org.jmol.modelset
public class Group extends Object
Field Summary | |
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protected Chain | chain |
protected int | firstAtomIndex |
static short | group3NameCount |
static String[] | group3Names |
protected short | groupID |
static Hashtable | htGroup |
protected boolean | isAmino |
static int | INSERTION_CODE_MASK |
protected int | lastAtomIndex |
int | minZ |
protected float | omega |
protected float | phi |
protected float | psi |
int | selectedIndex |
int | seqcode |
int | shapeVisibilityFlags |
protected float | straightness |
static int | SEQUENCE_NUMBER_FLAG |
static int | SEQUENCE_NUMBER_SHIFT |
Constructor Summary | |
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Group(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex) |
Method Summary | |
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static short | addGroup3Name(String group3) |
int | getBioPolymerIndex() |
int | getBioPolymerLength() |
char | getChainID() |
int | getFirstAtomIndex() |
char | getGroup1() |
String | getGroup3() |
static String | getGroup3(short groupID) |
short | getGroupID() |
static short | getGroupID(String group3) |
char | getInsertionCode() |
static char | getInsertionCode(int seqcode) |
static int | getInsertionCodeValue(int seqcode) |
int | getLastAtomIndex() |
Atom | getLeadAtom(Atom atom) |
Atom | getLeadAtom() |
int | getMinZ() |
Model | getModel()
BE CAREFUL: FAILURE TO NULL REFERENCES TO model WILL PREVENT FINALIZATION
AND CREATE A MEMORY LEAK.
|
int | getModelIndex() |
Hashtable | getMyInfo() |
float | getOmega() |
float | getPhi() |
int | getProteinStructureID() |
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) |
String | getSeqcodeString() |
static String | getSeqcodeString(int seqcode) |
int | getSeqNumber() |
static int | getSequenceNumber(int seqcode) |
float | getStraightness() |
Object | getStructure() |
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() |
boolean | isGroup3(String group3) |
boolean | isHetero() |
boolean | isNucleic() |
boolean | isProtein() |
boolean | isPurine() |
boolean | isPyrimidine() |
boolean | isRna() |
boolean | isSelected(BitSet bs) |
static short | lookupGroupID(String group3) |
protected int | scaleToScreen(int Z, int mar) |
void | selectAtoms(BitSet bs) |
void | setMinZ(int z) |
void | setModelSet(ModelSet modelSet) |
void | setOmega(float omega) |
void | setPhi(float phi) |
int | setProteinStructureType(byte iType, int monomerIndexCurrent) |
void | setPsi(float psi) |
void | setShapeVisibility(int visFlag, boolean isVisible) |
void | setStraightness(float straightness) |
String | toString() |
Returns: associated Model