Selecting the query and the database

To select the references for the calculation of the contacts you can use the select() method in both QueryProteins and MembraneDatabase objects. The selection parameter can be any of:

1. an MDAnalysis Atom, Residue or AtomGroup.

2. a string selection using the MDAnalysis selection syntax.

3. a mask using the macros metadata added.

The last option above is very useful for selecting individual proteins as the query for the contact calculation, as you can use any of the labels in target_system.query.list_proteins().

selection_mask = target_system.query.whole.macros == 'Protein0'
target_system.query.select(selection_mask)