org.jmol.modelsetbio

Class NucleicMonomer

public class NucleicMonomer extends PhosphorusMonomer

Field Summary
static byteC2
static byteC3Pr
static byteC4
static byteC5
static byteC6
static byteC8
booleanhasRnaO2Prime
static byteH3T
static byteH5T
static byte[]interestingNucleicAtomIDs
static byteN1
static byteN2
static byteN3
static byteN4
static byteN6
static byteN7
static byteN9
static byteNP
static byteO1P
static byteO2
static byteO2P
static byteO2Pr
static byteO3Pr
static byteO4
static byteO5Pr
static byteO6
static byte[]ring5OffsetIndexes
static byte[]ring6OffsetIndexes
Constructor Summary
NucleicMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
Method Summary
voidfindNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
voidgetBaseRing6Points(Point3f[] ring6Points)
AtomgetN1()
AtomgetN2()
AtomgetN3()
AtomgetN4()
AtomgetN6()
AtomgetO2()
AtomgetO4()
AtomgetO6()
bytegetProteinStructureType()
QuaterniongetQuaternion(char qType)
Point3fgetQuaternionFrameCenter(char qType)
AtomgetTerminatorAtom()
booleanisConnectedAfter(Monomer possiblyPreviousMonomer)
booleanisDna()
booleanisGuanine()
booleanisNucleicMonomer()
booleanisPurine()
booleanisPyrimidine()
booleanisRna()
booleanmaybeGetBaseRing5Points(Point3f[] ring5Points)
voidsetModelClickability()
static MonomervalidateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)

Field Detail

C2

private static final byte C2

C3Pr

private static final byte C3Pr

C4

private static final byte C4

C5

private static final byte C5

C6

static final byte C6

C8

private static final byte C8

hasRnaO2Prime

private boolean hasRnaO2Prime

H3T

private static final byte H3T

H5T

private static final byte H5T

interestingNucleicAtomIDs

static final byte[] interestingNucleicAtomIDs

N1

private static final byte N1

N2

private static final byte N2

N3

private static final byte N3

N4

private static final byte N4

N6

private static final byte N6

N7

private static final byte N7

N9

private static final byte N9

NP

private static final byte NP

O1P

private static final byte O1P

O2

private static final byte O2

O2P

private static final byte O2P

O2Pr

private static final byte O2Pr

O3Pr

private static final byte O3Pr

O4

private static final byte O4

O5Pr

private static final byte O5Pr

O6

private static final byte O6

ring5OffsetIndexes

private static final byte[] ring5OffsetIndexes

ring6OffsetIndexes

private static final byte[] ring6OffsetIndexes

Constructor Detail

NucleicMonomer

NucleicMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)

Method Detail

findNearestAtomIndex

public void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)

getBaseRing6Points

public void getBaseRing6Points(Point3f[] ring6Points)

getN1

Atom getN1()

getN2

Atom getN2()

getN3

Atom getN3()

getN4

Atom getN4()

getN6

Atom getN6()

getO2

Atom getO2()

getO4

Atom getO4()

getO6

Atom getO6()

getProteinStructureType

public byte getProteinStructureType()

getQuaternion

public Quaternion getQuaternion(char qType)

getQuaternionFrameCenter

Point3f getQuaternionFrameCenter(char qType)

getTerminatorAtom

Atom getTerminatorAtom()

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

isDna

public boolean isDna()

isGuanine

public boolean isGuanine()

isNucleicMonomer

public boolean isNucleicMonomer()

isPurine

public boolean isPurine()

isPyrimidine

public boolean isPyrimidine()

isRna

public boolean isRna()

maybeGetBaseRing5Points

public boolean maybeGetBaseRing5Points(Point3f[] ring5Points)

setModelClickability

public void setModelClickability()

validateAndAllocate

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