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  javax.vecmath.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, omega, phi, psi, shapeVisibilityFlags, straightness
 
Constructor Summary
private AminoMonomer(Chain chain, java.lang.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()
           
(package private)  javax.vecmath.Point3f getCarbonylCarbonAtomPoint()
           
(package private)  Atom getCarbonylOxygenAtom()
           
(package private)  javax.vecmath.Point3f getCarbonylOxygenAtomPoint()
           
(package private)  Atom getInitiatorAtom()
           
 boolean getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint, javax.vecmath.Vector3f vNH)
           
(package private)  Atom getNitrogenAtom()
           
(package private)  javax.vecmath.Point3f getNitrogenAtomPoint()
           
(package private)  javax.vecmath.Point3f getNitrogenHydrogenPoint()
           
 java.lang.String getProteinStructureTag()
           
 Quaternion getQuaternion(char qType)
           
(package private)  Atom getQuaternionFrameCenter(char qType)
           
 java.lang.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, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
           
 
Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructure, getProteinStructureType, getStrucNo, getStructure, isAlphaMonomer, isHelix, isSheet, setProteinStructureId, setProteinStructureType, setStructure
 
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getHelixData2, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getUniqueID, getWingAtom, getWingAtomPoint, isDna, isLeadAtom, isNucleic, isProtein, isRna, scanForOffsets, setBioPolymer, updateOffsetsForAlternativeLocations
 
Methods inherited from class org.jmol.modelset.Group
getChainID, getFirstAtomIndex, getGroup1, getGroup3, getGroupID, getGroupID, getGroupIndex, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLastAtomIndex, getLeadAtom, getModel, getModelIndex, getOmega, getPhi, getPsi, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isPurine, isPyrimidine, isSelected, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setModelSet, setOmega, setPhi, setPsi, setShapeVisibility, setStraightness, 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 javax.vecmath.Point3f ptTemp

beta

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

AminoMonomer

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

validateAndAllocate

static Monomer validateAndAllocate(Chain chain,
                                   java.lang.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

Atom getNitrogenAtom()

getNitrogenAtomPoint

javax.vecmath.Point3f getNitrogenAtomPoint()

getCarbonylCarbonAtom

Atom getCarbonylCarbonAtom()

getCarbonylCarbonAtomPoint

javax.vecmath.Point3f getCarbonylCarbonAtomPoint()

getCarbonylOxygenAtom

Atom getCarbonylOxygenAtom()

getCarbonylOxygenAtomPoint

javax.vecmath.Point3f getCarbonylOxygenAtomPoint()

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()
Overrides:
resetHydrogenPoint in class Monomer

getNitrogenHydrogenPoint

javax.vecmath.Point3f getNitrogenHydrogenPoint()

getNHPoint

public boolean getNHPoint(javax.vecmath.Point3f aminoHydrogenPoint,
                          javax.vecmath.Vector3f vNH)

getQuaternionFrameCenter

Atom getQuaternionFrameCenter(char qType)
Overrides:
getQuaternionFrameCenter in class AlphaMonomer

getQuaternion

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

isWithinStructure

public boolean isWithinStructure(byte type)
Overrides:
isWithinStructure in class Group

getStructureId

public java.lang.String getStructureId()
Overrides:
getStructureId in class Group

getProteinStructureTag

public java.lang.String getProteinStructureTag()
Overrides:
getProteinStructureTag in class Group