org.jmol.modelsetbio
Class AlphaMonomer

java.lang.Object
  extended by org.jmol.modelset.Group
      extended by org.jmol.modelsetbio.Monomer
          extended by org.jmol.modelsetbio.AlphaMonomer
Direct Known Subclasses:
AminoMonomer

public class AlphaMonomer
extends Monomer


Field Summary
(package private) static byte[] alphaOffsets
           
protected  javax.vecmath.Point3f nitrogenHydrogenPoint
           
protected  ProteinStructure proteinStructure
           
 
Fields inherited from class org.jmol.modelsetbio.Monomer
bioPolymer, monomerIndex, offsets
 
Fields inherited from class org.jmol.modelset.Group
chain, firstAtomIndex, groupID, isAmino, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
 
Constructor Summary
AlphaMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
 Atom getAtom(byte specialAtomID)
           
 javax.vecmath.Point3f getAtomPoint(byte specialAtomID)
           
 java.lang.Object getHelixData(int tokType, char qType, int mStep)
           
 ProteinStructure getProteinStructure()
           
 byte getProteinStructureSubType()
           
 byte getProteinStructureType()
           
 Quaternion getQuaternion(char qType)
           
(package private)  javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
           
 int getStrucNo()
           
 java.lang.Object getStructure()
           
(package private)  boolean isAlphaMonomer()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isHelix()
           
 boolean isProtein()
           
 boolean isSheet()
           
 void setProteinStructureId(int id)
           
 int setProteinStructureType(byte iType, int monomerIndexCurrent)
           
(package private)  void setStructure(ProteinStructure proteinStructure)
           
(package private) static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
           
 
Methods inherited from class org.jmol.modelsetbio.Monomer
calcBioParameters, checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setShapeVisibility, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

alphaOffsets

static final byte[] alphaOffsets

proteinStructure

protected ProteinStructure proteinStructure

nitrogenHydrogenPoint

protected javax.vecmath.Point3f nitrogenHydrogenPoint
Constructor Detail

AlphaMonomer

AlphaMonomer(Chain chain,
             java.lang.String group3,
             int seqcode,
             int firstAtomIndex,
             int lastAtomIndex,
             byte[] offsets)
Method Detail

isProtein

public boolean isProtein()
Overrides:
isProtein in class Monomer

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   java.lang.String group3,
                                   int seqcode,
                                   int firstIndex,
                                   int lastIndex,
                                   int[] specialAtomIndexes)

isAlphaMonomer

boolean isAlphaMonomer()

getProteinStructure

public ProteinStructure getProteinStructure()
Overrides:
getProteinStructure in class Monomer

getStructure

public java.lang.Object getStructure()
Overrides:
getStructure in class Group

setStructure

void setStructure(ProteinStructure proteinStructure)
Overrides:
setStructure in class Monomer

setProteinStructureId

public void setProteinStructureId(int id)
Overrides:
setProteinStructureId in class Monomer

getProteinStructureType

public byte getProteinStructureType()
Overrides:
getProteinStructureType in class Monomer

getProteinStructureSubType

public byte getProteinStructureSubType()
Overrides:
getProteinStructureSubType in class Group

getStrucNo

public int getStrucNo()
Overrides:
getStrucNo in class Group

isHelix

public boolean isHelix()
Overrides:
isHelix in class Monomer

isSheet

public boolean isSheet()
Overrides:
isSheet in class Monomer

setProteinStructureType

public int setProteinStructureType(byte iType,
                                   int monomerIndexCurrent)
Overrides:
setProteinStructureType in class Group
Parameters:
iType -
monomerIndexCurrent - a pointer to the current ProteinStructure
Returns:
a pointer to this ProteinStructure

getAtom

public final Atom getAtom(byte specialAtomID)

getAtomPoint

public final javax.vecmath.Point3f getAtomPoint(byte specialAtomID)

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
Specified by:
isConnectedAfter in class Monomer

getQuaternionFrameCenter

javax.vecmath.Point3f getQuaternionFrameCenter(char qType)
Overrides:
getQuaternionFrameCenter in class Monomer
Returns:
center

getHelixData

public java.lang.Object getHelixData(int tokType,
                                     char qType,
                                     int mStep)
Overrides:
getHelixData in class Group
Returns:
helix data of some sort

getQuaternion

public Quaternion getQuaternion(char qType)
Overrides:
getQuaternion in class Group
Returns:
quaternion