Package ffx.potential.bonded

Class MultiResidue

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.MSGroup

ffx.potential.bonded.Residue

ffx.potential.bonded.MultiResidue

All Implemented Interfaces:

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

public class MultiResidue
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/interfaces inherited from class ffx.potential.bonded.Residue

Residue.ResidueType, Residue.SSType

Field Summary

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
MultiResidue(Residue residue, ForceField forceField)	Constructor for MultiResidue.

Method Summary

Modifier and Type	Method	Description
MSNode	addMSNode(MSNode o)	Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup
void	addResidue(Residue newResidue)	addResidue.
void	assignBondedTerms(ForceField forceField)	assignBondedTerms
Joint	createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	createJoint(MSGroup group1, MSGroup group2, ForceField forceField)	Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
boolean	equals(Object o)
void	finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
void	findDangelingAtoms()	This method constructs a List of atoms which are under-constrained.
Residue	getActive()	getActive.
AminoAcidUtils.AminoAcid3	getAminoAcid3()	getAminoAcid3.
MSNode	getAngles()	Returns the MultiScaleGroup's angles FNode.
MSNode	getAtomNode()	Returns the AtomNode.
MSNode	getAtomNode(int index)	Returns the MSNode at the given index.
MSNode	getAtomNode(String n)	Returns the AtomNode specified by the String n.
List<MSNode>	getAtomNodeList()	Returns a List of the AtomNode's children.
Bond	getBond(int index)	Returns the Bond at the supplied index.
Bond	getBond(String id)	Returns the Bond with the given id.
MSNode	getBonds()	Returns the MultiScaleGroup's bonds FNode.
double[]	getCenter()	Returns the MultiScaleGroup's center as a double[3].
List<Residue>	getConsideredResidues()	Returns a copy of this MultiResidue's consideredResidues array.
List<Atom>	getDanglingAtoms()	Returns the MultiScaleGroup's dangling Atoms list.
List<Residue>	getInactive()	Returns a list of this MultiResidue's inactive residues.
double[]	getMultiScaleCenter(boolean w)	This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].
String	getName()	Returns the name of this MSNode.
int	getResidueCount()	getResidueCount.
Rotamer[]	getRotamers()	Return all currently set rotamers.
List<Atom>	getSideChainAtoms()	Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
MSNode	getTermNode()	Returns the MultiScaleGroup's terms FNode.
MSNode	getTorsions()	Returns the MultiScaleGroup's Torsion MSNode.
List<Atom>	getVariableAtoms()	Returns a list of atoms liable to change during dead-end elimination repacking.
int	hashCode()
boolean	isFinalized()	Returns true if the MultiScaleGroup is finalized.
void	reOrderAtoms()	reOrderAtoms
void	revertState(ResidueState state)	revertState.
boolean	setActiveResidue(int i)	Request the ith residue be set active.
boolean	setActiveResidue(AminoAcidUtils.AminoAcid3 aa)	Method may be redundant with requestSetActiveResidue.
boolean	setActiveResidue(Residue residue)	Setter for the field activeResidue.
void	setAngles(MSNode t)	Sets the Angles node to t.
void	setAtomNode(MSNode t)	Sets the Moieties node to t.
void	setBonds(MSNode t)	Sets the Bonds node to t.
void	setCenter(double[] d)	Set the value of Center to d.
void	setColor(RendererCache.ColorModel newColorModel, org.jogamp.vecmath.Color3f color, org.jogamp.java3d.Material mat)	setColor
void	setDanglingAtoms(List<Atom> a)	Sets the MultiScaleGroup's danglingAtoms member to a.
void	setFinalized(boolean t)	Specifies whether the MultiScaleGroup has been finalized.
void	setOutOfPlaneBends(MSNode t)	Sets the Out-of-Plane Bend node to t.
void	setPiOrbitalTorsions(MSNode t)	Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.
Rotamer[]	setRotamers(RotamerLibrary library)	Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
void	setStretchBends(MSNode t)	Sets the Stretch-Bends node to t.
void	setTerms(MSNode t)	Sets the MultiScaleGroup's terms node to t.
void	setTorsions(MSNode t)	Sets the MultiScaleGroup's torsion node to t.
void	setTorsionTorsions(MSNode t)	Sets the MultiScaleGroup's Torsion-Torsion node to t.
void	setUreyBradleys(MSNode t)	Sets the Urey-Bradley node to t.
void	setView(RendererCache.ViewModel newViewModel, List<org.jogamp.java3d.BranchGroup> newShapes)	setView
ResidueState	storeState()	storeState.
String	toString()
void	update()	update
void	updateAtoms()	updateAtoms
void	updateBonds()	updateBonds

