scripps.mol_data
Class Atom

java.lang.Object
  |
  +--harmonic.mz.data.SimpleNode
        |
        +--scripps.mol_data.MolElement
              |
              +--scripps.mol_data.Atom

All Implemented Interfaces:

harmonic.mz.data.DataNode, harmonic.meshGeom.math.MarkableObject

public class Atom

extends MolElement

Field Summary

harmonic.meshGeom.math.TMat

transform

Fields inherited from class scripps.mol_data.MolElement

hashIndex

Constructor Summary

Atom()

Method Summary

void	assignFromMetaFields(harmonic.mz.data.MetaFields mf)
void	assignToMetaFields(harmonic.mz.data.MetaFields mf)
Atom	findBondedAtom(java.lang.String name)
BondSet	getBonds()
Chain	getChain()
java.lang.String	getElement()
java.lang.String	getID()
harmonic.meshGeom.math.Pnt3f	getOrigPosition()
harmonic.meshGeom.math.Pnt3f	getPosition()
Residue	getResidue()
boolean	isHetAtom()
void	setElement(java.lang.String element)
void	setPosition(double[] coords)
void	setPosition(float[] coords)
void	setPosition(harmonic.meshGeom.math.Pnt3f pnt)

Methods inherited from class scripps.mol_data.MolElement

getMark, getMolecule, setMark, sortIndex, toString

Methods inherited from class harmonic.mz.data.SimpleNode

addField, addNode, addNodeListener, assignFromXMLAttributes, assignToXMLAttributes, at, canSelect, childCount, clearAttrib, createXMLElement, fileRoot, fromXMLNodes, getAttrib, getName, getNodeChildren, getNodeParent, getRemoteOwner, getSelect, getSerialNo, getTreeName, getTypeImage, getUpdateTime, getXMLNodes, isField, linkedTo, makeReferenced, makeUnreferenced, notifyListeners, purge, purgeFinal, removeNode, removeNodeListener, set, setAttrib, setIsField, setName, setNodeParent, setRemoteOwner, setSelect, setSerialNo, setUpdateTime, valueString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

transform

public harmonic.meshGeom.math.TMat transform

Constructor Detail

Atom

public Atom()

Method Detail

setElement

public void setElement(java.lang.String element)

setPosition

public void setPosition(float[] coords)

setPosition

public void setPosition(double[] coords)

setPosition

public void setPosition(harmonic.meshGeom.math.Pnt3f pnt)

isHetAtom

public boolean isHetAtom()

getID

public java.lang.String getID()

getElement

public java.lang.String getElement()

getOrigPosition

public harmonic.meshGeom.math.Pnt3f getOrigPosition()

getPosition

public harmonic.meshGeom.math.Pnt3f getPosition()

getResidue

public Residue getResidue()

getChain

public Chain getChain()

getBonds

public BondSet getBonds()

findBondedAtom

public Atom findBondedAtom(java.lang.String name)

assignToMetaFields

public void assignToMetaFields(harmonic.mz.data.MetaFields mf)

assignFromMetaFields

public void assignFromMetaFields(harmonic.mz.data.MetaFields mf)