org.jmol.modelsetbio

Class Monomer

public abstract class Monomer extends Group

Field Summary
BioPolymerbioPolymer
protected intmonomerIndex
protected byte[]offsets
Constructor Summary
protected Monomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)
Method Summary
protected static booleancheckOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)
voidfindNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
protected AtomgetAtomFromOffsetIndex(int offsetIndex)
BioPolymergetBioPolymer()
intgetBioPolymerIndex()
intgetBioPolymerLength()
AtomgetInitiatorAtom()
AtomgetLeadAtom()
intgetLeadAtomIndex()
Point3fgetLeadAtomPoint()
voidgetMonomerSequenceAtoms(BitSet bsInclude, BitSet bsResult)
HashtablegetMyInfo()
Point3fgetPointAtomPoint()
ProteinStructuregetProteinStructure()
bytegetProteinStructureType()
Point3fgetQuaternionFrameCenter(char qtype)
intgetSelectedMonomerCount()
intgetSelectedMonomerIndex()
protected AtomgetSpecialAtom(byte[] interestingIDs, byte specialAtomID)
protected Point3fgetSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)
static StringgetStructureTypeName(byte type)
AtomgetTerminatorAtom()
AtomgetWingAtom()
Point3fgetWingAtomPoint()
abstract booleanisConnectedAfter(Monomer possiblyPreviousMonomer)
booleanisDna()
booleanisHelix()
booleanisNucleic()
booleanisProtein()
booleanisRna()
booleanisSheet()
voidresetHydrogenPoint()
protected static byte[]scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)
voidsetBioPolymer(BioPolymer polymer, int index)
voidsetStructure(ProteinStructure proteinstructure)
voidupdateOffsetsForAlternativeLocations(BitSet bsSelected, int nAltLocInModel)

Field Detail

bioPolymer

BioPolymer bioPolymer

monomerIndex

protected int monomerIndex

offsets

protected final byte[] offsets

Constructor Detail

Monomer

protected Monomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)

Method Detail

checkOptional

protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)

findNearestAtomIndex

void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.

Parameters: x y closest madBegin madEnd

getAtomFromOffsetIndex

protected final Atom getAtomFromOffsetIndex(int offsetIndex)

getBioPolymer

public BioPolymer getBioPolymer()

getBioPolymerIndex

public int getBioPolymerIndex()

getBioPolymerLength

public int getBioPolymerLength()

getInitiatorAtom

Atom getInitiatorAtom()

getLeadAtom

public final Atom getLeadAtom()

getLeadAtomIndex

final int getLeadAtomIndex()

getLeadAtomPoint

final Point3f getLeadAtomPoint()

getMonomerSequenceAtoms

final void getMonomerSequenceAtoms(BitSet bsInclude, BitSet bsResult)

getMyInfo

public Hashtable getMyInfo()

getPointAtomPoint

final Point3f getPointAtomPoint()

getProteinStructure

public ProteinStructure getProteinStructure()

getProteinStructureType

public byte getProteinStructureType()

getQuaternionFrameCenter

Point3f getQuaternionFrameCenter(char qtype)

getSelectedMonomerCount

public int getSelectedMonomerCount()

getSelectedMonomerIndex

public int getSelectedMonomerIndex()

getSpecialAtom

protected final Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)

getSpecialAtomPoint

protected final Point3f getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)

getStructureTypeName

static String getStructureTypeName(byte type)

getTerminatorAtom

Atom getTerminatorAtom()

getWingAtom

public final Atom getWingAtom()

getWingAtomPoint

public final Point3f getWingAtomPoint()

isConnectedAfter

abstract boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

isDna

public boolean isDna()

isHelix

public boolean isHelix()

isNucleic

public final boolean isNucleic()

isProtein

public final boolean isProtein()

isRna

public boolean isRna()

isSheet

public boolean isSheet()

resetHydrogenPoint

public void resetHydrogenPoint()

scanForOffsets

protected static byte[] scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)

setBioPolymer

void setBioPolymer(BioPolymer polymer, int index)

setStructure

void setStructure(ProteinStructure proteinstructure)

updateOffsetsForAlternativeLocations

final void updateOffsetsForAlternativeLocations(BitSet bsSelected, int nAltLocInModel)