org.jmol.modelset
public class Group extends Object
| Field Summary | |
|---|---|
| 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 | |
|---|---|
| Group(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex) | |
| Method Summary | |
|---|---|
| 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