org.jmol.modelset
Class Group

java.lang.Object
  extended by org.jmol.modelset.Group
Direct Known Subclasses:
Monomer

public class Group
extends java.lang.Object


Field Summary
protected  Chain chain
           
 int firstAtomIndex
           
(package private) static short group3NameCount
           
(package private) static java.lang.String[] group3Names
           
protected  short groupID
           
private  int groupIndex
           
private static java.util.Map htGroup
           
private static int INSERTION_CODE_MASK
           
protected  boolean isAmino
           
 int lastAtomIndex
           
 int leadAtomIndex
           
private  float mu
           
private  float omega
           
private  float phi
           
private  float psi
           
(package private)  int selectedIndex
           
(package private)  int seqcode
           
private static int SEQUENCE_NUMBER_FLAG
           
private static int SEQUENCE_NUMBER_SHIFT
           
 int shapeVisibilityFlags
           
private  float straightness
           
private  float theta
           
 
Constructor Summary
Group(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
           
 
Method Summary
(package private) static short addGroup3Name(java.lang.String group3)
           
protected  boolean calcBioParameters()
           
 int getBioPolymerIndexInModel()
           
 int getBioPolymerLength()
           
 Atom getCarbonylOxygenAtom()
           
 char getChainID()
           
 boolean getCrossLinkLeadAtomIndexes(java.util.List vReturn)
           
 char getGroup1()
           
(package private)  java.lang.String getGroup3()
           
static java.lang.String getGroup3(short groupID)
           
 short getGroupID()
           
static short getGroupID(java.lang.String group3)
           
 int getGroupIndex()
           
 float getGroupParameter(int tok)
           
 java.lang.Object getHelixData(int tokType, char qType, int mStep)
           
 char getInsertionCode()
           
static char getInsertionCode(int seqcode)
           
static int getInsertionCodeValue(int seqcode)
           
 Atom getLeadAtom()
           
 Atom getLeadAtom(Atom atom)
           
 Model getModel()
          BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
 int getModelIndex()
           
 ModelSet getModelSet()
           
 int getMonomerIndex()
           
 Atom getNitrogenAtom()
           
 byte getProteinStructureSubType()
           
 java.lang.String getProteinStructureTag()
           
 byte getProteinStructureType()
           
 Quaternion getQuaternion(char qType)
           
 Quaternion getQuaternionFrame(Atom[] atoms)
           
 int getResno()
           
 int getSelectedGroupIndex()
           
 int getSelectedMonomerCount()
           
 int getSelectedMonomerIndex()
           
 int getSeqcode()
           
static int getSeqcode(int sequenceNumber, char insertionCode)
           
 java.lang.String getSeqcodeString()
           
static java.lang.String getSeqcodeString(int seqcode)
           
 int getSeqNumber()
           
static int getSequenceNumber(int seqcode)
           
 int getStrucNo()
           
 java.lang.Object getStructure()
           
 java.lang.String getStructureId()
           
 boolean haveParameters()
           
static boolean haveSequenceNumber(int seqcode)
           
protected  boolean isAtomHidden(int atomIndex)
           
 boolean isCarbohydrate()
           
 boolean isConnectedPrevious()
           
 boolean isCrossLinked(Group g)
           
protected  boolean isCursorOnTopOf(Atom atom, int x, int y, int radius, Atom champ)
           
 boolean isDna()
           
(package private)  boolean isGroup3(java.lang.String group3)
           
(package private)  boolean isHetero()
           
 boolean isLeadAtom(int atomIndex)
           
 boolean isNucleic()
           
 boolean isProtein()
           
 boolean isPurine()
           
 boolean isPyrimidine()
           
 boolean isRna()
           
 boolean isSelected(java.util.BitSet bs)
           
 boolean isWithinStructure(byte type)
           
static short lookupGroupID(java.lang.String group3)
           
protected  int scaleToScreen(int Z, int mar)
           
 int selectAtoms(java.util.BitSet bs)
           
 void setGroupIndex(int groupIndex)
           
 void setGroupParameter(int tok, float f)
           
 void setModelSet(ModelSet modelSet)
           
 void setProteinStructureId(int i)
           
 int setProteinStructureType(byte iType, int monomerIndexCurrent)
           
 void setShapeVisibility(int visFlag, boolean isVisible)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

groupIndex

private int groupIndex

chain

protected Chain chain

seqcode

int seqcode

groupID

protected short groupID

isAmino

protected boolean isAmino

selectedIndex

int selectedIndex

firstAtomIndex

public int firstAtomIndex

lastAtomIndex

public int lastAtomIndex

leadAtomIndex

public int leadAtomIndex

SEQUENCE_NUMBER_FLAG

private static final int SEQUENCE_NUMBER_FLAG
See Also:
Constant Field Values

INSERTION_CODE_MASK

private static final int INSERTION_CODE_MASK
See Also:
Constant Field Values

SEQUENCE_NUMBER_SHIFT

private static final int SEQUENCE_NUMBER_SHIFT
See Also:
Constant Field Values

shapeVisibilityFlags

public int shapeVisibilityFlags

phi

private float phi

psi

private float psi

omega

private float omega

straightness

private float straightness

mu

private float mu

theta

private float theta

htGroup

private static java.util.Map htGroup

group3Names

static java.lang.String[] group3Names

group3NameCount

static short group3NameCount
Constructor Detail

Group

public Group(Chain chain,
             java.lang.String group3,
             int seqcode,
             int firstAtomIndex,
             int lastAtomIndex)
Method Detail

