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Have LinearDensity support updating AtomGroups, more intuitive names, save bins #2508

lilyminium opened this issue Feb 6, 2020 · 3 comments


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@lilyminium lilyminium commented Feb 6, 2020

Is your feature request related to a problem? Please describe.

  1. This mailing list issue is a good use case of Linear Density but is foiled by the class not supporting UpdatingAtomGroups.

  2. It is not intuitive to me that LinearDensity.results['x']['pos'] refers to the mass-weighted density in g/cm^3 of the selection. pos makes me think of coordinates. char makes me think of characters.

  3. If the class saves the bins from np.histogram, it would be far easier to take advantage of existing histogram plotting tools. Also, using np.histogramdd seems easier.

  4. The output is just an array of floats and the documentation doesn't say which units the density is in. These are not the normal units of MDAnalysis (amu for mass, Angstrom for length, e for charge) so they need special documentation. Also, the units written in the header of the file output are inaccurate for the charge. See #2507 for more

Describe the solution you'd like

  1. Move the code below to _single_frame() so it updates.
        # Get masses and charges for the selection
        try:  # in case it's not an atom
            self.masses = np.array([elem.total_mass() for elem in group])
            self.charges = np.array([elem.total_charge() for elem in group])
        except AttributeError:  # much much faster for atoms
            self.masses = self._ags[0].masses
            self.charges = self._ags[0].charges

        self.totalmass = np.sum(self.masses)
  1. Call them .mass_density and .charge_density in their own NumPy arrays. Have the results as Numpy arrays instead of dictionaries.

  2. Save the bins

  3. Not change the units.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Happy to do this at some point, if people are ok with breaking scripts that have coded the original .results['x']['pos'] indexing into them

@lilyminium lilyminium mentioned this issue Feb 7, 2020
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@orbeckst orbeckst commented Feb 13, 2020

This all sounds extremely sensible to me.

For 1.0 we could break the API but if there's a way to keep the old data structures around (maybe hide them behind managed attributes that create them on the fly from the new real data structures) then that would help users who just want their old stuff to still work with the last py2 release but set us up for a clean removal for 2.0.

With properties for the old attributes we can also easily issue deprecation warnings.


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@hmacdope hmacdope commented Mar 2, 2020

Hey all,
I would love to work on this if possible?


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@lilyminium lilyminium commented Mar 2, 2020

@hmacdope please go ahead! Here is a notebook that shows a bit of the current behaviour of the class. #2507 has some notes about the units of the output.

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