ffe.lang
Class Residue

java.lang.Object
  javax.swing.tree.DefaultMutableTreeNode
      ffe.lang.FNode
          ffe.lang.FGroup
              ffe.lang.Residue

All Implemented Interfaces:

java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable, javax.swing.tree.TreeNode

public final class Residue

extends FGroup

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

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.tree.DefaultMutableTreeNode

Field Summary

static int	HELIX
static int	NONE
(package private) static java.lang.StringBuffer	s
static int	SHEET
static javax.vecmath.Color3f[]	ssColors
static int	TURN

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

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

Residue(java.lang.String name, boolean bk)

Residue(java.lang.String name, int num, boolean bk)
Name is the residue's 3 letter abbreviation and num is its position in the Polymer.

Residue(java.lang.String name, int num, FNode atoms, boolean bk)
As above, with atoms being a FNode with this Residue's atoms as child nodes

Method Summary

void	addFNode(FNode o) Allows adding Atom FNodes to the Residue.
void	drawLabel(Graphics3D graphics, javax.media.j3d.J3DGraphics2D g2d, javax.media.j3d.Node node, boolean labelAtoms, boolean labelResidues)
boolean	equals(java.lang.Object object) Overidden equals method that return true if object is not equals to this, is of the same class, has the same parent Polymer and the same sequence number.
void	finalize(boolean finalizeGeometry) The Finalize method should be called once all atoms have been added to the Residue.
javax.vecmath.Vector3d	getAlpha3d() Returns the position of this Residue's Alpha Carbon (if it is an amino acid).
double	getHydrophobicity() Returns this Residue's Hydrophobicity value.
static double	getHydrophobicity(java.lang.String aa) Returns the Hydrophobicity of the Residue provided as an arguement.
java.lang.String	getPolymer() Returns this Residues Parent Polymer name.
int	getResidueNumber() Returns this Residue's sequence number.
static int	parseSSType(java.lang.String ss)
void	print() Prints "Residue Number: x" to stdout.
void	printSidePolymerCOM()
void	setNumber(int n)
void	setPolymer(java.lang.String n)
void	setSSType(int i)
void	switchColor(int colortype, javax.vecmath.Color3f color, javax.media.j3d.Material mat)
java.lang.String	toString() Returns the Moieties name.

Methods inherited from class ffe.lang.FGroup

collectBonds, ConstructGeometry, destroy, findCenter, findDangelingAtoms, getAngles, getBond, getBond, getBonds, getBondsKnown, getCenter, getDangelingAtoms, getDihedrals, getFGroupList, getFGroups, getFNode, getFNode, getTerms, isFinalized, joiner, joiner, reInit, removeLeaves, setAngles, setBonds, setBondsKnown, setCenter, setDangelingAtoms, setDihedrals, setFGroups, setFinalized, setTerms, updateAtoms, updateBonds

Methods inherited from class ffe.lang.FNode

getAtomList, getBondList, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, getTermList, isSelected, setName, setSelected, switchView

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, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

s

static java.lang.StringBuffer s

NONE

public static int NONE

HELIX

public static int HELIX

TURN

public static int TURN

SHEET

public static int SHEET

ssColors

public static javax.vecmath.Color3f[] ssColors

Constructor Detail

Residue

public Residue(int num)

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

Residue

public Residue(java.lang.String name,
               boolean bk)

Residue

public Residue(java.lang.String name,
               int num,
               boolean bk)

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

Residue

public Residue(java.lang.String name,
               int num,
               FNode atoms,
               boolean bk)

As above, with atoms being a FNode with this Residue's atoms as child nodes

Method Detail

equals

public boolean equals(java.lang.Object object)

Overidden equals method that return true if object is not equals to this, is of the same class, has the same parent Polymer and the same sequence number.

Overrides:

equals in class FNode

addFNode

public void addFNode(FNode o)

Allows adding Atom FNodes to the Residue.

Specified by:

addFNode in class FGroup

toString

public java.lang.String toString()

Description copied from class: FGroup

Returns the Moieties name.

Overrides:

toString in class FGroup

print

public void print()

Prints "Residue Number: x" to stdout.

Overrides:

print in class FGroup

drawLabel

public void drawLabel(Graphics3D graphics,
                      javax.media.j3d.J3DGraphics2D g2d,
                      javax.media.j3d.Node node,
                      boolean labelAtoms,
                      boolean labelResidues)

Overrides:

drawLabel in class FNode

switchColor

public void switchColor(int colortype,
                        javax.vecmath.Color3f color,
                        javax.media.j3d.Material mat)

Overrides:

switchColor in class FGroup

printSidePolymerCOM

public void printSidePolymerCOM()

finalize

public void finalize(boolean finalizeGeometry)

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 (Dangeling) atoms.

Specified by:

finalize in class FGroup

getResidueNumber

public int getResidueNumber()

Returns this Residue's sequence number.

getPolymer

public java.lang.String getPolymer()

Returns this Residues Parent Polymer name.

getAlpha3d

public javax.vecmath.Vector3d getAlpha3d()

Returns the position of this Residue's Alpha Carbon (if it is an amino acid).

getHydrophobicity

public double getHydrophobicity()

Returns this Residue's Hydrophobicity value.

getHydrophobicity

public static double getHydrophobicity(java.lang.String aa)

Returns the Hydrophobicity of the Residue provided as an arguement. (Must be the 3-letter abreviation)

setNumber

public void setNumber(int n)

setPolymer

public void setPolymer(java.lang.String n)

setSSType

public void setSSType(int i)

parseSSType

public static int parseSSType(java.lang.String ss)