Tutorial:Selecting subsets of atoms

NOTE: TUTORIAL WRITING IN PROGRESS DO NOT FOLLOW THIS

This is an example on how to select atoms and residues with MSL, following the example program example_selecting_atoms_and_residues.cpp in the examples/ subdirectory.

Complete source of example_selecting_atoms_and_residues

Background

MSL objects can be selected if they inherit the Selectable object. So far, Atoms and Residues are Selectable. The requirement for being selectable is to implement the virtual "addSelectableFunctions", which define what properties of the object can be selected upon.

Selection By Name Can select based on selection flags that are inside each Atom. By default every atom has an "all" selection flag set.

You can create selection flags for atoms by:

• Using Atom object:

    
    a.setSelectionFlag("foobar")

• Using AtomSelection object:

    as.select("foobar, chain A")

Selection By Property Using AtomSelection Object, to select all atoms of chain A:

    as.select("chain A")

To compile

% make bin/example_selecting_atoms_and_residues

To run the program

Go to the main directory and run the command (note, the location of the exampleFiles subdirectory needs to be provided as an argument)

% bin/example_selecting_atoms_and_residues exampleFiles

Program description

• Creating an AtomSelection object

	
	AtomSelection sel(sys.getAtomPointers());

• Basic selection 'all'

	AtomPointerVector allAts = sel.select("all");

• Select chain A atoms and store as "chA" for easy retrieval

	AtomPointerVector chainAAts = sel.select("chA, chain A");

• Expanding the selection logic , first a long-hand selection string is used. second a short-hand version of the same selection is used.

	AtomPointerVector backbone    = sel.select("bb, (((name CA OR name N) OR name C) OR name O)");

	AtomPointerVector bbShortHand = sel.select("bb2, name CA+N+C+O");

• Selections using names from previous selections

	AtomPointerVector test = sel.select("new, bb AND name O");

• Selections using NOT operator

	AtomPointerVector notBB = sel.select("notBB, not name CA+C+O+N");

• Selections using range "-" operator.

	AtomPointerVector res26 = sel.select("res26, resi 2-6");

• Selection using distances to a sub-selection

	AtomPointerVector oxygensHbondSer = sel.select("oxygensHbondSer, name O WITHIN 3.5 OF name OG");

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