43 improve check logic in molecular dynamics normalizers #44
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| @@ -68,6 +68,11 @@ class BeadGroup(object): | |||
| def __init__(self, atoms, compound='fragments'): | |||
| """Initialize with an AtomGroup instance. | |||
| Will split based on keyword 'compounds' (residues or fragments). | |||
| self._atoms: AtomGroup (total number of atoms) | |||
| self.compound: str (dictates type of grouping) | |||
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We need to make sure that things like "grouping" and "compound" (line 75) are explained in the documentation.
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This compound/fragments concept is an MDAnalysis thing, tbh I don't fully understand the full usage. Only that 'fragments' is the correct keyword to grab molecules for some reason (at least in the examples that I have seen)
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If there is something that you think we specifically need to add to the documentation, could you make an issue about it so we don't forget?
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| if ags_by_moltype.masses is not None: | ||
| ags_by_moltype = ags_by_moltype[ | ||
| ags_by_moltype.masses > abs(1e-2) |
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Do we need to remove the virtual sites from the uploads, or would keeping them in the trajectory but "ignoring" them during postprocessing a better option?
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This is purely so that the RDFs/MSDs are not calculated for the virtual sites. Otherwise, I think they should be fully supported to upload.
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Ok, then it is like I was suggesting.
JFRudzinski
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@Bernadette-Mohr I still need to do some tests, but you can review when you have a chance. Try to think if any other checks might be useful.