Fixed
A place to store all the atoms of the wild-type molecules in a conf space, where each atom is unambiguously assigned to either the static region or a design position.
The 'fixed' atoms in a conformation space are the atoms that do not get modified when swiching conformations at design positions.
Among the fixed atoms, the 'dyanmic' atoms are the atoms whose forcefield parameters change when switching conformations, since switching conformations can cause the forcefield parameters of nearby atoms to change.
The remaining fixed atoms are the 'static' atoms.
Dynamic fixed atoms are migrated to the atom lists of the design positions in the compiled conformation space, so their forcefield parameters can be applied correctly after a conformation change.
Each static fixed atom is also assigned an index, so it can be efficiently referred to in the compiled conf space.
Constructors
Types
Functions
Returns the static atoms in the indexed order.
Remove all dyanmic atoms from the fixed atoms. Moves any remaining fixed atoms into the static atoms list. The fixed atoms list will be empty afterwards.