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hannahbaumann
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Check if this works for triclinic boxes. From Irfan: There might also be code in MDAnalysis that does the math also working for triclinic boxes. |
…e runners for the matrix
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hannahbaumann
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| center = self.central_ag.center_of_mass() | ||
| box = self.central_ag.dimensions[:3] | ||
| center = self.reference.center_of_mass() | ||
| box = triclinic_vectors(ts.dimensions) |
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Nice this is great that it works with all boxes.
src/openfe_analysis/rmsd.py
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| for frag in prot.fragments: | ||
| make_whole(frag, reference_atom=frag[0]) |
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Showing the limits of my MDAnalysis knowledge, but does this not need to be added to the trajectory transformations?
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I actually just realized that we don't need this, since that's done in the unwrap tranformation. Removed it.
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| nope = NoJump(prot) | ||
| minnie = Minimiser(prot, ligand) | ||
| # Unwrap all atoms | ||
| unwrap_tr = unwrap(prot) |
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Here I changed the NoJump to unwrap since NoJump only corrects the COM. Should we do the same for the ligand below? @IAlibay , do you know what was the reason for implementing this new NoJump transformation instead of using the MDanalysis unwrap?
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After #70 (merged in that branch into this PR to fix tests)
Fixes #30