Class AtomSelectionOptions

java.lang.Object
ffx.potential.cli.AtomSelectionOptions

public class AtomSelectionOptions extends Object
Represents command line options for scripts that support atom selections.
Since:
1.0
Author:
Michael J. Schnieders
  • Constructor Details

    • AtomSelectionOptions

      public AtomSelectionOptions()
  • Method Details

    • actOnAtoms

      public static void actOnAtoms(@Nonnull MolecularAssembly assembly, @Nullable String selection, @Nonnull BiConsumer<Atom,Boolean> action, @Nonnull String description)
    • getActiveAtoms

      public String getActiveAtoms()
      --aa or --activeAtoms Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].
      Returns:
      Returns active atoms.
    • setActiveAtoms

      public void setActiveAtoms(MolecularAssembly molecularAssembly)
      Set active atoms for a MolecularAssembly.
      Parameters:
      molecularAssembly - a MolecularAssembly object.
    • getInactiveAtoms

      public String getInactiveAtoms()
      --ia or --inactiveAtoms Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].
      Returns:
      Returns inactive atoms.
    • isAtomSelectionSet

      public boolean isAtomSelectionSet()
      Check if either the active or inactive atom selection is set.
      Returns:
      True if one of the fields is not empty.