Building a Universe

[lilyminium]

Story: As a user, I want to concatenate selections of trajectories, so that I can use principal component analysis to compare them in a lower dimensional space. [Notebook example]

Story: As a user, I want to build my own Universe from scratch, so that I can generate random molecules as test cases. [Notebook example]

Acceptance criteria:

• I understand how Universe.empty() works.
• I understand how to load in coordinates manually.
• I understand how to add and delete atoms/residues
• I understand how to create a new Universe with Merge.
• I have a link to the Topology section.

[richardjgowers]

Another relevant example here might be the genconf/editconf example of tiling out an existing Universe using mda.Merge/U.empty()

[orbeckst]

As a user, I want to concatenate selections of trajectories,

Do you mean concatenating trajectories? If so, this means understanding what the ChainReader does.

[orbeckst]

The MemoryReader is also a good tool for these universe building hacks, see https://www.mdanalysis.org/mdanalysis/documentation_pages/coordinates/memory.html#creating-an-in-memory-trajectory-of-a-sub-system

[lilyminium]

Do you mean concatenating trajectories? If so, this means understanding what the ChainReader does.

I meant being able to select and concatenate AtomGroups from different Universes. One common reason for this would be to perform principal component analysis to compare variance of different trajectories on a lower dimensional space. As far as I know, you can only do this by constructing a new Universe with Merge, and loading copied coordinates with MemoryReader.

e.g.

def copy_coords(universe):
    
    def copy_pos(atom_group):
        return atom_group.positions.copy()
    
    selected = universe.select_atoms('protein')
    analysis = AnalysisFromFunction(copy_pos, selected)
    analysis.run()
    return analysis.results

pgp_coords = copy_coords(pgp)
pgp_atp_coords = copy_coords(pgp_atp)
pgp_atp_morphine_coords = copy_coords(pgp_atp_morphine)

combined_coords = np.vstack([pgp_coords, pgp_atp_coords, pgp_atp_morphine_coords])

combined = mda.Merge(pgp.select_atoms('protein'))
combined.load_new(combined_coords, format=MemoryReader)

[lilyminium]

Closed by #14 .