org.jmol.modelsetbio

Class AminoMonomer

public class AminoMonomer extends AlphaMonomer

Field Summary
static floatbeta
static byteC
static byteCA
static byte[]interestingAminoAtomIDs
booleannhChecked
static byteN
static byteO
static byteOT
Point3fptTemp
Constructor Summary
AminoMonomer(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)
AtomgetCarbonylCarbonAtom()
Point3fgetCarbonylCarbonAtomPoint()
AtomgetCarbonylOxygenAtom()
Point3fgetCarbonylOxygenAtomPoint()
AtomgetInitiatorAtom()
booleangetNHPoint(Point3f aminoHydrogenPoint, Vector3f vNH)
AtomgetNitrogenAtom()
Point3fgetNitrogenAtomPoint()
Point3fgetNitrogenHydrogenPoint()
QuaterniongetQuaternion(char qType)
Point3fgetQuaternionFrameCenter(char qType)
AtomgetTerminatorAtom()
booleanhasOAtom()
booleanisAminoMonomer()
static booleanisBondedCorrectly(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
static booleanisBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
booleanisConnectedAfter(Monomer possiblyPreviousMonomer)
voidresetHydrogenPoint()
static MonomervalidateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)

Field Detail

beta

private static final float beta

C

private static final byte C

CA

private static final byte CA

interestingAminoAtomIDs

static final byte[] interestingAminoAtomIDs

nhChecked

boolean nhChecked

N

private static final byte N

O

private static final byte O

OT

private static final byte OT

ptTemp

private final Point3f ptTemp

Constructor Detail

AminoMonomer

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

Method Detail

findNearestAtomIndex

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

getCarbonylCarbonAtom

Atom getCarbonylCarbonAtom()

getCarbonylCarbonAtomPoint

Point3f getCarbonylCarbonAtomPoint()

getCarbonylOxygenAtom

Atom getCarbonylOxygenAtom()

getCarbonylOxygenAtomPoint

Point3f getCarbonylOxygenAtomPoint()

getInitiatorAtom

Atom getInitiatorAtom()

getNHPoint

public boolean getNHPoint(Point3f aminoHydrogenPoint, Vector3f vNH)

getNitrogenAtom

Atom getNitrogenAtom()

getNitrogenAtomPoint

Point3f getNitrogenAtomPoint()

getNitrogenHydrogenPoint

Point3f getNitrogenHydrogenPoint()

getQuaternion

public Quaternion getQuaternion(char qType)

getQuaternionFrameCenter

Point3f getQuaternionFrameCenter(char qType)

getTerminatorAtom

Atom getTerminatorAtom()

hasOAtom

boolean hasOAtom()

isAminoMonomer

boolean isAminoMonomer()

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)

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

resetHydrogenPoint

public void resetHydrogenPoint()

validateAndAllocate

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