Methods inherited from class ffx.potential.bonded.Residue

compareTo, drawLabel, getBackboneAtoms, getChainID, getNextResidue, getNucleicAcid3, getNucleicAcid3, getPreviousResidue, getReferenceAtom, getResidueNumber, getResidueType, getRotamer, getSegID, getTitrationUtils, initializeDefaultAtomicCoordinates, print, setChainID, setName, setNumber, setRotamer, setRotamers, setSegID, setTitrationUtils, storeCoordinateArray, toFormattedString, toString

Methods inherited from class ffx.potential.bonded.MSGroup

getAtomByName, removeLeaves, setAngleTorsions, setImproperTorsions, setStretchTorsions

Methods inherited from class ffx.potential.bonded.MSNode

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

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, 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

Constructor Details

MultiResidue

public MultiResidue(Residue residue,
 ForceField forceField)

Constructor for MultiResidue.

Parameters:

residue - a Residue object.

forceField - a ForceField object.

Method Details

addMSNode

public MSNode addMSNode(MSNode o)

Abstract method that should specify how to add various MSNodes subclasses (such as Atoms, Residues and Polymers) to the MSGroup

Allows adding Atoms to the Residue.

Overrides:

addMSNode in class Residue

Parameters:

o - a MSNode object.

Returns:

a MSNode object.

addResidue

public void addResidue(Residue newResidue)

addResidue.

Parameters:

newResidue - a Residue object.

assignBondedTerms

public void assignBondedTerms(ForceField forceField)

assignBondedTerms

Overrides:

assignBondedTerms in class MSGroup

Parameters:

forceField - the ForceField to use when creating bonded terms.

createJoint

public Joint createJoint(Bond bond,
 MSGroup group1,
 MSGroup group2,
 ForceField forceField)

Create a joint between two chemical groups.

Overrides:

createJoint in class MSGroup

Parameters:

bond - Bond

group1 - a MSGroup object.

group2 - a MSGroup object.

forceField - the ForceField parameters to use when creating the joint.

Returns:

Joint the created Joint.

createJoint

public Joint createJoint(MSGroup group1,
 MSGroup group2,
 ForceField forceField)

Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.

Overrides:

createJoint in class MSGroup

Parameters:

group1 - a MSGroup object.

group2 - a MSGroup object.

forceField - the ForceField parameters to use when creating the joint.

Returns:

a Joint object.

equals

public boolean equals(Object o)

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

Overridden equals method that return true if object is not equals to this, is of the same class, has the same parent Polymer, the same sequence number, the same ResidueType, and the same AA3/NA3.

Overrides:

equals in class Residue

finalize

public void finalize(boolean finalizeGeometry,
 ForceField forceField)

Abstract method that should specify how to finalize a MSGroup

The Finalize method should be called once all atoms have been added to the Residue. Geometry objects (Bonds, Angles, etc) are then formed, followed by a determination of under-constrained (Dangling) atoms.

Overrides:

finalize in class Residue

Parameters:

finalizeGeometry - a boolean.

forceField - the ForceField parameters to use when finalizing the MSGroup.

findDangelingAtoms

public void findDangelingAtoms()

This method constructs a List of atoms which are under-constrained. (i.e. They can except more bonds)

Overrides:

findDangelingAtoms in class MSGroup

getActive

public Residue getActive()

getActive.

Returns:

a Residue object.

getAminoAcid3

public AminoAcidUtils.AminoAcid3 getAminoAcid3()

getAminoAcid3.

Returns the AminoAcid3 of the active residue.

Overrides:

getAminoAcid3 in class Residue

Returns:

a AminoAcidUtils.AminoAcid3 object.

getAngles

public MSNode getAngles()

Returns the MultiScaleGroup's angles FNode.

Overrides:

getAngles in class MSGroup

Returns:

a MSNode object.

setAngles

public void setAngles(MSNode t)

Sets the Angles node to t.

Overrides:

setAngles in class MSGroup

Parameters:

t - a MSNode object.

getAtomNode

public MSNode getAtomNode()

Returns the AtomNode.

Overrides:

getAtomNode in class MSGroup

Returns:

a MSNode object.

setAtomNode

public void setAtomNode(MSNode t)

Sets the Moieties node to t.

