Package ffx.potential.bonded

Class MultiTerminus

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.MSGroup

ffx.potential.bonded.Residue

ffx.potential.bonded.MultiTerminus

All Implemented Interfaces:

ROLS, Serializable, Cloneable, Comparable<Residue>, MutableTreeNode, TreeNode

public class MultiTerminus
extends Residue

The MultiResidue class allows switching between residues for uses such as sequence optimization.

Since:

1.0

Author:

Will Tollefson, Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	MultiTerminus.BB_TYPE
static enum	MultiTerminus.END

Nested classes/interfaces inherited from class ffx.potential.bonded.Residue

Residue.ResidueType, Residue.SSType

Field Summary

Fields

Modifier and Type	Field	Description
final MultiTerminus.END	end
boolean	isCharged	Charge state of the termini.

Fields inherited from class ffx.potential.bonded.Residue

Ramachandran

Fields inherited from class ffx.potential.bonded.MSGroup

angleTime, angleTorsionTime, bondTime, improperTorsionTime, outOfPlaneBendTime, piOrbitalTorsionTime, stretchBendTime, stretchTorsionTime, torsionTime, torsionTorsionTime, ureyBradleyTime

Fields inherited from class ffx.potential.bonded.MSNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ffx.potential.bonded.ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
MultiTerminus(Residue residue, ForceField forceField, ForceFieldEnergy forceFieldEnergy, MolecularAssembly molecularAssembly)	Constructor for MultiTerminus.

Method Summary

Modifier and Type	Method	Description
void	add(MutableTreeNode mtn)
boolean	equals(Object object)
boolean	isCharged()	isCharged.
void	titrateTerminus_v0()	Changes the charge state of this MultiTerminus.

Methods inherited from class ffx.potential.bonded.Residue

addMSNode, compareTo, drawLabel, finalize, getAminoAcid3, getBackboneAtoms, getChainID, getNextResidue, getNucleicAcid3, getNucleicAcid3, getPreviousResidue, getReferenceAtom, getResidueNumber, getResidueType, getRotamer, getRotamers, getSegID, getSideChainAtoms, getTitrationUtils, getVariableAtoms, hashCode, initializeDefaultAtomicCoordinates, print, revertState, setChainID, setColor, setName, setNumber, setRotamer, setRotamers, setSegID, setTitrationUtils, storeCoordinateArray, storeState, toFormattedString, toString, toString

Methods inherited from class ffx.potential.bonded.MSGroup

assignBondedTerms, createJoint, createJoint, findDangelingAtoms, getAngles, getAtomByName, getAtomNode, getAtomNode, getAtomNode, getAtomNodeList, getBond, getBond, getBonds, getCenter, getDangelingAtoms, getMultiScaleCenter, getTermNode, getTorsions, isFinalized, removeLeaves, reOrderAtoms, setAngles, setAngleTorsions, setAtomNode, setBonds, setCenter, setDangelingAtoms, setFinalized, setImproperTorsions, setOutOfPlaneBends, setPiOrbitalTorsions, setStretchBends, setStretchTorsions, setTerms, setTorsions, setTorsionTorsions, setUreyBradleys, setView, update, updateAtoms, updateBonds

Methods inherited from class ffx.potential.bonded.MSNode

contains, destroy, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getDescendants, getExtent, getImproperTorsionList, getList, getMSCount, getMSNode, getMultiScaleLevel, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, isSelected, removeChild, setSelected

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Details

end

public final MultiTerminus.END end

isCharged

public boolean isCharged

Charge state of the termini.

Constructor Details

MultiTerminus

public MultiTerminus(Residue residue,
 ForceField forceField,
 ForceFieldEnergy forceFieldEnergy,
 MolecularAssembly molecularAssembly)

Constructor for MultiTerminus.

Parameters:

residue - a Residue object.

forceField - a ForceField object.

forceFieldEnergy - a ForceFieldEnergy object.

molecularAssembly - a MolecularAssembly object.

Method Details

add

public void add(MutableTreeNode mtn)

Overrides:

add in class DefaultMutableTreeNode

equals

public boolean equals(Object object)

MSNode equality := same class and same name. Consider replacing with a Comparator<MSNode> for cases where non-reference equality is desired.

Overrides:

equals in class Residue

isCharged

public boolean isCharged()

isCharged.

Returns:

a boolean.

titrateTerminus_v0

public void titrateTerminus_v0()

Changes the charge state of this MultiTerminus. Keep existing Atom objects but updates types, bonded terms, and builds new proton if necessary.