Package ffx.potential.bonded

Class Residue

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.MSGroup

ffx.potential.bonded.Residue

All Implemented Interfaces:

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

Direct Known Subclasses:

MultiResidue

public class Residue
extends MSGroup
implements Comparable<Residue>

The Residue class represents individual amino acids or nucleic acid bases.

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	Residue.ResidueType	Residue type [NA, AA, UNK].
static enum	Residue.SSType

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	Ramachandran	Constant Ramachandran="new String[17]"

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
Residue(int num, Residue.ResidueType residueType)	Default Constructor where num is this Residue's position in the Polymer.
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
Residue(String name, int num, Residue.ResidueType residueType)	Name is the residue's 3 letter abbreviation and num is its position in the Polymer.
Residue(String name, int resNumber, Residue.ResidueType residueType, Character chainID, String segID)	Name is the residue's 3 letter abbreviation and num is its position in the Polymer.
Residue(String name, Residue.ResidueType residueType)	Constructor for Residue.

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
int	compareTo(Residue o)
void	drawLabel(org.jogamp.java3d.Canvas3D canvas, org.jogamp.java3d.J3DGraphics2D g2d, org.jogamp.java3d.Node node)	drawLabel
boolean	equals(Object o)
void	finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
AminoAcidUtils.AminoAcid3	getAminoAcid3()	getAminoAcid3.
Atom	getAtomInitial()
List<Atom>	getBackboneAtoms()	Returns a list of backbone atoms; for our purposes, nucleic acid backbone atoms are those of the nucleobase.
Character	getChainID()	Returns this Residues Parent Polymer name.
Residue	getNextResidue()	Returns the Residue bonded to this Residue at this Residue's 3' or C-terminal end.
NucleicAcidUtils.NucleicAcid3	getNucleicAcid3()	getNucleicAcid3.
NucleicAcidUtils.NucleicAcid3	getNucleicAcid3(boolean matchShortName)	Returns the NucleicAcid3 corresponding to this Residue, with additional robust checking for 1- or 2-letter names.
Residue	getPreviousResidue()	Returns the Residue bonded to this Residue at this Residue's 5' or N-terminal end.
Atom	getReferenceAtom()	Returns a reference Atom for a Residue, primarily intended for rough distance calculations.
int	getResidueNumber()	Returns this Residue's sequence number.
Residue.ResidueType	getResidueType()	Getter for the field residueType.
Rotamer	getRotamer()	Get the current rotamer.
Rotamer[]	getRotamers()	Return all currently set rotamers.
String	getSegID()	Getter for the field segID.
List<Atom>	getSideChainAtoms()	Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
TitrationUtils	getTitrationUtils()
List<Atom>	getVariableAtoms()	Returns a list of atoms liable to change during dead-end elimination repacking.
int	hashCode()
void	initializeDefaultAtomicCoordinates()	Initializes this (presumably nucleic acid) Residue's C1s, O4s, C4s, O3sNorth, and O3sSouth default coordinates based on default PDB atom locations; to preserve rotamer independence, this must be called before any NA rotamers are applied.
boolean	isTitrateConformers()
void	print()	Prints the MSNode's name
void	revertState(ResidueState state)	revertState.
void	setAtomInitial(Atom atomInitial)
void	setChainID(Character c)	Setter for the field chainID.
void	setColor(RendererCache.ColorModel newColorModel, org.jogamp.vecmath.Color3f color, org.jogamp.java3d.Material mat)	setColor
void	setName(String name)	Sets the name of this NodeObject to n.
void	setNumber(int n)	setNumber
void	setRotamer(Rotamer rotamer)	Set the current rotamer.
Rotamer[]	setRotamers()	Sets the original coordinate rotamers for titratable residues RotamerLibrary's original coordinates rotamer flag has been set.
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	setSegID(String segID)	Setter for the field segID.
void	setTitrateConformers(boolean titrateConformers)
void	setTitrationUtils(TitrationUtils titrationUtils)
double[][]	storeCoordinateArray()	Returns the coordinates of all atoms in this Residue as a 2D array.
ResidueState	storeState()	storeState.
String	toFormattedString(boolean addResType, boolean addChainID)	Formats this residue with some optional inclusions.
String	toString()
String	toString(Rotamer rotamer)	A descriptive string based on a given rotamer.

