org.jmol.modelsetbio
Class AminoMonomer

java.lang.Object
  extended by org.jmol.modelset.Group
      extended by org.jmol.modelsetbio.Monomer
          extended by org.jmol.modelsetbio.AlphaMonomer
              extended by org.jmol.modelsetbio.AminoMonomer

public class AminoMonomer
extends AlphaMonomer


Field Summary
private static float beta
           
private static byte C
           
private static byte CA
           
(package private) static byte[] interestingAminoAtomIDs
           
private static byte N
           
(package private)  boolean nhChecked
           
private static byte O
           
private static byte OT
           
private  Point3f ptTemp
           
 
Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets, nitrogenHydrogenPoint, 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
private AminoMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
(package private)  void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
          Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
(package private)  Atom getCarbonylCarbonAtom()
           
 Atom getCarbonylOxygenAtom()
           
(package private)  Point3f getExplicitNH()
           
(package private)  Atom getInitiatorAtom()
           
 boolean getNHPoint(Point3f aminoHydrogenPoint, Vector3f vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
           
 Atom getNitrogenAtom()
           
(package private)  Point3f getNitrogenHydrogenPoint()
           
 String getProteinStructureTag()
           
 Quaternion getQuaternion(char qType)
           
(package private)  Point3f getQuaternionFrameCenter(char qType)
           
 String getStructureId()
           
(package private)  Atom getTerminatorAtom()
           
(package private)  boolean hasOAtom()
           
(package private)  boolean isAminoMonomer()
           
private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
           
private static boolean isBondedCorrectly(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isWithinStructure(byte type)
           
 void resetHydrogenPoint()
           
(package private) static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
           
 
Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructure, getProteinStructureSubType, getProteinStructureType, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, setProteinStructureId, setProteinStructureType, setStructure, validateAndAllocate
 
Methods inherited from class org.jmol.modelsetbio.Monomer
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLink, getCrossLinkLeadAtomIndexes, getHelixData2, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getUniqueID, getWingAtom, haveParameters, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getChainID, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupParameter, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getModel, getModelIndex, getModelSet, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isPurine, isPyrimidine, isRna, isSelected, 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

CA

private static final byte CA
See Also:
Constant Field Values

O

private static final byte O
See Also:
Constant Field Values

N

private static final byte N
See Also:
Constant Field Values

C

private static final byte C
See Also:
Constant Field Values

OT

private static final byte OT
See Also:
Constant Field Values

interestingAminoAtomIDs

static final byte[] interestingAminoAtomIDs

nhChecked

boolean nhChecked

ptTemp

private final Point3f ptTemp

beta

private static final float beta
See Also:
Constant Field Values
Constructor Detail

AminoMonomer

private AminoMonomer(Chain chain,
                     String group3,
                     int seqcode,
                     int firstAtomIndex,
                     int lastAtomIndex,
                     byte[] offsets)
Method Detail

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   String group3,
                                   int seqcode,
                                   int firstAtomIndex,
                                   int lastAtomIndex,
                                   int[] specialAtomIndexes,
                                   Atom[] atoms)

isBondedCorrectly

private static boolean isBondedCorrectly(int offset1,
                                         int offset2,
                                         int firstAtomIndex,
                                         byte[] offsets,
                                         Atom[] atoms)

isBondedCorrectly

private static boolean isBondedCorrectly(int firstAtomIndex,
                                         byte[] offsets,
                                         Atom[] atoms)

isAminoMonomer

boolean isAminoMonomer()

getNitrogenAtom

public Atom getNitrogenAtom()
Overrides:
getNitrogenAtom in class Group

getCarbonylCarbonAtom

Atom getCarbonylCarbonAtom()

getCarbonylOxygenAtom

public Atom getCarbonylOxygenAtom()
Overrides:
getCarbonylOxygenAtom in class Group

getInitiatorAtom

Atom getInitiatorAtom()
Overrides:
getInitiatorAtom in class Monomer

getTerminatorAtom

Atom getTerminatorAtom()
Overrides:
getTerminatorAtom in class Monomer

hasOAtom

boolean hasOAtom()

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
Overrides:
isConnectedAfter in class AlphaMonomer

findNearestAtomIndex

void findNearestAtomIndex(int x,
                          int y,
                          Atom[] closest,
                          short madBegin,
                          short madEnd)
Description copied from class: Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.

Overrides:
findNearestAtomIndex in class Monomer

resetHydrogenPoint

public void resetHydrogenPoint()

getNitrogenHydrogenPoint

Point3f getNitrogenHydrogenPoint()

getExplicitNH

Point3f getExplicitNH()

getNHPoint

public boolean getNHPoint(Point3f aminoHydrogenPoint,
                          Vector3f vNH,
                          boolean jmolHPoint,
                          boolean dsspIgnoreHydrogens)

getQuaternionFrameCenter

Point3f getQuaternionFrameCenter(char qType)
Overrides:
getQuaternionFrameCenter in class AlphaMonomer
Returns:
center

getQuaternion

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

isWithinStructure

public boolean isWithinStructure(byte type)
Overrides:
isWithinStructure in class Group
Returns:
T/F

getStructureId

public String getStructureId()
Overrides:
getStructureId in class Monomer

getProteinStructureTag

public String getProteinStructureTag()
Overrides:
getProteinStructureTag in class Group