Uses of Class
ffx.potential.bonded.MSNode

Packages that use MSNode

Package	Description
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.

Uses of MSNode in ffx.potential

Subclasses of MSNode in ffx.potential

Modifier and Type	Class	Description
class	MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Methods in ffx.potential that return MSNode

Modifier and Type	Method	Description
MSNode	MolecularAssembly.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup

Methods in ffx.potential that return types with arguments of type MSNode

Modifier and Type	Method	Description
List<MSNode>	MolecularAssembly.getAllBondedEntities()	Gets all bonded entities in this MolecularAssembly, where an entity can be a polymer, molecule, monoatomic ion, or monoatomic gas (i.e. noble gas atoms).
List<MSNode>	MolecularAssembly.getIons()	Getter for the field ions.
List<MSNode>	MolecularAssembly.getMolecules()	Getter for the field molecules.
List<MSNode>	MolecularAssembly.getNodeList()	getNodeList
List<MSNode>	MolecularAssembly.getWater()	getWater

Methods in ffx.potential with parameters of type MSNode

Modifier and Type	Method	Description
MSNode	MolecularAssembly.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
void	Renderer.arm(MSNode node, boolean t, boolean v, RendererCache.ViewModel vtype, boolean c, RendererCache.ColorModel ctype)	arm

Method parameters in ffx.potential with type arguments of type MSNode

Modifier and Type	Method	Description
void	Renderer.arm(ArrayList<MSNode> nodes, boolean t, boolean v, RendererCache.ViewModel vtype, boolean c, RendererCache.ColorModel ctype)	This node arms UpdateBehavior with a graphics operation to carry out

Constructors in ffx.potential with parameters of type MSNode

Modifier	Constructor	Description
	MolecularAssembly(String name, MSNode Polymers)	Constructor for MolecularAssembly.
	MolecularAssembly(String name, MSNode Polymers, org.apache.commons.configuration2.CompositeConfiguration properties)	Constructor for MolecularAssembly.

Uses of MSNode in ffx.potential.bonded

Subclasses of MSNode in ffx.potential.bonded

Modifier and Type	Class	Description
class	Angle	The Angle class represents an angle formed between three linearly bonded atoms.
class	AngleTorsion	The AngleTorsion class represents an angle torsion coupling between four bonded atoms.
class	Atom	The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
class	Bond	The Bond class represents a covalent bond formed between two atoms.
class	BondedTerm	The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).
class	ImproperTorsion	The ImproperTorsion class represents an Improper Torsion.
class	Joint	The Joint class contains the geometry produced by the FGroup Joiner method.
class	Molecule	The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.
class	MSGroup	The MSGroup class has one sub-node containing atoms, and one that contains molecular mechanics/geometry terms.
class	MSRoot	The MSRoot class is the root of the Force Field X data structure.
class	MultiResidue	The MultiResidue class allows switching between residues for uses such as sequence optimization.
class	OutOfPlaneBend	The OutOfPlaneBend class represents an Out-Of-Plane Bend.
class	PiOrbitalTorsion	The Pi-Orbital Torsion class.
class	Polymer	The Polymer class encapsulates a peptide or nucleotide chain.
class	Residue	The Residue class represents individual amino acids or nucleic acid bases.
class	RestrainDistance	RestraintDistance class.
class	RestraintTorsion
class	ROLSP	The ROLSP class is used for Proof-Of-Concept Parallel Recusive Over Length Scales (ROLS) Methods (currently only on shared memory systems).
class	StretchBend	The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.
class	StretchTorsion	The StretchTorsion class represents a coupling between a torsional angle and the three bonds contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.
class	Torsion	The Torsion class represents a torsional angle formed between four bonded atoms.
class	TorsionTorsion	The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.
class	UreyBradley	The UreyBradley class.

