org.jmol.modelsetbio

Class AlphaMonomer

public class AlphaMonomer extends Monomer

Field Summary
static byte[]alphaOffsets
protected Point3fnitrogenHydrogenPoint
ProteinStructureproteinStructure
Constructor Summary
AlphaMonomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
Method Summary
AtomgetAtom(byte specialAtomID)
Point3fgetAtomPoint(byte specialAtomID)
ProteinStructuregetProteinStructure()
intgetProteinStructureID()
bytegetProteinStructureType()
ObjectgetStructure()
booleanisAlphaMonomer()
booleanisConnectedAfter(Monomer possiblyPreviousMonomer)
booleanisHelix()
booleanisSheet()
intsetProteinStructureType(byte iType, int monomerIndexCurrent)
voidsetStructure(ProteinStructure proteinStructure)
static MonomervalidateAndAllocate(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes, Atom[] atoms)

Field Detail

alphaOffsets

static final byte[] alphaOffsets

nitrogenHydrogenPoint

protected Point3f nitrogenHydrogenPoint

proteinStructure

private ProteinStructure proteinStructure

Constructor Detail

AlphaMonomer

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

Method Detail

getAtom

public final Atom getAtom(byte specialAtomID)

getAtomPoint

public final Point3f getAtomPoint(byte specialAtomID)

getProteinStructure

public ProteinStructure getProteinStructure()

getProteinStructureID

public int getProteinStructureID()

getProteinStructureType

public byte getProteinStructureType()

getStructure

public Object getStructure()

isAlphaMonomer

boolean isAlphaMonomer()

isConnectedAfter

boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

isHelix

public boolean isHelix()

isSheet

public boolean isSheet()

setProteinStructureType

public int setProteinStructureType(byte iType, int monomerIndexCurrent)

Parameters: iType monomerIndexCurrent a pointer to the current ProteinStructure

Returns: a pointer to this ProteinStructure

setStructure

void setStructure(ProteinStructure proteinStructure)

validateAndAllocate

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