Superposition: Cast universes w and w/o models to atom groups

[dominiquesydow]

Description

Universes can come with or without models. Currently, we only consider universes with models in our superposition module: the first model is selected for the alignment. After this selection, the object type changes from an MDA Universe to AtomGroup.

Example:

# With models
structures = [Structure.from_pdbid("4y72"), Structure.from_pdbid("1xqz"), Structure.from_pdbid("1m17")]
align(structures, user_select=False, method=METHODS["mda"]);

# Without models (casting an MDA NoDataError)
f1, f2, f3 = ...  # Path to PDB files*
structures = [Structure.from_string(f1), Structure.from_string(f2), Structure.from_string(f3)]
align(structures, user_select=False, method=METHODS["mda"]);

*Download PBD files (terminal):

for pdb in 4y72 1xqz 1m17; do wget https://www.rcsb.org/structure/$pdb -o $pdb.pdb; done

Solution

Cast all universes (regardless of whether they contain models or not) to AtomGroup objects.

Todos

• [x] Add _universe_to_atomgroup function
• [x] Apply function to reference and all mobile structures before the alignment
• [x] [Off-topic] Make opencadd.structure.superposition.api.align parameter user_select optional (default is False); this will allow back-compatibility with earlier version when user_select was not a parameter, yet.

Status

• [x] Ready to go

[codecov-commenter]

Codecov Report

Merging #149 (656f6b3) into master (097e3b5) will decrease coverage by 0.02%. The diff coverage is 83.33%.

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