Methods in ffx.potential.bonded that return MSNode

Modifier and Type	Method	Description
MSNode	Molecule.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
abstract MSNode	MSGroup.addMSNode(MSNode m)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	MultiResidue.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	Polymer.addMSNode(MSNode msNode)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	Residue.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	MSNode.contains(MSNode msNode)	If this MSNode or any MSNode below it equals the argument, that MSNode is returned.
MSNode	MSGroup.getAngles()	Returns the MultiScaleGroup's angles FNode.
MSNode	MultiResidue.getAngles()	Returns the MultiScaleGroup's angles FNode.
MSNode	MSGroup.getAtomNode()	Returns the AtomNode.
MSNode	MSGroup.getAtomNode(int index)	Returns the MSNode at the given index.
MSNode	MSGroup.getAtomNode(String n)	Returns the AtomNode specified by the String n.
MSNode	MultiResidue.getAtomNode()	Returns the AtomNode.
MSNode	MultiResidue.getAtomNode(int index)	Returns the MSNode at the given index.
MSNode	MultiResidue.getAtomNode(String n)	Returns the AtomNode specified by the String n.
MSNode	MSGroup.getBonds()	Returns the MultiScaleGroup's bonds FNode.
MSNode	MultiResidue.getBonds()	Returns the MultiScaleGroup's bonds FNode.
MSNode	MSGroup.getTermNode()	Returns the MultiScaleGroup's terms FNode.
MSNode	MultiResidue.getTermNode()	Returns the MultiScaleGroup's terms FNode.
MSNode	MSGroup.getTorsions()	Returns the MultiScaleGroup's Torsion MSNode.
MSNode	MultiResidue.getTorsions()	Returns the MultiScaleGroup's Torsion MSNode.

Methods in ffx.potential.bonded that return types with arguments of type MSNode

Modifier and Type	Method	Description
List<MSNode>	MSGroup.getAtomNodeList()	Returns a List of the AtomNode's children.
List<MSNode>	MultiResidue.getAtomNodeList()	Returns a List of the AtomNode's children.
List<MSNode>	MSNode.getChildList()	Returns a List of the MSNode's Children (instead of using an Enumeration).

Methods in ffx.potential.bonded with parameters of type MSNode

Modifier and Type	Method	Description
MSNode	Molecule.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
abstract MSNode	MSGroup.addMSNode(MSNode m)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	MultiResidue.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	Polymer.addMSNode(MSNode msNode)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	Residue.addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
MSNode	MSNode.contains(MSNode msNode)	If this MSNode or any MSNode below it equals the argument, that MSNode is returned.
void	MSNode.removeChild(MSNode child)	removeChild.
void	MSGroup.setAngles(MSNode t)	Sets the Angles node to t.
void	MultiResidue.setAngles(MSNode t)	Sets the Angles node to t.
void	MSGroup.setAngleTorsions(MSNode t)	Sets the MultiScaleGroup's angle-torsion node to t.
void	MSGroup.setAtomNode(MSNode t)	Sets the Moieties node to t.
void	MultiResidue.setAtomNode(MSNode t)	Sets the Moieties node to t.
void	MSGroup.setBonds(MSNode t)	Sets the Bonds node to t.
void	MultiResidue.setBonds(MSNode t)	Sets the Bonds node to t.
void	MSGroup.setImproperTorsions(MSNode t)	Sets the ImproperTorsion node to t.
void	MSGroup.setOutOfPlaneBends(MSNode t)	Sets the Out-of-Plane Bend node to t.
void	MultiResidue.setOutOfPlaneBends(MSNode t)	Sets the Out-of-Plane Bend node to t.
void	MSGroup.setPiOrbitalTorsions(MSNode t)	Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
void	MultiResidue.setPiOrbitalTorsions(MSNode t)	Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
void	MSGroup.setStretchBends(MSNode t)	Sets the Stretch-Bends node to t.
void	MultiResidue.setStretchBends(MSNode t)	Sets the Stretch-Bends node to t.
void	MSGroup.setStretchTorsions(MSNode t)	Sets the MultiScaleGroup's stretch-torsion node to t.
void	MSGroup.setTerms(MSNode t)	Sets the MultiScaleGroup's terms node to t.
void	MultiResidue.setTerms(MSNode t)	Sets the MultiScaleGroup's terms node to t.
void	MSGroup.setTorsions(MSNode t)	Sets the MultiScaleGroup's torsion node to t.
void	MultiResidue.setTorsions(MSNode t)	Sets the MultiScaleGroup's torsion node to t.
void	MSGroup.setTorsionTorsions(MSNode t)	Sets the MultiScaleGroup's Torsion-Torsion node to t.
void	MultiResidue.setTorsionTorsions(MSNode t)	Sets the MultiScaleGroup's Torsion-Torsion node to t.
void	MSGroup.setUreyBradleys(MSNode t)	Sets the Urey-Bradley node to t.
void	MultiResidue.setUreyBradleys(MSNode t)	Sets the Urey-Bradley node to t.

