public class Group
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private BS |
bsAdded |
Chain |
chain |
int |
firstAtomIndex |
char |
group1 |
static java.lang.String[] |
group3Names |
short |
groupID |
int |
groupIndex |
static java.util.Map<java.lang.String,java.lang.Short> |
htGroup |
private static int |
INSERTION_CODE_MASK |
int |
lastAtomIndex |
int |
leadAtomIndex |
(package private) int |
selectedIndex |
int |
seqcode |
private static int |
SEQUENCE_NUMBER_FLAG |
private static int |
SEQUENCE_NUMBER_SHIFT |
int |
shapeVisibilityFlags |
static java.lang.String[] |
specialAtomNames |
static java.lang.String |
standardGroupList |
Constructor and Description |
---|
Group() |
Modifier and Type | Method and Description |
---|---|
void |
addAtoms(int atomIndex) |
private void |
checkMinZ(Atom atom,
int[] minZ) |
void |
fixIndices(int atomsDeleted,
BS bsDeleted) |
int |
getAtomIndex(java.lang.String name,
int offset) |
int |
getBioPolymerIndexInModel() |
int |
getBioPolymerLength() |
BS |
getBSSideChain() |
Atom |
getCarbonylOxygenAtom() |
boolean |
getCrossLinkLead(javajs.util.Lst<java.lang.Integer> vReturn) |
char |
getGroup1() |
java.lang.String |
getGroup3() |
java.util.Map<java.lang.String,java.lang.Object> |
getGroupInfo(int igroup,
javajs.util.P3 ptTemp) |
float |
getGroupParameter(int tok)
Monomers only
|
Group[] |
getGroups() |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
char |
getInsertionCode() |
static char |
getInsertionCodeChar(int seqcode) |
static int |
getInsertionCodeFor(int seqcode) |
Atom |
getLeadAtom() |
Atom |
getLeadAtomOr(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() |
int |
getMonomerIndex() |
Atom |
getNitrogenAtom() |
STR |
getProteinStructureSubType() |
java.lang.String |
getProteinStructureTag() |
STR |
getProteinStructureType() |
javajs.util.Quat |
getQuaternion(char qType) |
javajs.util.Quat |
getQuaternionFrame(Atom[] atoms) |
int |
getResno() |
int |
getSelectedGroupIndex() |
int |
getSelectedMonomerCount() |
int |
getSelectedMonomerIndex() |
static int |
getSeqcodeFor(int seqNo,
char insCode) |
java.lang.String |
getSeqcodeString() |
static java.lang.String |
getSeqcodeStringFor(int seqcode) |
static int |
getSeqNumberFor(int seqcode) |
int |
getStrucNo() |
java.lang.Object |
getStructure() |
java.lang.String |
getStructureId() |
static boolean |
haveSequenceNumber(int seqcode) |
boolean |
isAdded(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 |
isHetero() |
boolean |
isLeadAtom(int atomIndex) |
boolean |
isNucleic() |
boolean |
isProtein() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
boolean |
isSelected(BS bs) |
boolean |
isWithinStructure(STR type) |
protected float |
scaleToScreen(int Z,
int mar) |
int |
selectAtoms(BS bs) |
Group |
setGroup(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex) |
protected void |
setGroupID(java.lang.String group3) |
int |
setProteinStructureType(STR type,
int monomerIndexCurrent) |
void |
setShapeVisibility(int visFlag,
boolean isVisible) |
void |
setStrucNo(int i) |
java.lang.String |
toString() |
public int groupIndex
public char group1
public Chain chain
public int firstAtomIndex
public int leadAtomIndex
public int lastAtomIndex
public int seqcode
public short groupID
int selectedIndex
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 BS bsAdded
public static java.util.Map<java.lang.String,java.lang.Short> htGroup
public static java.lang.String standardGroupList
public static java.lang.String[] group3Names
public static java.lang.String[] specialAtomNames
public Group setGroup(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
protected void setGroupID(java.lang.String group3)
group3
- public final void setShapeVisibility(int visFlag, boolean isVisible)
public java.lang.String getGroup3()
public char getGroup1()
public int getBioPolymerLength()
public int getMonomerIndex()
public Group[] getGroups()
public java.lang.Object getStructure()
public int getStrucNo()
public STR getProteinStructureType()
public STR getProteinStructureSubType()
public int setProteinStructureType(STR 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()
public final int getResno()
public static final int getSeqNumberFor(int seqcode)
public static final boolean haveSequenceNumber(int seqcode)
public final java.lang.String getSeqcodeString()
public static int getSeqcodeFor(int seqNo, char insCode)
public static java.lang.String getSeqcodeStringFor(int seqcode)
public char getInsertionCode()
public static int getInsertionCodeFor(int seqcode)
public static char getInsertionCodeChar(int seqcode)
public boolean isAdded(int atomIndex)
public void addAtoms(int atomIndex)
public int selectAtoms(BS bs)
public boolean isSelected(BS bs)
boolean isHetero()
public java.lang.String toString()
toString
in class java.lang.Object
protected float scaleToScreen(int Z, int mar)
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 javajs.util.Quat getQuaternion(char qType)
qType
- public javajs.util.Quat getQuaternionFrame(Atom[] atoms)
public void setStrucNo(int i)
i
- public java.lang.Object getHelixData(int tokType, char qType, int mStep)
tokType
- qType
- mStep
- public boolean isWithinStructure(STR type)
type
- public java.lang.String getProteinStructureTag()
public java.lang.String getStructureId()
public int getBioPolymerIndexInModel()
public boolean isCrossLinked(Group g)
g
- public boolean getCrossLinkLead(javajs.util.Lst<java.lang.Integer> vReturn)
vReturn
- public boolean isConnectedPrevious()
public Atom getNitrogenAtom()
public Atom getCarbonylOxygenAtom()
public void fixIndices(int atomsDeleted, BS bsDeleted)
public java.util.Map<java.lang.String,java.lang.Object> getGroupInfo(int igroup, javajs.util.P3 ptTemp)
public void getMinZ(Atom[] atoms, int[] minZ)
private void checkMinZ(Atom atom, int[] minZ)
public float getGroupParameter(int tok)
tok
- public int getAtomIndex(java.lang.String name, int offset)
name
- offset
- public BS getBSSideChain()