org.jmol.modelsetbio
public abstract class Monomer extends Group
Field Summary | |
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BioPolymer | bioPolymer |
protected int | monomerIndex |
protected byte[] | offsets |
Constructor Summary | |
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protected | Monomer(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets) |
Method Summary | |
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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.
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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