public class Group
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private java.util.BitSet |
bsAdded |
protected Chain |
chain |
int |
firstAtomIndex |
(package private) static short |
group3NameCount |
(package private) static java.lang.String[] |
group3Names |
protected short |
groupID |
protected int |
groupIndex |
private static java.util.Map<java.lang.String,java.lang.Short> |
htGroup |
private static int |
INSERTION_CODE_MASK |
protected boolean |
isProtein |
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 and Description |
---|
Group(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex) |
Modifier and Type | Method and Description |
---|---|
void |
addAtoms(int atomIndex) |
(package private) static short |
addGroup3Name(java.lang.String group3) |
protected boolean |
calcBioParameters() |
private void |
checkMinZ(Atom atom,
int[] minZ) |
void |
fixIndices(int atomsDeleted,
java.util.BitSet bsDeleted) |
int |
getBioPolymerIndexInModel() |
int |
getBioPolymerLength() |
Atom |
getCarbonylOxygenAtom() |
char |
getChainID() |
boolean |
getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn) |
char |
getGroup1() |
java.lang.String |
getGroup3() |
static java.lang.String |
getGroup3(short groupID) |
short |
getGroupID() |
static short |
getGroupID(java.lang.String group3) |
int |
getGroupIndex() |
protected java.util.Map<java.lang.String,java.lang.Object> |
getGroupInfo(int igroup) |
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) |
void |
getMinZ(Atom[] atoms,
int[] minZ) |
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() |
EnumStructure |
getProteinStructureSubType() |
java.lang.String |
getProteinStructureTag() |
EnumStructure |
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) |
boolean |
isAdded(int atomIndex) |
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(EnumStructure 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(EnumStructure type,
int monomerIndexCurrent) |
void |
setShapeVisibility(int visFlag,
boolean isVisible) |
java.lang.String |
toString() |
protected int groupIndex
protected Chain chain
int seqcode
protected short groupID
protected boolean isProtein
int selectedIndex
public int firstAtomIndex
public int leadAtomIndex
public int lastAtomIndex
private static final int SEQUENCE_NUMBER_FLAG
private static final int INSERTION_CODE_MASK
private static final int SEQUENCE_NUMBER_SHIFT
public int shapeVisibilityFlags
private float phi
private float psi
private float omega
private float straightness
private float mu
private float theta
private static java.util.Map<java.lang.String,java.lang.Short> htGroup
static java.lang.String[] group3Names
static short group3NameCount
private java.util.BitSet bsAdded
public Group(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
public int getGroupIndex()
public void setGroupIndex(int groupIndex)
protected boolean calcBioParameters()
public boolean haveParameters()
public void setGroupParameter(int tok, float f)
public float getGroupParameter(int tok)
public void setModelSet(ModelSet modelSet)
public final void setShapeVisibility(int visFlag, boolean isVisible)
final boolean isGroup3(java.lang.String group3)
public final java.lang.String getGroup3()
public static java.lang.String getGroup3(short groupID)
public final char getGroup1()
public final short getGroupID()
public final ModelSet getModelSet()
public final char getChainID()
public int getBioPolymerLength()
public int getMonomerIndex()
public java.lang.Object getStructure()
public int getStrucNo()
public EnumStructure getProteinStructureType()
public EnumStructure getProteinStructureSubType()
public int setProteinStructureType(EnumStructure type, int monomerIndexCurrent)
type
- monomerIndexCurrent
- public boolean isProtein()
public boolean isNucleic()
public boolean isDna()
public boolean isRna()
public boolean isPurine()
public boolean isPyrimidine()
public boolean isCarbohydrate()
static short addGroup3Name(java.lang.String group3)
public static short getGroupID(java.lang.String group3)
public static short lookupGroupID(java.lang.String group3)
public final int getResno()
public final int getSeqcode()
public final int getSeqNumber()
public static final int getSequenceNumber(int seqcode)
public static final int getInsertionCodeValue(int seqcode)
public static final boolean haveSequenceNumber(int seqcode)
public final java.lang.String getSeqcodeString()
public static int getSeqcode(int sequenceNumber, char insertionCode)
public static java.lang.String getSeqcodeString(int seqcode)
public char getInsertionCode()
public static char getInsertionCode(int seqcode)
public boolean isAdded(int atomIndex)
public void addAtoms(int atomIndex)
public int selectAtoms(java.util.BitSet bs)
public boolean isSelected(java.util.BitSet bs)
boolean isHetero()
public java.lang.String toString()
toString
in class java.lang.Object
protected int scaleToScreen(int Z, int mar)
protected boolean isAtomHidden(int atomIndex)
public Model getModel()
public int getModelIndex()
public int getSelectedMonomerCount()
public int getSelectedMonomerIndex()
public int getSelectedGroupIndex()
public boolean isLeadAtom(int atomIndex)
atomIndex
- public Atom getLeadAtom()
public Quaternion getQuaternion(char qType)
qType
- public Quaternion getQuaternionFrame(Atom[] atoms)
public void setProteinStructureId(int i)
i
- public java.lang.Object getHelixData(int tokType, char qType, int mStep)
tokType
- qType
- mStep
- public boolean isWithinStructure(EnumStructure type)
type
- public java.lang.String getProteinStructureTag()
public java.lang.String getStructureId()
public int getBioPolymerIndexInModel()
public boolean isCrossLinked(Group g)
g
- public boolean getCrossLinkLeadAtomIndexes(java.util.List<java.lang.Integer> vReturn)
vReturn
- public boolean isConnectedPrevious()
public Atom getNitrogenAtom()
public Atom getCarbonylOxygenAtom()
public void fixIndices(int atomsDeleted, java.util.BitSet bsDeleted)
protected java.util.Map<java.lang.String,java.lang.Object> getGroupInfo(int igroup)
public void getMinZ(Atom[] atoms, int[] minZ)
private void checkMinZ(Atom atom, int[] minZ)