org.jmol.modelset
Class Group
java.lang.Object
org.jmol.modelset.Group
- Direct Known Subclasses:
- Monomer
public class Group
- extends java.lang.Object
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)
|
int |
getBioPolymerIndex()
|
int |
getBioPolymerLength()
|
char |
getChainID()
|
int |
getFirstAtomIndex()
|
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()
|
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep)
|
char |
getInsertionCode()
|
static char |
getInsertionCode(int seqcode)
|
static int |
getInsertionCodeValue(int seqcode)
|
int |
getLastAtomIndex()
|
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()
|
java.util.Hashtable |
getMyInfo()
|
float |
getOmega()
|
float |
getPhi()
|
java.lang.String |
getProteinStructureTag()
|
byte |
getProteinStructureType()
|
float |
getPsi()
|
Quaternion |
getQuaternion(char qtype)
|
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)
|
float |
getStraightness()
|
int |
getStrucNo()
|
java.lang.Object |
getStructure()
|
java.lang.String |
getStructureId()
|
static boolean |
haveSequenceNumber(int seqcode)
|
protected boolean |
isAtomHidden(int atomIndex)
|
boolean |
isCarbohydrate()
|
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 |
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)
|
void |
selectAtoms(java.util.BitSet bs)
|
void |
setGroupIndex(int groupIndex)
|
void |
setModelSet(ModelSet modelSet)
|
void |
setOmega(float omega)
|
void |
setPhi(float phi)
|
void |
setProteinStructureId(int i)
|
int |
setProteinStructureType(byte iType,
int monomerIndexCurrent)
|
void |
setPsi(float psi)
|
void |
setShapeVisibility(int visFlag,
boolean isVisible)
|
void |
setStraightness(float straightness)
|
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
groupIndex
private int groupIndex
chain
protected Chain chain
seqcode
int seqcode
groupID
protected short groupID
isAmino
protected boolean isAmino
selectedIndex
int selectedIndex
firstAtomIndex
protected int firstAtomIndex
lastAtomIndex
protected int lastAtomIndex
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
protected float phi
psi
protected float psi
omega
protected float omega
straightness
protected float straightness
htGroup
private static java.util.Hashtable htGroup
group3Names
static java.lang.String[] group3Names
group3NameCount
static short group3NameCount
Group
public Group(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex)
getGroupIndex
public int getGroupIndex()
setGroupIndex
public void setGroupIndex(int groupIndex)
getFirstAtomIndex
public int getFirstAtomIndex()
getLastAtomIndex
public int getLastAtomIndex()
getStraightness
public float getStraightness()
setStraightness
public void setStraightness(float straightness)
getPhi
public float getPhi()
setPhi
public void setPhi(float phi)
getPsi
public float getPsi()
setPsi
public void setPsi(float psi)
setOmega
public void setOmega(float omega)
getOmega
public float getOmega()
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()
getChainID
public final char getChainID()
getBioPolymerLength
public int getBioPolymerLength()
getBioPolymerIndex
public int getBioPolymerIndex()
getStructure
public java.lang.Object getStructure()
getStrucNo
public int getStrucNo()
getProteinStructureType
public byte getProteinStructureType()
setProteinStructureType
public int setProteinStructureType(byte iType,
int monomerIndexCurrent)
getMyInfo
public java.util.Hashtable getMyInfo()
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 void 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()
getLeadAtom
public Atom getLeadAtom(Atom atom)
getLeadAtom
public Atom getLeadAtom()
getQuaternion
public Quaternion getQuaternion(char qtype)
setProteinStructureId
public void setProteinStructureId(int i)
getHelixData
public java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
isWithinStructure
public boolean isWithinStructure(byte type)
getProteinStructureTag
public java.lang.String getProteinStructureTag()
getStructureId
public java.lang.String getStructureId()