Method parameters in ffx.potential.bonded with type arguments of type MSNode

Modifier and Type	Method	Description
static void	PolymerUtils.resolvePolymerLinks(List<MSNode> molecules, MolecularAssembly molecularAssembly, List<Bond> bondList)	Resolves links between polymeric hetero groups; presently only functional for cyclic molecules.

Constructors in ffx.potential.bonded with parameters of type MSNode

Modifier	Constructor	Description
	Joint(MSGroup group1, MSGroup group2, MSNode bondNode, MSNode angleNode, MSNode stretchBendNode, MSNode ureyBradleyNode, MSNode outOfPlaneNode, MSNode torsionNode, MSNode improperTorsionNode, MSNode stretchTorsionNode, MSNode angleTorsionNode, MSNode piOrbitalTorsionNode, MSNode torsionTorsionNode)	Constructs a Joint between Group 1 and Group 2.
	MSGroup(String n, MSNode node)	Constructs a MultiScaleGroup object with name n and sets its AtomGroup node equals to node.
	Polymer(Character chainID, String segID, MSNode residues)	Polymer Constructor.
	Residue(String name, int resNumber, MSNode atoms, Residue.ResidueType residueType, ForceField forceField)	As above, with atoms being a MSNode with this Residue's atoms as child nodes

Uses of MSNode in ffx.potential.nonbonded

Subclasses of MSNode in ffx.potential.nonbonded

Modifier and Type	Class	Description
class	RestrainPosition	Restrain the position of atoms to their initial coordinates.

Uses of MSNode in ffx.potential.parsers

Method parameters in ffx.potential.parsers with type arguments of type MSNode

Modifier and Type	Method	Description
void	CIFFilter.writePropertiesFile(String dir, String fileName, String spacegroup, List<MSNode> entities)	Write a properties file.

Uses of MSNode in ffx.ui

Subclasses of MSNode in ffx.ui

Modifier and Type	Class	Description
class	FFXSystem	The FFXSystem class contains extensions to the generic MolecularAssembly class.

Methods in ffx.ui that return MSNode

Modifier and Type	Method	Description
MSNode	Hierarchy.getActiveNode()	Getter for the field activeNode.

Methods in ffx.ui with parameters of type MSNode

Modifier and Type	Method	Description
void	Hierarchy.groupSelection(MSNode f1, MSNode f2)	groupSelection
void	MainPanel.merge(MSNode[] nodesToMerge)	merge
void	ModelingShell.select(MSNode node)	select
static Selection	Selection.select(MSNode m, Class<? extends Object> scale, String criteria)	select
static Selection	Selection.select(MSNode m, String scale, String criteria)	select
void	GraphicsCanvas.setColorModel(String model, MSNode node)	Operates on the passed node.
void	GraphicsCanvas.setPosition(MSNode node)	setPosition
void	GraphicsCanvas.setViewModel(String model, MSNode node)	Operates on the supplied node.
void	GraphicsCanvas.updateScene(MSNode n, boolean t, boolean v, RendererCache.ViewModel newViewModel, boolean c, RendererCache.ColorModel newColorModel)	updateScene

Method parameters in ffx.ui with type arguments of type MSNode

Modifier and Type	Method	Description
void	Hierarchy.addSelections(ArrayList<MSNode> a)	addSelections
void	Hierarchy.removeSelections(ArrayList<MSNode> a)	removeSelections
void	Hierarchy.toggleSelections(ArrayList<MSNode> a)	toggleSelections
void	GraphicsCanvas.updateScene(ArrayList<MSNode> n, boolean t, boolean v, RendererCache.ViewModel newViewModel, boolean c, RendererCache.ColorModel newColorModel)	updateScene