org.jmol.modelset

Class Group

public class Group extends Object

Field Summary
protected Chainchain
protected intfirstAtomIndex
static shortgroup3NameCount
static String[]group3Names
protected shortgroupID
static HashtablehtGroup
protected booleanisAmino
static intINSERTION_CODE_MASK
protected intlastAtomIndex
intminZ
protected floatomega
protected floatphi
protected floatpsi
intselectedIndex
intseqcode
intshapeVisibilityFlags
protected floatstraightness
static intSEQUENCE_NUMBER_FLAG
static intSEQUENCE_NUMBER_SHIFT
Constructor Summary
Group(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
Method Summary
static shortaddGroup3Name(String group3)
intgetBioPolymerIndex()
intgetBioPolymerLength()
chargetChainID()
intgetFirstAtomIndex()
chargetGroup1()
StringgetGroup3()
static StringgetGroup3(short groupID)
shortgetGroupID()
static shortgetGroupID(String group3)
chargetInsertionCode()
static chargetInsertionCode(int seqcode)
static intgetInsertionCodeValue(int seqcode)
intgetLastAtomIndex()
AtomgetLeadAtom(Atom atom)
AtomgetLeadAtom()
intgetMinZ()
ModelgetModel()
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
intgetModelIndex()
HashtablegetMyInfo()
floatgetOmega()
floatgetPhi()
intgetProteinStructureID()
bytegetProteinStructureType()
floatgetPsi()
QuaterniongetQuaternion(char qtype)
intgetResno()
intgetSelectedGroupIndex()
intgetSelectedMonomerCount()
intgetSelectedMonomerIndex()
intgetSeqcode()
static intgetSeqcode(int sequenceNumber, char insertionCode)
StringgetSeqcodeString()
static StringgetSeqcodeString(int seqcode)
intgetSeqNumber()
static intgetSequenceNumber(int seqcode)
floatgetStraightness()
ObjectgetStructure()
static booleanhaveSequenceNumber(int seqcode)
protected booleanisAtomHidden(int atomIndex)
booleanisCarbohydrate()
protected booleanisCursorOnTopOf(Atom atom, int x, int y, int radius, Atom champ)
booleanisDna()
booleanisGroup3(String group3)
booleanisHetero()
booleanisNucleic()
booleanisProtein()
booleanisPurine()
booleanisPyrimidine()
booleanisRna()
booleanisSelected(BitSet bs)
static shortlookupGroupID(String group3)
protected intscaleToScreen(int Z, int mar)
voidselectAtoms(BitSet bs)
voidsetMinZ(int z)
voidsetModelSet(ModelSet modelSet)
voidsetOmega(float omega)
voidsetPhi(float phi)
intsetProteinStructureType(byte iType, int monomerIndexCurrent)
voidsetPsi(float psi)
voidsetShapeVisibility(int visFlag, boolean isVisible)
voidsetStraightness(float straightness)
StringtoString()

Field Detail

chain

protected Chain chain

firstAtomIndex

protected int firstAtomIndex

group3NameCount

static short group3NameCount

group3Names

static String[] group3Names

groupID

protected short groupID

htGroup

private static Hashtable htGroup

isAmino

protected boolean isAmino

INSERTION_CODE_MASK

private static final int INSERTION_CODE_MASK

lastAtomIndex

protected int lastAtomIndex

minZ

private int minZ

omega

protected float omega

phi

protected float phi

psi

protected float psi

selectedIndex

int selectedIndex

seqcode

int seqcode

shapeVisibilityFlags

public int shapeVisibilityFlags

straightness

protected float straightness

SEQUENCE_NUMBER_FLAG

private static final int SEQUENCE_NUMBER_FLAG

SEQUENCE_NUMBER_SHIFT

private static final int SEQUENCE_NUMBER_SHIFT

Constructor Detail

Group

public Group(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)

Method Detail

addGroup3Name

static short addGroup3Name(String group3)

getBioPolymerIndex

public int getBioPolymerIndex()

getBioPolymerLength

public int getBioPolymerLength()

getChainID

public final char getChainID()

getFirstAtomIndex

public int getFirstAtomIndex()

getGroup1

public final char getGroup1()

getGroup3

final String getGroup3()

getGroup3

public static String getGroup3(short groupID)

getGroupID

public final short getGroupID()

getGroupID

public static short getGroupID(String group3)

getInsertionCode

public char getInsertionCode()

getInsertionCode

public static char getInsertionCode(int seqcode)

getInsertionCodeValue

public static final int getInsertionCodeValue(int seqcode)

getLastAtomIndex

public int getLastAtomIndex()

getLeadAtom

public Atom getLeadAtom(Atom atom)

getLeadAtom

public Atom getLeadAtom()

getMinZ

public int getMinZ()

getModel

public Model getModel()
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.

Returns: associated Model

getModelIndex

public int getModelIndex()

getMyInfo

public Hashtable getMyInfo()

getOmega

public float getOmega()

getPhi

public float getPhi()

getProteinStructureID

public int getProteinStructureID()

getProteinStructureType

public byte getProteinStructureType()

getPsi

public float getPsi()

getQuaternion

public Quaternion getQuaternion(char qtype)

getResno

public final int getResno()

getSelectedGroupIndex

public int getSelectedGroupIndex()

getSelectedMonomerCount

public int getSelectedMonomerCount()

getSelectedMonomerIndex

public int getSelectedMonomerIndex()

getSeqcode

public final int getSeqcode()

getSeqcode

public static int getSeqcode(int sequenceNumber, char insertionCode)

getSeqcodeString

public final String getSeqcodeString()

getSeqcodeString

public static String getSeqcodeString(int seqcode)

getSeqNumber

public final int getSeqNumber()

getSequenceNumber

public static final int getSequenceNumber(int seqcode)

getStraightness

public float getStraightness()

getStructure

public Object getStructure()

haveSequenceNumber

public static final boolean haveSequenceNumber(int seqcode)

isAtomHidden

protected boolean isAtomHidden(int atomIndex)

isCarbohydrate

public boolean isCarbohydrate()

isCursorOnTopOf

protected boolean isCursorOnTopOf(Atom atom, int x, int y, int radius, Atom champ)

isDna

public boolean isDna()

isGroup3

final boolean isGroup3(String group3)

isHetero

boolean isHetero()

isNucleic

public boolean isNucleic()

isProtein

public boolean isProtein()

isPurine

public boolean isPurine()

isPyrimidine

public boolean isPyrimidine()

isRna

public boolean isRna()

isSelected

public boolean isSelected(BitSet bs)

lookupGroupID

public static short lookupGroupID(String group3)

scaleToScreen

protected int scaleToScreen(int Z, int mar)

selectAtoms

public final void selectAtoms(BitSet bs)

setMinZ

public void setMinZ(int z)

setModelSet

public void setModelSet(ModelSet modelSet)

setOmega

public void setOmega(float omega)

setPhi

public void setPhi(float phi)

setProteinStructureType

public int setProteinStructureType(byte iType, int monomerIndexCurrent)

setPsi

public void setPsi(float psi)

setShapeVisibility

public final void setShapeVisibility(int visFlag, boolean isVisible)

setStraightness

public void setStraightness(float straightness)

toString

public String toString()