Overrides:

setAtomNode in class MSGroup

Parameters:

t - a MSNode object.

getAtomNode

public MSNode getAtomNode(int index)

Returns the MSNode at the given index.

Overrides:

getAtomNode in class MSGroup

Parameters:

index - The index of the AtomNode to return.

Returns:

a MSNode object.

getAtomNode

public MSNode getAtomNode(String n)

Returns the AtomNode specified by the String n.

Overrides:

getAtomNode in class MSGroup

Parameters:

n - a String object.

Returns:

a MSNode object.

getAtomNodeList

public List<MSNode> getAtomNodeList()

Returns a List of the AtomNode's children.

Overrides:

getAtomNodeList in class MSGroup

Returns:

a List object.

getBond

public Bond getBond(String id)

Returns the Bond with the given id.

Overrides:

getBond in class MSGroup

Parameters:

id - a String object.

Returns:

a Bond object.

getBond

public Bond getBond(int index)

Returns the Bond at the supplied index.

Overrides:

getBond in class MSGroup

Parameters:

index - The index of the Bond to return.

Returns:

a Bond object.

getBonds

public MSNode getBonds()

Returns the MultiScaleGroup's bonds FNode.

Overrides:

getBonds in class MSGroup

Returns:

a MSNode object.

setBonds

public void setBonds(MSNode t)

Sets the Bonds node to t.

Overrides:

setBonds in class MSGroup

Parameters:

t - a MSNode object.

getCenter

public double[] getCenter()

Returns the MultiScaleGroup's center as a double[3].

Overrides:

getCenter in class MSGroup

Returns:

an array of double.

setCenter

public void setCenter(double[] d)

Set the value of Center to d.

Overrides:

setCenter in class MSGroup

Parameters:

d - an array of double.

getConsideredResidues

public List<Residue> getConsideredResidues()

Returns a copy of this MultiResidue's consideredResidues array.

Returns:

a new List of the considered residues.

getDanglingAtoms

public List<Atom> getDanglingAtoms()

Returns the MultiScaleGroup's dangling Atoms list.

Overrides:

getDanglingAtoms in class MSGroup

Returns:

a List object.

setDanglingAtoms

public void setDanglingAtoms(List<Atom> a)

Sets the MultiScaleGroup's danglingAtoms member to a.

Overrides:

setDanglingAtoms in class MSGroup

Parameters:

a - a List object.

getInactive

public List<Residue> getInactive()

Returns a list of this MultiResidue's inactive residues. Adding/removing from the returned list does nothing.

Returns:

a new List of inactive residues.

getMultiScaleCenter

public double[] getMultiScaleCenter(boolean w)

This method finds the Geometrical center of this MultiScaleGroup, or the atomicWeight-weighted center if w is set to true, and returns it as a double[3].

Overrides:

getMultiScaleCenter in class MSGroup

Parameters:

w - a boolean.

Returns:

an array of double.

getName

public String getName()

Returns the name of this MSNode.

Overrides:

getName in class MSNode

Returns:

a String object.

getResidueCount

public int getResidueCount()

getResidueCount.

Returns:

The number of residues in this MultiResidue.

getRotamers

public Rotamer[] getRotamers()

Return all currently set rotamers.

Overrides:

getRotamers in class Residue

Returns:

All current rotamers for this residue.

setRotamers

public Rotamer[] setRotamers(RotamerLibrary library)

Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.

Any rotamers that were set previously are deleted.

Overrides:

setRotamers in class Residue

Parameters:

library - Rotamer library to use

Returns:

An array of Rotamer.

getSideChainAtoms

public List<Atom> getSideChainAtoms()

Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.

Overrides:

getSideChainAtoms in class Residue

Returns:

List of side chain (or nucleic backbone) atoms.

getTermNode

public MSNode getTermNode()

Returns the MultiScaleGroup's terms FNode.

Overrides:

getTermNode in class MSGroup

Returns:

a MSNode object.

getTorsions

public MSNode getTorsions()

Returns the MultiScaleGroup's Torsion MSNode.

Overrides:

getTorsions in class MSGroup

Returns:

a MSNode object.

setTorsions

public void setTorsions(MSNode t)

Sets the MultiScaleGroup's torsion node to t.

