org.jmol.modelsetbio
Class AminoMonomer
public
class
AminoMonomer
extends AlphaMonomer
Method Summary |
void | findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd) |
Atom | getCarbonylCarbonAtom() |
Point3f | getCarbonylCarbonAtomPoint() |
Atom | getCarbonylOxygenAtom() |
Point3f | getCarbonylOxygenAtomPoint() |
Atom | getInitiatorAtom() |
boolean | getNHPoint(Point3f aminoHydrogenPoint, Vector3f vNH) |
Atom | getNitrogenAtom() |
Point3f | getNitrogenAtomPoint() |
Point3f | getNitrogenHydrogenPoint() |
Quaternion | getQuaternion(char qType) |
Point3f | getQuaternionFrameCenter(char qType) |
Atom | getTerminatorAtom() |
boolean | hasOAtom() |
boolean | isAminoMonomer() |
static boolean | isBondedCorrectly(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms) |
static boolean | isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms) |
boolean | isConnectedAfter(Monomer possiblyPreviousMonomer) |
void | resetHydrogenPoint() |
static Monomer | validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms) |
private static final float beta
private static final byte C
private static final byte CA
static final byte[] interestingAminoAtomIDs
boolean nhChecked
private static final byte N
private static final byte O
private static final byte OT
private final Point3f ptTemp
private AminoMonomer(
Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
void findNearestAtomIndex(int x, int y,
Atom[] closest, short madBegin, short madEnd)
Atom getCarbonylCarbonAtom()
Point3f getCarbonylCarbonAtomPoint()
Atom getCarbonylOxygenAtom()
Point3f getCarbonylOxygenAtomPoint()
public boolean getNHPoint(Point3f aminoHydrogenPoint, Vector3f vNH)
Point3f getNitrogenAtomPoint()
Point3f getNitrogenHydrogenPoint()
Point3f getQuaternionFrameCenter(char qType)
boolean hasOAtom()
boolean isAminoMonomer()
private static boolean isBondedCorrectly(int offset1, int offset2, int firstAtomIndex, byte[] offsets,
Atom[] atoms)
private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets,
Atom[] atoms)
boolean isConnectedAfter(
Monomer possiblyPreviousMonomer)
public void resetHydrogenPoint()
static
Monomer validateAndAllocate(
Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes,
Atom[] atoms)