Package ffx.potential.bonded

Class Molecule

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.MSGroup

ffx.potential.bonded.Molecule

All Implemented Interfaces:

ROLS, Serializable, Cloneable, MutableTreeNode, TreeNode

public class Molecule
extends MSGroup

The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Field Summary

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
Molecule(String name)	Constructor for Molecule.
Molecule(String name, int residueNum, Character chainID, String segID)	Constructor for Molecule.

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
boolean	equals(Object o)
void	finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
Atom	getAtom(String name)	getAtom
Character	getChainID()	Getter for the field chainID.
String	getKey()
String	getResidueName()	Getter for the field residueName.
int	getResidueNumber()	getResidueNumber
String	getSegID()	Getter for the field segID.
int	hashCode()
void	setChainID(Character c)	Setter for the field chainID.
void	setName(String name)	Sets the name of this NodeObject to n.
void	setResidueNum(int residueNum)	Setter for the field residueNum.

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, print, removeLeaves, reOrderAtoms, setAngles, setAngleTorsions, setAtomNode, setBonds, setCenter, setColor, setDanglingAtoms, setFinalized, setImproperTorsions, setOutOfPlaneBends, setPiOrbitalTorsions, setStretchBends, setStretchTorsions, setTerms, setTorsions, setTorsionTorsions, setUreyBradleys, setView, toString, update, updateAtoms, updateBonds

Methods inherited from class ffx.potential.bonded.MSNode

contains, destroy, drawLabel, 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

Constructor Details

Molecule

public Molecule(String name)

Constructor for Molecule.

Parameters:

name - a String object.

Molecule

public Molecule(String name,
 int residueNum,
 Character chainID,
 String segID)

Constructor for Molecule.

Parameters:

name - a String object.

residueNum - The residue number.

chainID - a Character object.

segID - a String object.

Method Details

setChainID

public void setChainID(Character c)

Setter for the field chainID.

Parameters:

c - a Character object.

setResidueNum

public void setResidueNum(int residueNum)

Setter for the field residueNum.

Parameters:

residueNum - The molecule number.

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 Atom MSNodes to the Molecule.

Specified by:

addMSNode in class MSGroup

Parameters:

o - a MSNode object.

Returns:

a MSNode object.

equals

public boolean equals(Object o)

Description copied from class: MSNode

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

Specified by:

finalize in class MSGroup

Parameters:

finalizeGeometry - a boolean.

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

getAtom

public Atom getAtom(String name)

getAtom

Parameters:

name - a String object.

Returns:

a Atom object.

getChainID

public Character getChainID()

Getter for the field chainID.

Returns:

a Character object.

getKey

public String getKey()

getResidueName

public String getResidueName()

Getter for the field residueName.

Returns:

a String object.

getResidueNumber

public int getResidueNumber()

getResidueNumber

Returns:

The residue number.

getSegID

public String getSegID()

Getter for the field segID.

Returns:

a String object.

hashCode

public int hashCode()

Description copied from class: MSNode

Overrides:

hashCode in class MSNode

setName

public void setName(String name)

Sets the name of this NodeObject to n.

Overrides:

setName in class MSNode

Parameters:

name - a String object.