Methods inherited from class ffx.potential.bonded.MSGroup

assignBondedTerms, createJoint, createJoint, findDangelingAtoms, getAngles, getAtomByName, getAtomNode, getAtomNode, getAtomNode, getAtomNodeList, getBond, getBond, getBonds, getCenter, getDanglingAtoms, getMultiScaleCenter, getTermNode, getTorsions, isFinalized, removeLeaves, reOrderAtoms, setAngles, setAngleTorsions, setAtomNode, setBonds, setCenter, setDanglingAtoms, 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, getExtent, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, 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

Field Details

Ramachandran

public static String[] Ramachandran

Constant Ramachandran="new String[17]"

Constructor Details

Residue

public Residue(int num,
 Residue.ResidueType residueType)

Default Constructor where num is this Residue's position in the Polymer.

Parameters:

num - The residue number.

residueType - The residue type.

Residue

public Residue(String name,
 Residue.ResidueType residueType)

Constructor for Residue.

Parameters:

name - The residue name.

residueType - The residue type.

Residue

public Residue(String name,
 int num,
 Residue.ResidueType residueType)

Name is the residue's 3 letter abbreviation and num is its position in the Polymer.

Parameters:

name - The residue name.

num - The residue number.

residueType - The residue type.

Residue

public Residue(String name,
 int resNumber,
 Residue.ResidueType residueType,
 Character chainID,
 String segID)

Name is the residue's 3 letter abbreviation and num is its position in the Polymer.

Parameters:

name - The residue name.

resNumber - The residue number.

residueType - The residue type.

chainID - The chain ID.

segID - The segment ID.

Residue

public 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

Parameters:

name - The residue name.

resNumber - The residue number.

atoms - a MSNode object.

residueType - The residue type.

forceField - the ForceField to use when created bonded terms.

Method Details

isTitrateConformers

public boolean isTitrateConformers()

setTitrateConformers

public void setTitrateConformers(boolean titrateConformers)

getAtomInitial

public Atom getAtomInitial()

setAtomInitial

public void setAtomInitial(Atom atomInitial)

setName

public void setName(String name)

Description copied from class: MSNode

Sets the name of this NodeObject to n.

Overrides:

setName in class MSNode

Parameters:

name - a String object.

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.

Specified by:

addMSNode in class MSGroup

Parameters:

o - a MSNode object.

Returns:

a MSNode object.

compareTo

public int compareTo(Residue o)

Specified by:

compareTo in interface Comparable<Residue>

drawLabel

public void drawLabel(org.jogamp.java3d.Canvas3D canvas,
 org.jogamp.java3d.J3DGraphics2D g2d,
 org.jogamp.java3d.Node node)

drawLabel

Specified by:

drawLabel in interface ROLS

Overrides:

drawLabel in class MSNode

Parameters:

canvas - a Canvas3D object.

g2d - a J3DGraphics2D object.

node - a Node 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.

Overrides:

equals in class MSNode

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.

Specified by:

finalize in class MSGroup

Parameters:

finalizeGeometry - a boolean.

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

setTitrationUtils

public void setTitrationUtils(TitrationUtils titrationUtils)

getTitrationUtils

public TitrationUtils getTitrationUtils()

getAminoAcid3

public AminoAcidUtils.AminoAcid3 getAminoAcid3()

getAminoAcid3.

Returns:

a AminoAcidUtils.AminoAcid3 object.

getBackboneAtoms

public List<Atom> getBackboneAtoms()

Returns a list of backbone atoms; for our purposes, nucleic acid backbone atoms are those of the nucleobase.

Returns:

List of backbone (or nucleobase) atoms.

getChainID

public Character getChainID()

Returns this Residues Parent Polymer name.

Returns:

a Character object.

setChainID

public void setChainID(Character c)

Setter for the field chainID.

Parameters:

c - a Character object.

setSegID

public void setSegID(String segID)

Setter for the field segID.

Parameters:

segID - The segID to use.

getNextResidue

public Residue getNextResidue()

Returns the Residue bonded to this Residue at this Residue's 3' or C-terminal end. Any use of this method to add Residues to a sliding window or similar MUST not add that residue if that residue has no Rotamers, as several algorithms (such as the distance matrix) assume that all Residues being optimized have Rotamers.

