Selections

PILOTS supports two selection sources:

• Atom groups from [groups] based on dump fields, regions, id/type/mol, and similar predicates.

• Topology groups from [topo_groups] based on bonds, connectivity, components, and related topology-derived queries.

Both are converted into a per-frame atom set. Measures can combine them with boolean logic at measure scope.

Atom groups

Atom groups are defined under [groups]. Example:

[groups]
backbone = type==1
slab = region:slab zmin=0 zmax=10

Topology groups

Topology groups are defined under [topo_groups] and always produce an atom set. They require topology bonds to be loaded.

[topo_groups]
bonded = atoms_in_any_bond
big_components = atoms_in_component_size>=100

Measure-level combination

Each measure may specify:

• group: atom-group expression (default: all)

• topo_group: topo-group expression (default: all)

• combine: boolean expression over A and T (default: A&T)

The complement operators !A and !T are defined with respect to the current frame’s atom universe. Many time-correlation measures additionally require the resulting selection to be static across frames.