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, seqcode, shapeVisibilityFlags
Constructor and Description |
---|
Monomer() |
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,
BS 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,
JmolList<java.lang.Integer> vReturn) |
private boolean |
getCrossLinkGroup(int i,
JmolList<java.lang.Integer> vReturn,
Group group) |
boolean |
getCrossLinkLead(JmolList<java.lang.Integer> vReturn) |
Group[] |
getGroups() |
protected java.lang.Object |
getHelixData2(int tokType,
char qType,
int mStep) |
(package private) Atom |
getInitiatorAtom() |
Atom |
getLeadAtom() |
int |
getMonomerIndex() |
(package private) void |
getMonomerSequenceAtoms(BS bsInclude,
BS bsResult) |
java.util.Map<java.lang.String,java.lang.Object> |
getMyInfo() |
ProteinStructure |
getProteinStructure() |
EnumStructure |
getProteinStructureType() |
(package private) P3 |
getQuaternionFrameCenter(char qtype) |
int |
getSelectedMonomerCount() |
int |
getSelectedMonomerIndex() |
protected Atom |
getSpecialAtom(byte[] interestingIDs,
byte specialAtomID) |
protected P3 |
getSpecialAtomPoint(byte[] interestingIDs,
byte specialAtomID) |
java.lang.String |
getStructureId() |
(package private) Atom |
getTerminatorAtom() |
java.lang.String |
getUniqueID() |
Atom |
getWingAtom() |
protected static boolean |
have(byte[] offsets,
byte n) |
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) |
protected Monomer |
set2(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] interestingAtomOffsets) |
(package private) void |
setBioPolymer(BioPolymer polymer,
int index) |
void |
setStrucNo(int id) |
(package private) void |
setStructure(ProteinStructure proteinstructure) |
(package private) void |
updateOffsetsForAlternativeLocations(Atom[] atoms,
BS bsSelected) |
addAtoms, fixIndices, getCarbonylOxygenAtom, getChainID, getGroup1, getGroup3, getGroup3For, getGroupID, getGroupIdFor, getGroupIndex, getGroupInfo, getGroupParameter, getHelixData, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, getStructure, haveSequenceNumber, isAdded, isAtomHidden, isCarbohydrate, isCursorOnTopOf, isDna, isNucleic, isProtein, isPurine, isPyrimidine, isRna, isSelected, isWithinStructure, lookupGroupID, scaleToScreen, selectAtoms, setGroup, setGroupIndex, setGroupParameter, setModelSet, setProteinStructureType, setShapeVisibility, toString
BioPolymer bioPolymer
protected byte[] offsets
int monomerIndex
protected static boolean have(byte[] offsets, byte n)
protected Monomer set2(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)
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 setStrucNo(int id)
setStrucNo
in class Group
protected final Atom getAtomFromOffsetIndex(int offsetIndex)
protected final Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)
protected final P3 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 java.util.Map<java.lang.String,java.lang.Object> getMyInfo()
public java.lang.String getStructureId()
getStructureId
in class Group
void getConformation(Atom[] atoms, BS bsConformation, int conformationIndex)
atoms
- bsConformation
- conformationIndex
- will be >= 0final void updateOffsetsForAlternativeLocations(Atom[] atoms, BS bsSelected)
protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)
P3 getQuaternionFrameCenter(char qtype)
qtype
- protected java.lang.Object getHelixData2(int tokType, char qType, int mStep)
public java.lang.String getUniqueID()
public boolean isCrossLinked(Group g)
isCrossLinked
in class Group
public boolean getCrossLinkLead(JmolList<java.lang.Integer> vReturn)
getCrossLinkLead
in class Group
protected boolean getCrossLink(int i, JmolList<java.lang.Integer> vReturn)
private boolean getCrossLinkGroup(int i, JmolList<java.lang.Integer> vReturn, Group group)
public boolean isConnectedPrevious()
isConnectedPrevious
in class Group