org.jmol.modelsetbio
public abstract class Monomer extends Group
Modifier and Type | Field and Description |
---|---|
(package private) BioPolymer |
bioPolymer |
(package private) int |
monomerIndex |
protected byte[] |
offsets |
chain, firstAtomIndex, groupID, groupIndex, isProtein, lastAtomIndex, leadAtomIndex, shapeVisibilityFlags
Modifier | Constructor and Description |
---|---|
protected |
Monomer(Chain chain,
String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] interestingAtomOffsets) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
calcBioParameters() |
protected static boolean |
checkOptional(byte[] offsets,
byte atom,
int firstAtomIndex,
int index) |
(package private) 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 |
getBioPolymerIndexInModel() |
int |
getBioPolymerLength() |
(package private) void |
getConformation(Atom[] atoms,
BitSet bsConformation,
int conformationIndex)
clear out bits that are not associated with the nth conformation
counting for each residue from the beginning of the file listing
|
protected boolean |
getCrossLink(int i,
List<Integer> vReturn) |
private boolean |
getCrossLink(int i,
List<Integer> vReturn,
Group group) |
boolean |
getCrossLinkLeadAtomIndexes(List<Integer> vReturn) |
protected Object |
getHelixData2(int tokType,
char qType,
int mStep) |
(package private) Atom |
getInitiatorAtom() |
Atom |
getLeadAtom() |
int |
getMonomerIndex() |
(package private) void |
getMonomerSequenceAtoms(BitSet bsInclude,
BitSet bsResult) |
Map<String,Object> |
getMyInfo() |
ProteinStructure |
getProteinStructure() |
EnumStructure |
getProteinStructureType() |
(package private) Point3f |
getQuaternionFrameCenter(char qtype) |
int |
getSelectedMonomerCount() |
int |
getSelectedMonomerIndex() |
protected Atom |
getSpecialAtom(byte[] interestingIDs,
byte specialAtomID) |
protected Point3f |
getSpecialAtomPoint(byte[] interestingIDs,
byte specialAtomID) |
String |
getStructureId() |
(package private) Atom |
getTerminatorAtom() |
String |
getUniqueID() |
Atom |
getWingAtom() |
boolean |
haveParameters() |
(package private) abstract boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isConnectedPrevious() |
boolean |
isCrossLinked(Group g) |
boolean |
isHelix() |
boolean |
isLeadAtom(int atomIndex) |
boolean |
isSheet() |
protected static byte[] |
scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs) |
(package private) void |
setBioPolymer(BioPolymer polymer,
int index) |
void |
setProteinStructureId(int id) |
(package private) void |
setStructure(ProteinStructure proteinstructure) |
(package private) void |
updateOffsetsForAlternativeLocations(Atom[] atoms,
BitSet bsSelected) |
addAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3, getGroupID, getGroupID, getGroupIndex, getGroupInfo, getGroupParameter, getHelixData, getInsertionCode, getInsertionCode, getInsertionCodeValue, getLeadAtom, getMinZ, getModel, getModelIndex, getModelSet, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcode, getSeqcode, getSeqcodeString, getSeqcodeString, getSeqNumber, getSequenceNumber, getStrucNo, getStructure, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isProtein, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, toString
BioPolymer bioPolymer
protected final byte[] offsets
int monomerIndex
void setBioPolymer(BioPolymer polymer, int index)
public int getSelectedMonomerCount()
getSelectedMonomerCount
in class Group
public int getSelectedMonomerIndex()
getSelectedMonomerIndex
in class Group
public BioPolymer getBioPolymer()
public int getBioPolymerLength()
getBioPolymerLength
in class Group
public int getMonomerIndex()
getMonomerIndex
in class Group
public int getBioPolymerIndexInModel()
getBioPolymerIndexInModel
in class Group
protected static byte[] scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)
void setStructure(ProteinStructure proteinstructure)
proteinstructure
- public ProteinStructure getProteinStructure()
public EnumStructure getProteinStructureType()
getProteinStructureType
in class Group
public boolean isHelix()
public boolean isSheet()
public void setProteinStructureId(int id)
setProteinStructureId
in class Group
protected final Atom getAtomFromOffsetIndex(int offsetIndex)
protected final Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)
protected final Point3f getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)
public boolean isLeadAtom(int atomIndex)
isLeadAtom
in class Group
public final Atom getLeadAtom()
getLeadAtom
in class Group
public final Atom getWingAtom()
Atom getInitiatorAtom()
Atom getTerminatorAtom()
abstract boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
x
- y
- closest
- madBegin
- madEnd
- protected boolean calcBioParameters()
calcBioParameters
in class Group
public boolean haveParameters()
haveParameters
in class Group
public String getStructureId()
getStructureId
in class Group
void getConformation(Atom[] atoms, BitSet bsConformation, int conformationIndex)
atoms
- bsConformation
- conformationIndex
- will be >= 0final void updateOffsetsForAlternativeLocations(Atom[] atoms, BitSet bsSelected)
protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)
Point3f getQuaternionFrameCenter(char qtype)
qtype
- protected Object getHelixData2(int tokType, char qType, int mStep)
public String getUniqueID()
public boolean isCrossLinked(Group g)
isCrossLinked
in class Group
public boolean getCrossLinkLeadAtomIndexes(List<Integer> vReturn)
getCrossLinkLeadAtomIndexes
in class Group
public boolean isConnectedPrevious()
isConnectedPrevious
in class Group