Apply image shifting by fragment#124
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #124 +/- ##
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+ Coverage 98.26% 98.27% +0.01%
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Files 9 9
Lines 461 465 +4
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+ Hits 453 457 +4
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hannahbaumann
changed the title
| @@ -58,11 +58,15 @@ def apply_complex_alignment_transformations( | |||
| # 1. Make molecules whole (protein + optional ligand) | |||
| transforms = [unwrap(group)] | |||
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This now makes the alignment very very slow. Unwrap loops over the fragments and before (when there was no bond information), there were a lot of fragments that were very small.
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How much of a problem is this in practice?
IAlibay
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IAlibay
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One thing to fix, one question, and a missing news entry.
Otherwise it looks great to me!
| @@ -58,11 +58,15 @@ def apply_complex_alignment_transformations( | |||
| # 1. Make molecules whole (protein + optional ligand) | |||
| transforms = [unwrap(group)] | |||
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How much of a problem is this in practice?
| chains = [seg.atoms for seg in protein.segments] | ||
| shift_targets = chains[1:] + ligands | ||
| # 2. Closest image shift for protein fragments + ligand (if present) | ||
| fragments = list(protein.fragments) |
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Is it worth checking for bonds in protein before you do this?
| skip = max(n_frames // 500, 1) | ||
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| u_top = mda.Universe(pdb_topology) | ||
| u_top.select_atoms("protein").guess_bonds() |
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I believe you have to avoid doing this if there is no protein, otherwise it'll crash out.
| u_top.select_atoms("protein").guess_bonds() | |
| protein = u_top.select_atoms("protein") | |
| if protein: | |
| protein.guess_bonds() |
Note: this also shows that we don't have any tests that are solvent only - we should raise an issue to deal with that.
2 participants
When two chains of a protein have the same
segid, the PBC are not handled correctly during alignment since they would appear as one segment. This PR switches to use theprotein.fragmentsinstead. For fragments to be recognized correctly, we first need to guess the bonds in the protein.Having the large fragments now makes
unwrap()very slow which is fragment based.