org.jmol.modelsetbio
Class NucleicMonomer
public
class
NucleicMonomer
extends PhosphorusMonomer
Method Summary |
void | findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd) |
void | getBaseRing6Points(Point3f[] ring6Points) |
Atom | getN1() |
Atom | getN2() |
Atom | getN3() |
Atom | getN4() |
Atom | getN6() |
Atom | getO2() |
Atom | getO4() |
Atom | getO6() |
byte | getProteinStructureType() |
Quaternion | getQuaternion(char qType) |
Point3f | getQuaternionFrameCenter(char qType) |
Atom | getTerminatorAtom() |
boolean | isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean | isDna() |
boolean | isGuanine() |
boolean | isNucleicMonomer() |
boolean | isPurine() |
boolean | isPyrimidine() |
boolean | isRna() |
boolean | maybeGetBaseRing5Points(Point3f[] ring5Points) |
void | setModelClickability() |
static Monomer | validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) |
private static final byte C2
private static final byte C3Pr
private static final byte C4
private static final byte C5
static final byte C6
private static final byte C8
private boolean hasRnaO2Prime
private static final byte H3T
private static final byte H5T
static final byte[] interestingNucleicAtomIDs
private static final byte N1
private static final byte N2
private static final byte N3
private static final byte N4
private static final byte N6
private static final byte N7
private static final byte N9
private static final byte NP
private static final byte O1P
private static final byte O2
private static final byte O2P
private static final byte O2Pr
private static final byte O3Pr
private static final byte O4
private static final byte O5Pr
private static final byte O6
private static final byte[] ring5OffsetIndexes
private static final byte[] ring6OffsetIndexes
NucleicMonomer(
Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
public void findNearestAtomIndex(int x, int y,
Atom[] closest, short madBegin, short madEnd)
public void getBaseRing6Points(Point3f[] ring6Points)
public byte getProteinStructureType()
Point3f getQuaternionFrameCenter(char qType)
boolean isConnectedAfter(
Monomer possiblyPreviousMonomer)
public boolean isDna()
public boolean isGuanine()
public boolean isNucleicMonomer()
public boolean isPurine()
public boolean isPyrimidine()
public boolean isRna()
public boolean maybeGetBaseRing5Points(Point3f[] ring5Points)
public void setModelClickability()
public static
Monomer validateAndAllocate(
Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes,
Atom[] atoms)