasing resolution
hannahbaumann Jun 2, 2026
5fba3ae
Update render
hannahbaumann Jun 2, 2026
386fbdc
Address review comments
hannahbaumann Jun 8, 2026
b733ebb
Add link to mda docs
hannahbaumann Jun 8, 2026
23016f3
Address review comments
hannahbaumann Jun 10, 2026
f907d97
Remove unused images
hannahbaumann Jun 10, 2026
eae7810
Switch to c-f install
hannahbaumann Jun 10, 2026
9234a2e
Some more edits
hannahbaumann Jun 10, 2026
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1 change: 1 addition & 0 deletions environment.yaml
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Expand Up @@ -9,6 +9,7 @@ dependencies:
- nglview
- notebook
- numpy <2.4.0 # https://github.com/OpenFreeEnergy/cinnabar/issues/198
- openfe-analysis>=0.5.0
- pip
- pytest
- pytest-cov
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879 changes: 879 additions & 0 deletions simulation_visualization/simulation_visualization.ipynb
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