Overrides:

setTorsions in class MSGroup

Parameters:

t - a MSNode object.

getVariableAtoms

public List<Atom> getVariableAtoms()

Returns a list of atoms liable to change during dead-end elimination repacking. For ordinary amino acids: side chain atoms. For ordinary nucleic acids: sugar/phosphate backbone atoms. MultiResidue over-rides this to return all atoms (as backbone atom types are non-constant).

Returns all atoms (all atoms are variable during DEE).

Overrides:

getVariableAtoms in class Residue

Returns:

Atoms changeable during DEE.

hashCode

public int hashCode()

Overrides:

hashCode in class Residue

isFinalized

public boolean isFinalized()

Returns true if the MultiScaleGroup is finalized.

Overrides:

isFinalized in class MSGroup

Returns:

a boolean.

setFinalized

public void setFinalized(boolean t)

Specifies whether the MultiScaleGroup has been finalized.

Overrides:

setFinalized in class MSGroup

Parameters:

t - a boolean.

reOrderAtoms

public void reOrderAtoms()

reOrderAtoms

Overrides:

reOrderAtoms in class MSGroup

setActiveResidue

public boolean setActiveResidue(int i)

Request the ith residue be set active.

Parameters:

i - The index of the residue to set active.

Returns:

true if the ith residue was set active, false otherwise.

setActiveResidue

public boolean setActiveResidue(Residue residue)

Setter for the field activeResidue.

Parameters:

residue - a Residue object.

Returns:

a boolean.

setActiveResidue

public boolean setActiveResidue(AminoAcidUtils.AminoAcid3 aa)

Method may be redundant with requestSetActiveResidue. Will not function correctly if there is more than one residue of type UNK (unknown).

Parameters:

aa - a AminoAcidUtils.AminoAcid3 object.

Returns:

True if successful

setColor

public void setColor(RendererCache.ColorModel newColorModel,
 org.jogamp.vecmath.Color3f color,
 org.jogamp.java3d.Material mat)

setColor

Specified by:

setColor in interface ROLS

Overrides:

setColor in class Residue

Parameters:

newColorModel - a RendererCache.ColorModel object.

color - a Color3f object.

mat - a Material object.

setOutOfPlaneBends

public void setOutOfPlaneBends(MSNode t)

Sets the Out-of-Plane Bend node to t.

Overrides:

setOutOfPlaneBends in class MSGroup

Parameters:

t - a MSNode object.

setPiOrbitalTorsions

public void setPiOrbitalTorsions(MSNode t)

Sets the MultiScaleGroup's Pi-Orbital Torsion node to t.

Overrides:

setPiOrbitalTorsions in class MSGroup

Parameters:

t - a MSNode object.

setStretchBends

public void setStretchBends(MSNode t)

Sets the Stretch-Bends node to t.

Overrides:

setStretchBends in class MSGroup

Parameters:

t - a MSNode object.

setTerms

public void setTerms(MSNode t)

Sets the MultiScaleGroup's terms node to t.

Overrides:

setTerms in class MSGroup

Parameters:

t - a MSNode object.

setTorsionTorsions

public void setTorsionTorsions(MSNode t)

Sets the MultiScaleGroup's Torsion-Torsion node to t.

Overrides:

setTorsionTorsions in class MSGroup

Parameters:

t - a MSNode object.

setUreyBradleys

public void setUreyBradleys(MSNode t)

Sets the Urey-Bradley node to t.

Overrides:

setUreyBradleys in class MSGroup

Parameters:

t - a MSNode object.

setView

public void setView(RendererCache.ViewModel newViewModel,
 List<org.jogamp.java3d.BranchGroup> newShapes)

setView

Specified by:

setView in interface ROLS

Overrides:

setView in class MSGroup

Parameters:

newViewModel - a RendererCache.ViewModel object.

newShapes - a List object.

storeState

public ResidueState storeState()

storeState.

Publicly accessible method for storing a MultiResidue state.

Overrides:

storeState in class Residue

Returns:

a ResidueState object.

toString

public String toString()

Overridden toString method returns the MSNode's name

Returns the MSGroup's name.

Overrides:

toString in class Residue

update

public void update()

update

Specified by:

update in interface ROLS

Overrides:

update in class MSGroup

updateAtoms

public void updateAtoms()

updateAtoms

Overrides:

updateAtoms in class MSGroup

updateBonds

public void updateBonds()

updateBonds

Overrides:

updateBonds in class MSGroup

revertState

public void revertState(ResidueState state)

Description copied from class: Residue

revertState.

Overrides:

revertState in class Residue

Parameters:

state - a ResidueState object.