org.jmol.modelsetbio
Class NucleicMonomer

java.lang.Object
  extended by org.jmol.modelset.Group
      extended by org.jmol.modelsetbio.Monomer
          extended by org.jmol.modelsetbio.PhosphorusMonomer
              extended by org.jmol.modelsetbio.NucleicMonomer

public class NucleicMonomer
extends PhosphorusMonomer


Field Summary
private static byte C2
           
private static byte C3Pr
           
private static byte C4
           
private static byte C5
           
(package private) static byte C6
           
private static byte C8
           
private static byte H3T
           
private static byte H5T
           
private  boolean hasRnaO2Prime
           
(package private) static byte[] interestingNucleicAtomIDs
           
private static byte N1
           
private static byte N2
           
private static byte N3
           
private static byte N4
           
private static byte N6
           
private static byte N7
           
private static byte N9
           
private static byte NP
           
private static byte O1P
           
private static byte O2
           
private static byte O2P
           
private static byte O2Pr
           
private static byte O3Pr
           
private static byte O4
           
private static byte O5Pr
           
private static byte O6
           
private static byte[] ring5OffsetIndexes
           
private static byte[] ring6OffsetIndexes
           
 
Fields inherited from class org.jmol.modelsetbio.PhosphorusMonomer
isPurine, isPyrimidine
 
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
NucleicMonomer(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
           
 
Method Summary
 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.
 void getBaseRing6Points(javax.vecmath.Point3f[] ring6Points)
           
 java.lang.Object getHelixData(int tokType, char qType, int mStep)
           
(package private)  Atom getN1()
           
(package private)  Atom getN2()
           
(package private)  Atom getN3()
           
(package private)  Atom getN4()
           
(package private)  Atom getN6()
           
(package private)  Atom getO2()
           
(package private)  Atom getO4()
           
(package private)  Atom getO6()
           
 byte getProteinStructureType()
           
 Quaternion getQuaternion(char qType)
           
(package private)  Atom getQuaternionFrameCenter(char qType)
           
(package private)  Atom getTerminatorAtom()
           
(package private)  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
           
 boolean isDna()
           
 boolean isGuanine()
           
 boolean isNucleicMonomer()
           
 boolean isPurine()
           
 boolean isPyrimidine()
           
 boolean isRna()
           
 boolean maybeGetBaseRing5Points(javax.vecmath.Point3f[] ring5Points)
           
 void setModelClickability()
           
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.PhosphorusMonomer
getStructure, isPhosphorusMonomer
 
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getBioPolymer, getBioPolymerIndex, getBioPolymerLength, getHelixData2, getInitiatorAtom, getLeadAtom, getLeadAtomIndex, getLeadAtomPoint, getMonomerSequenceAtoms, getMyInfo, getPointAtomPoint, getProteinStructure, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureTypeName, getUniqueID, getWingAtom, getWingAtomPoint, isHelix, isNucleic, isProtein, isSheet, resetHydrogenPoint, scanForOffsets, setBioPolymer, setProteinStructureId, setStructure, 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, getProteinStructureTag, getPsi, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStraightness, getStrucNo, getStructureId, haveSequenceNumber, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setModelSet, setOmega, setPhi, setProteinStructureType, setPsi, setShapeVisibility, setStraightness, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

C6

static final byte C6
See Also:
Constant Field Values

O2Pr

private static final byte O2Pr
See Also:
Constant Field Values

C5

private static final byte C5
See Also:
Constant Field Values

N1

private static final byte N1
See Also:
Constant Field Values

C2

private static final byte C2
See Also:
Constant Field Values

N3

private static final byte N3
See Also:
Constant Field Values

C4

private static final byte C4
See Also:
Constant Field Values

O2

private static final byte O2
See Also:
Constant Field Values

N7

private static final byte N7
See Also:
Constant Field Values

C8

private static final byte C8
See Also:
Constant Field Values

N9

private static final byte N9
See Also:
Constant Field Values

O4

private static final byte O4
See Also:
Constant Field Values

O6

private static final byte O6
See Also:
Constant Field Values

N4

private static final byte N4
See Also:
Constant Field Values

NP

private static final byte NP
See Also:
Constant Field Values

N6

private static final byte N6
See Also:
Constant Field Values

N2

private static final byte N2
See Also:
Constant Field Values

H5T

private static final byte H5T
See Also:
Constant Field Values

O5Pr

private static final byte O5Pr
See Also:
Constant Field Values

H3T

private static final byte H3T
See Also:
Constant Field Values

O3Pr

private static final byte O3Pr
See Also:
Constant Field Values

C3Pr

private static final byte C3Pr
See Also:
Constant Field Values

O1P

private static final byte O1P
See Also:
Constant Field Values

O2P

private static final byte O2P
See Also:
Constant Field Values

interestingNucleicAtomIDs

static final byte[] interestingNucleicAtomIDs

hasRnaO2Prime

private boolean hasRnaO2Prime

ring6OffsetIndexes

private static final byte[] ring6OffsetIndexes

ring5OffsetIndexes

private static final byte[] ring5OffsetIndexes
Constructor Detail

NucleicMonomer

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

validateAndAllocate

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

isNucleicMonomer

public boolean isNucleicMonomer()

isDna

public boolean isDna()
Overrides:
isDna in class PhosphorusMonomer

isRna

public boolean isRna()
Overrides:
isRna in class PhosphorusMonomer

isPurine

public boolean isPurine()
Overrides:
isPurine in class PhosphorusMonomer

isPyrimidine

public boolean isPyrimidine()
Overrides:
isPyrimidine in class PhosphorusMonomer

isGuanine

public boolean isGuanine()

getProteinStructureType

public byte getProteinStructureType()
Overrides:
getProteinStructureType in class PhosphorusMonomer

getN1

Atom getN1()

getN3

Atom getN3()

getN2

Atom getN2()

getO2

Atom getO2()

getO6

Atom getO6()

getN4

Atom getN4()

getN6

Atom getN6()

getO4

Atom getO4()

getTerminatorAtom

Atom getTerminatorAtom()
Overrides:
getTerminatorAtom in class Monomer

getBaseRing6Points

public void getBaseRing6Points(javax.vecmath.Point3f[] ring6Points)

maybeGetBaseRing5Points

public boolean maybeGetBaseRing5Points(javax.vecmath.Point3f[] ring5Points)

isConnectedAfter

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

findNearestAtomIndex

public 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

setModelClickability

public void setModelClickability()

getQuaternionFrameCenter

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

getHelixData

public java.lang.Object getHelixData(int tokType,
                                     char qType,
                                     int mStep)
Overrides:
getHelixData in class Group

getQuaternion

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