Uses of Class
ffx.potential.bonded.Molecule

Packages that use Molecule

Package	Description
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of Molecule in ffx.algorithms.optimize

Constructors in ffx.algorithms.optimize with parameters of type Molecule

Modifier	Constructor	Description
	ConformationScan(MolecularAssembly molecularAssembly, Molecule[] systemOne, Molecule[] systemTwo, double minimizeEps, int minimizeMaxIterations, boolean staticTorsionScan, boolean excludeExtraHydrogen, boolean minimize)
	TorsionSearch(MolecularAssembly molecularAssembly, Molecule molecule, int nTorsionsPerBond, int returnedStates)

Uses of Molecule in ffx.potential

Methods in ffx.potential that return Molecule

Modifier and Type	Method	Description
Molecule[]	MolecularAssembly.getMoleculeArray()

Methods in ffx.potential with parameters of type Molecule

Modifier and Type	Method	Description
void	MolecularAssembly.deleteMolecule(Molecule molecule)	deleteMolecule

Uses of Molecule in ffx.realspace

Methods in ffx.realspace that return types with arguments of type Molecule

Modifier and Type	Method	Description
List<List<Molecule>>	RealSpaceData.getAltMolecules()	getAltMolecules

Uses of Molecule in ffx.xray

Methods in ffx.xray that return types with arguments of type Molecule

Modifier and Type	Method	Description
List<List<Molecule>>	DataContainer.getAltMolecules()	getAltMolecules
List<List<Molecule>>	DiffractionData.getAltMolecules()	getAltMolecules
List<List<Molecule>>	RefinementModel.getAltMolecules()	Getter for the field altMolecules.