getGroupIndex

public int getGroupIndex()

setGroupIndex

public void setGroupIndex(int groupIndex)

calcBioParameters

protected boolean calcBioParameters()

haveParameters

public boolean haveParameters()

setGroupParameter

public void setGroupParameter(int tok,
                              float f)

getGroupParameter

public float getGroupParameter(int tok)

setModelSet

public void setModelSet(ModelSet modelSet)

setShapeVisibility

public final void setShapeVisibility(int visFlag,
                                     boolean isVisible)

isGroup3

final boolean isGroup3(java.lang.String group3)

getGroup3

final java.lang.String getGroup3()

getGroup3

public static java.lang.String getGroup3(short groupID)

getGroup1

public final char getGroup1()

getGroupID

public final short getGroupID()

getModelSet

public final ModelSet getModelSet()

getChainID

public final char getChainID()

getBioPolymerLength

public int getBioPolymerLength()

getMonomerIndex

public int getMonomerIndex()

getStructure

public java.lang.Object getStructure()

getStrucNo

public int getStrucNo()

getProteinStructureType

public byte getProteinStructureType()

getProteinStructureSubType

public byte getProteinStructureSubType()

setProteinStructureType

public int setProteinStructureType(byte iType,
                                   int monomerIndexCurrent)
Parameters:
iType -
monomerIndexCurrent -
Returns:
type

isProtein

public boolean isProtein()

isNucleic

public boolean isNucleic()

isDna

public boolean isDna()

isRna

public boolean isRna()

isPurine

public boolean isPurine()

isPyrimidine

public boolean isPyrimidine()

isCarbohydrate

public boolean isCarbohydrate()

addGroup3Name

static short addGroup3Name(java.lang.String group3)

getGroupID

public static short getGroupID(java.lang.String group3)

lookupGroupID

public static short lookupGroupID(java.lang.String group3)

getResno

public final int getResno()

getSeqcode

public final int getSeqcode()

getSeqNumber

public final int getSeqNumber()

getSequenceNumber

public static final int getSequenceNumber(int seqcode)

getInsertionCodeValue

public static final int getInsertionCodeValue(int seqcode)

haveSequenceNumber

public static final boolean haveSequenceNumber(int seqcode)

getSeqcodeString

public final java.lang.String getSeqcodeString()

getSeqcode

public static int getSeqcode(int sequenceNumber,
                             char insertionCode)

getSeqcodeString

public static java.lang.String getSeqcodeString(int seqcode)

getInsertionCode

public char getInsertionCode()

getInsertionCode

public static char getInsertionCode(int seqcode)

selectAtoms

public final int selectAtoms(java.util.BitSet bs)

isSelected

public boolean isSelected(java.util.BitSet bs)

isHetero

boolean isHetero()

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

scaleToScreen

protected int scaleToScreen(int Z,
                            int mar)

isCursorOnTopOf

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

isAtomHidden

protected boolean isAtomHidden(int atomIndex)

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()

getSelectedMonomerCount

public int getSelectedMonomerCount()

getSelectedMonomerIndex

public int getSelectedMonomerIndex()

getSelectedGroupIndex

public int getSelectedGroupIndex()

isLeadAtom

public boolean isLeadAtom(int atomIndex)
Parameters:
atomIndex -
Returns:
T/F

getLeadAtom

public Atom getLeadAtom(Atom atom)

getLeadAtom

public Atom getLeadAtom()

getQuaternion

public Quaternion getQuaternion(char qType)
Parameters:
qType -
Returns:
quaternion

getQuaternionFrame

public Quaternion getQuaternionFrame(Atom[] atoms)

setProteinStructureId

public void setProteinStructureId(int i)
Parameters:
i -

getHelixData

public java.lang.Object getHelixData(int tokType,
                                     char qType,
                                     int mStep)
Parameters:
tokType -
qType -
mStep -
Returns:
helix data of some sort

isWithinStructure

public boolean isWithinStructure(byte type)
Parameters:
type -
Returns:
T/F

getProteinStructureTag

public java.lang.String getProteinStructureTag()

getStructureId

public java.lang.String getStructureId()

getBioPolymerIndexInModel

public int getBioPolymerIndexInModel()

isCrossLinked

public boolean isCrossLinked(Group g)
Parameters:
g -
Returns:
T/F

getCrossLinkLeadAtomIndexes

public boolean getCrossLinkLeadAtomIndexes(java.util.List vReturn)
Parameters:
vReturn -
Returns:
T/F

isConnectedPrevious

public boolean isConnectedPrevious()

getNitrogenAtom

public Atom getNitrogenAtom()

getCarbonylOxygenAtom

public Atom getCarbonylOxygenAtom()