atoms_and_chains (
        asets,
        ilists,
        load_atoms,
        )

sublist ( list,  indices )

select_nearby (
        distance,
        load_atoms,
        displayed_only,
        )

Select atoms and chains near the currently selected atoms and chains.

all_multiscale_chains ()

atomic_contacts (
        asets1,
        asets2,
        distance,
        load_atoms,
        )

Find atomic contacts between two sets of multiscale chains. Return contact atoms, optionally loading atoms if needed.

chain_atom_subset ( ca )

Make Atom_Set for subset of atoms from multiscale chain.

molecule_atom_set ( ma )

Make Atom_Set for subset of atoms not in a multiscale chain.

chain_atom_sets ( cplist )

Get chain coordinates and transforms. Chains that differ only by a transform use the same Numeric array of coordinates.

group_atoms ( atoms )

xform_numeric_array ( xf )

select_contacts (
        distance,
        load_atoms,
        displayed_only,
        )

Select contacts between selected and unselected atoms and chains

remove_undisplayed_table_atoms ( table )

select_atoms_and_chains ( atoms,  cplist )

atom_shown ( a )

Check if atom, ribbon or multiscale surface is shown for an atom.

TODO: Would like to check MSMS surface representation too.

chain_transform ( cp )

selected_and_unselected_atom_sets ( displayed_only )

Deal with loaded and unloaded atoms, multiscale and non-multiscale models, and atom and multiscale chain selections.

subtract_lists ( list1,  list2 )

all_atoms ()

selected_multiscale_chains ()

all_atoms_and_chains ( asets,  load_atoms )

Atom_Set