| Interface | Description |
|---|---|
| DipoleSource |
Interface for something that can calculate the dipole of a molecule.
|
| IMolecule |
Interface for an IMolecule
|
| IMoleculeKinetic |
Interface for an molecule that holds vectors for velocity.
|
| IMoleculeList |
Interface for a set of IMolecules.
|
| IMoleculeOriented |
Interface for a IAtom that includes an IVector that defines the atom's
position.
|
| IMoleculeOrientedKinetic |
Interface for an Atom that has a position, orientation, velocity and angular
velocity.
|
| IMoleculePositionDefinition |
Returns a vector given a molecule, thereby defining the position
of the molecule.
|
| IMoleculePositioned | |
| MoleculeAgentManager.MoleculeAgentSource<E> |
Interface for an object that wants an agent associated with each
IMolecule a Box.
|
| MoleculeSource |
Interface for objects when return atoms (meeting some specification)
from a box.
|
| MoleculeToIndex |
Interface for class that associates an integer with an atom.
|
| MoleculeToMoleculeList |
Interface for class that determines an AtomArrayList given an atom.
|
| OrientationCalc |
Interface for a class that can calculate the orientation of a molecule or
to set the orientation of a molecule.
|
| OrientationCalcQuaternion |
OrientationCalc interface that handles quaternions (as a a double array)
instead of an Orientation object.
|
| Class | Description |
|---|---|
| Molecule | |
| MoleculeAgentManager<E> |
MoleculeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every IMolecule in a box.
|
| MoleculeArrayList | |
| MoleculeOriented |
Molecule class appropriate for a rigid molecule.
|
| MoleculeOrientedDynamic |
Molecule class appropriate for a rigid molecule in a dynamic context.
|
| MoleculePair |
Data structure that contains two mutable atom instances.
|
| MoleculePositionCOM |
Calculates the center of mass (COM) over a set of atoms.
|
| MoleculePositionFirstAtom |
Returns the position of the first child leaf atom.
|
| MoleculePositionGeometricCenter |
Calculates the geometric center over a set of atoms.
|
| MoleculePositionGeometricCenterAlkaneEH |
Calculates the geometric center over a set of atoms.
|
| MoleculePositionGeometricCenterPBC |
Calculates the geometric center over a set of atoms.
|
| MoleculeSetSinglet |
Data structure that contains a single mutable atom instance.
|
| MoleculeSourceRandomMolecule |
MoleculeSource that returns a completely random molecule.
|
| MoleculeToMoleculeListSpecies | |
| MoleculeToMoleculeSetFixed | |
| OrientationCalcAtom |
OrientationCalc implementation that handles a monotomic oriented molecule.
|