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)
|
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 |
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
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)
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()