Modifier and Type | Field and Description |
---|---|
private BS |
bsAdded |
Chain |
chain |
int |
firstAtomIndex |
private static short |
group3NameCount |
private static String[] |
group3Names |
protected short |
groupID |
protected int |
groupIndex |
private static Map<String,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 |
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() |
Modifier and Type | Method and Description |
---|---|
void |
addAtoms(int atomIndex) |
private static short |
addGroup3Name(String group3) |
protected boolean |
calcBioParameters() |
private void |
checkMinZ(Atom atom,
int[] minZ) |
void |
fixIndices(int atomsDeleted,
BS bsDeleted) |
int |
getBioPolymerIndexInModel() |
int |
getBioPolymerLength() |
Atom |
getCarbonylOxygenAtom() |
int |
getChainID() |
boolean |
getCrossLinkLead(javajs.util.List<Integer> vReturn) |
char |
getGroup1() |
String |
getGroup3() |
static String |
getGroup3For(short groupID) |
short |
getGroupID() |
private static short |
getGroupIdFor(String group3) |
int |
getGroupIndex() |
Map<String,Object> |
getGroupInfo(int igroup) |
float |
getGroupParameter(int tok) |
Group[] |
getGroups() |
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() |
EnumStructure |
getProteinStructureSubType() |
String |
getProteinStructureTag() |
EnumStructure |
getProteinStructureType() |
Quaternion |
getQuaternion(char qType) |
Quaternion |
getQuaternionFrame(Atom[] atoms) |
int |
getResno() |
int |
getSelectedGroupIndex() |
int |
getSelectedMonomerCount() |
int |
getSelectedMonomerIndex() |
static int |
getSeqcodeFor(int seqNo,
char insCode) |
String |
getSeqcodeString() |
static String |
getSeqcodeStringFor(int seqcode) |
static int |
getSeqNumberFor(int seqcode) |
int |
getStrucNo() |
Object |
getStructure() |
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 |
isHetero() |
boolean |
isLeadAtom(int atomIndex) |
boolean |
isNucleic() |
boolean |
isProtein() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
boolean |
isSelected(BS bs) |
boolean |
isWithinStructure(EnumStructure type) |
static short |
lookupGroupID(String group3) |
protected float |
scaleToScreen(int Z,
int mar) |
int |
selectAtoms(BS bs) |
Group |
setGroup(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex) |
void |
setGroupIndex(int groupIndex) |
void |
setGroupParameter(int tok,
float f) |
void |
setModelSet(ModelSet modelSet) |
int |
setProteinStructureType(EnumStructure type,
int monomerIndexCurrent) |
void |
setShapeVisibility(int visFlag,
boolean isVisible) |
void |
setStrucNo(int i) |
String |
toString() |
protected int groupIndex
public Chain chain
public int firstAtomIndex
public int leadAtomIndex
public int lastAtomIndex
public int seqcode
protected short groupID
protected boolean isProtein
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 float phi
private float psi
private float omega
private float straightness
private float mu
private float theta
private static String[] group3Names
private static short group3NameCount
private BS bsAdded
public int getGroupIndex()
public void setGroupIndex(int groupIndex)
public Group setGroup(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex)
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)
public final String getGroup3()
public static String getGroup3For(short groupID)
public final char getGroup1()
public final short getGroupID()
public final int getChainID()
public int getBioPolymerLength()
public int getMonomerIndex()
public Group[] getGroups()
public 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()
private static short addGroup3Name(String group3)
private static short getGroupIdFor(String group3)
public static short lookupGroupID(String group3)
public final int getResno()
public static final int getSeqNumberFor(int seqcode)
public static final boolean haveSequenceNumber(int seqcode)
public final String getSeqcodeString()
public static int getSeqcodeFor(int seqNo, char insCode)
public static 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()
protected float 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 setStrucNo(int i)
i
- public Object getHelixData(int tokType, char qType, int mStep)
tokType
- qType
- mStep
- public boolean isWithinStructure(EnumStructure type)
type
- public String getProteinStructureTag()
public String getStructureId()
public int getBioPolymerIndexInModel()
public boolean isCrossLinked(Group g)
g
- public boolean getCrossLinkLead(javajs.util.List<Integer> vReturn)
vReturn
- public boolean isConnectedPrevious()
public Atom getNitrogenAtom()
public Atom getCarbonylOxygenAtom()
public void fixIndices(int atomsDeleted, BS bsDeleted)
public void getMinZ(Atom[] atoms, int[] minZ)
private void checkMinZ(Atom atom, int[] minZ)