org.jmol.modelsetbio
public abstract class Monomer extends Group
| Field Summary | |
|---|---|
| BioPolymer | bioPolymer |
| protected int | monomerIndex |
| protected byte[] | offsets |
| Constructor Summary | |
|---|---|
| protected | Monomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets) |
| Method Summary | |
|---|---|
| protected static boolean | checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index) |
| void | findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Selects LeadAtom when this Monomer is clicked iff it is
closer to the user.
|
| protected Atom | getAtomFromOffsetIndex(int offsetIndex) |
| BioPolymer | getBioPolymer() |
| int | getBioPolymerIndex() |
| int | getBioPolymerLength() |
| Atom | getInitiatorAtom() |
| Atom | getLeadAtom() |
| int | getLeadAtomIndex() |
| Point3f | getLeadAtomPoint() |
| void | getMonomerSequenceAtoms(BitSet bsInclude, BitSet bsResult) |
| Hashtable | getMyInfo() |
| Point3f | getPointAtomPoint() |
| ProteinStructure | getProteinStructure() |
| byte | getProteinStructureType() |
| Point3f | getQuaternionFrameCenter(char qtype) |
| int | getSelectedMonomerCount() |
| int | getSelectedMonomerIndex() |
| protected Atom | getSpecialAtom(byte[] interestingIDs, byte specialAtomID) |
| protected Point3f | getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID) |
| static String | getStructureTypeName(byte type) |
| Atom | getTerminatorAtom() |
| Atom | getWingAtom() |
| Point3f | getWingAtomPoint() |
| abstract boolean | isConnectedAfter(Monomer possiblyPreviousMonomer) |
| boolean | isDna() |
| boolean | isHelix() |
| boolean | isNucleic() |
| boolean | isProtein() |
| boolean | isRna() |
| boolean | isSheet() |
| void | resetHydrogenPoint() |
| protected static byte[] | scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs) |
| void | setBioPolymer(BioPolymer polymer, int index) |
| void | setStructure(ProteinStructure proteinstructure) |
| void | updateOffsetsForAlternativeLocations(BitSet bsSelected, int nAltLocInModel) |
Parameters: x y closest madBegin madEnd