Refactor RMSD analyses into MDAnalysis AnaysisBase classes#90
Refactor RMSD analyses into MDAnalysis AnaysisBase classes#90hannahbaumann wants to merge 3 commits intomainfrom
AnaysisBase classes#90Conversation
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@talagayev and @jthorton : This is a first go at the refactor into the individual RMSD classes, based on the MDAnalysis |
hannahbaumann
changed the title
AnaysisBase classes
src/openfe_analysis/rmsd.py
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| class LigandRMSD(AnalysisBase): | ||
| """ | ||
| 1D RMSD time series for a ligand AtomGroup. | ||
| """ | ||
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| def __init__(self, atomgroup, **kwargs): | ||
| super(LigandRMSD, self).__init__(atomgroup.universe.trajectory, **kwargs) | ||
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| self._ag = atomgroup | ||
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| def _prepare(self): | ||
| self.results.rmsd = [] | ||
| self._reference = self._ag.positions | ||
| self._weights = self._ag.masses / np.mean(self._ag.masses) | ||
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| def _single_frame(self): | ||
| rmsd = rms.rmsd( | ||
| self._ag.positions, | ||
| self._reference, | ||
| self._weights, | ||
| center=False, | ||
| superposition=False, | ||
| ) | ||
| self.results.rmsd.append(rmsd) | ||
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| def _conclude(self): | ||
| self.results.rmsd = np.asarray(self.results.rmsd) |
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2 initial thoughts:
- Can we make a more general RMSD class that can be reused for protein and ligand analysis, basically it should work on any atom group and does this not already exist in MDAnalysis?
- Do we not want to switch to use the symmetry RMSD (spyrmsd I think its called)?
talagayev
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talagayev
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@hannahbaumann I like it, looks very good to me :) also the structure is like for the MDAnalysis AnalysisBase classes, which is I think @IAlibay wanted to have and also adressing it that it takes any atom group adressing @jthorton comment is good.
Overall Looks good to me :)
3 participants
Refactor the rmsd analysis using this example: https://docs.mdanalysis.org/2.7.0/documentation_pages/analysis/base.html
gather_rms_datafunction but access the individual analysis classes directly in the openfeProtocolmake_Universefunction go into utils?