Returns:

The next Residue.

getNucleicAcid3

public NucleicAcidUtils.NucleicAcid3 getNucleicAcid3()

getNucleicAcid3.

Returns:

a NucleicAcidUtils.NucleicAcid3 object.

getNucleicAcid3

public NucleicAcidUtils.NucleicAcid3 getNucleicAcid3(boolean matchShortName)

Returns the NucleicAcid3 corresponding to this Residue, with additional robust checking for 1- or 2-letter names.

Parameters:

matchShortName - Try to match 1- or 2-letter names (e.g. A to ADE).

Returns:

a NucleicAcidUtils.NucleicAcid3 object.

getPreviousResidue

public Residue getPreviousResidue()

Returns the Residue bonded to this Residue at this Residue's 5' or N-terminal end. Any use of this method to add Residues to a sliding window or similar MUST not add that residue if that residue has no Rotamers, as several algorithms (such as the distance matrix) assume that all Residues being optimized have Rotamers.

Returns:

The previous Residue.

getReferenceAtom

public Atom getReferenceAtom()

Returns a reference Atom for a Residue, primarily intended for rough distance calculations. This atom should be roughly centrally located within the residue, and be invariant.

Returns:

A reference Atom.

getResidueNumber

public int getResidueNumber()

Returns this Residue's sequence number.

Returns:

The sequence number.

getResidueType

public Residue.ResidueType getResidueType()

Getter for the field residueType.

Returns:

a Residue.ResidueType object.

getRotamer

public Rotamer getRotamer()

Get the current rotamer.

Returns:

a Rotamer object.

setRotamer

public void setRotamer(Rotamer rotamer)

Set the current rotamer.

Parameters:

rotamer - a Rotamer object.

getRotamers

public Rotamer[] getRotamers()

Return all currently set rotamers.

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.

Parameters:

library - Rotamer library to use

Returns:

An array of Rotamer.

setRotamers

public Rotamer[] setRotamers()

Sets the original coordinate rotamers for titratable residues RotamerLibrary's original coordinates rotamer flag has been set.

Any rotamers that were set previously are deleted.

Returns:

An array of Rotamer.

getSegID

public String getSegID()

Getter for the field segID.

Returns:

a String object.

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.

Returns:

List of side chain (or nucleic backbone) atoms.

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:

Atoms changeable during DEE.

hashCode

public int hashCode()

Overrides:

hashCode in class MSNode

initializeDefaultAtomicCoordinates

public void initializeDefaultAtomicCoordinates()

Initializes this (presumably nucleic acid) Residue's C1s, O4s, C4s, O3sNorth, and O3sSouth default coordinates based on default PDB atom locations; to preserve rotamer independence, this must be called before any NA rotamers are applied.

print

public void print()

Prints the MSNode's name

Prints the MultiScaleGroup's Atoms and Bonds.

Prints "Residue Number: x" to stdout.

Overrides:

print in class MSGroup

revertState

public void revertState(ResidueState state)

revertState.

Parameters:

state - a ResidueState object.

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 MSGroup

Parameters:

newColorModel - a RendererCache.ColorModel object.

color - a Color3f object.

mat - a Material object.

setNumber

public void setNumber(int n)

setNumber

Parameters:

n - The residue number.

storeCoordinateArray

public double[][] storeCoordinateArray()

Returns the coordinates of all atoms in this Residue as a 2D array.

Returns:

the coordinates of all atoms in this Residue as a 2D array.

storeState

public ResidueState storeState()

storeState.

Returns:

a ResidueState object.

toFormattedString

public String toFormattedString(boolean addResType,
 boolean addChainID)

Formats this residue with some optional inclusions.

[residue type]-[chain ID]ResNumber-Name.

Parameters:

addResType - Include the residue type

addChainID - Include the chain ID.

Returns:

A descriptive string.

toString

public String toString(Rotamer rotamer)

A descriptive string based on a given rotamer.

[chain ID]ResNumber-RotamerName.

Parameters:

rotamer - The rotamer to use.

Returns:

A descriptive string.

toString

public String toString()

Overridden toString method returns the MSNode's name

Returns the MSGroup's name.

Overrides:

toString in class MSGroup