Fix multi chain RMSD analysis #64
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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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## main #64 +/- ##
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- Coverage 88.16% 87.28% -0.89%
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Lines 338 346 +8
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hannahbaumann
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pre-commit.ci autofix |
| 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.
| # this only works for orthogonal boxes | ||
| ag.positions -= np.rint(vec / box) * box | ||
| frac = np.linalg.solve(box.T, vec) # fractional coordinates | ||
| shift = np.dot(np.round(frac), box) # nearest image |
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Maybe comment round to get the nearest image, then compute the shift
| 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?
After #70 (merged in that branch into this PR to fix tests)
Fixes #30