public abstract class Monomer extends Group
| Modifier and Type | Field and Description |
|---|---|
boolean |
backboneBlockVis |
BioPolymer |
bioPolymer |
(package private) int |
monomerIndex |
private float |
mu |
protected byte[] |
offsets |
private float |
omega |
private float |
phi |
private float |
psi |
private float |
straightness |
private float |
theta |
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList| Constructor and Description |
|---|
Monomer() |
| Modifier and Type | Method and Description |
|---|---|
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) |
int |
getAtomIndex(java.lang.String name,
int offset) |
int |
getBioPolymerIndexInModel() |
int |
getBioPolymerLength() |
protected boolean |
getCrossLinkGroup(int i,
javajs.util.Lst<java.lang.Integer> vReturn,
Group group,
boolean crosslinkCovalent,
boolean crosslinkHBond,
boolean isNotCheck) |
boolean |
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond) |
char |
getGroup1() |
protected char |
getGroup1b() |
float |
getGroupParameter(int tok)
Monomers only
|
protected java.lang.Object |
getHelixData2(int tokType,
char qType,
int mStep) |
(package private) Atom |
getInitiatorAtom() |
Atom |
getLeadAtom() |
int |
getMonomerIndex() |
(package private) void |
getMonomerSequenceAtoms(javajs.util.BS bsInclude,
javajs.util.BS bsResult) |
java.util.Map<java.lang.String,java.lang.Object> |
getMyInfo(javajs.util.P3 ptTemp) |
STR |
getProteinStructureType() |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qtype) |
int |
getSelectedMonomerCount() |
int |
getSelectedMonomerIndex() |
protected Atom |
getSpecialAtom(byte[] interestingIDs,
byte specialAtomID) |
protected javajs.util.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) |
(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 |
setGroupID(java.lang.String group3) |
(package private) void |
setGroupParameter(int tok,
float f) |
protected void |
setLeadAtomIndex() |
void |
setStrucNo(int id) |
(package private) void |
updateOffsetsForAlternativeLocations(Atom[] atoms,
javajs.util.BS bsSelected) |
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getHelixData, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternion, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, getStructure, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isProtein, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toStringpublic BioPolymer bioPolymer
protected byte[] offsets
int monomerIndex
private float phi
private float psi
private float omega
private float straightness
private float mu
private float theta
public boolean backboneBlockVis
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)
protected void setLeadAtomIndex()
void setBioPolymer(BioPolymer polymer, int index)
public int getSelectedMonomerCount()
getSelectedMonomerCount in class Grouppublic int getSelectedMonomerIndex()
getSelectedMonomerIndex in class Grouppublic int getBioPolymerLength()
getBioPolymerLength in class Grouppublic int getMonomerIndex()
getMonomerIndex in class Grouppublic int getAtomIndex(java.lang.String name,
int offset)
getAtomIndex in class Grouppublic int getBioPolymerIndexInModel()
getBioPolymerIndexInModel in class Groupprotected static byte[] scanForOffsets(int firstAtomIndex,
int[] specialAtomIndexes,
byte[] interestingAtomIDs)
public STR getProteinStructureType()
getProteinStructureType in class Grouppublic boolean isHelix()
public boolean isSheet()
public void setStrucNo(int id)
setStrucNo in class Groupprotected final Atom getAtomFromOffsetIndex(int offsetIndex)
protected final Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)
protected final javajs.util.P3 getSpecialAtomPoint(byte[] interestingIDs,
byte specialAtomID)
public boolean isLeadAtom(int atomIndex)
isLeadAtom in class Grouppublic final Atom getLeadAtom()
getLeadAtom in class Grouppublic 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 - public java.util.Map<java.lang.String,java.lang.Object> getMyInfo(javajs.util.P3 ptTemp)
public java.lang.String getStructureId()
getStructureId in class Groupfinal void updateOffsetsForAlternativeLocations(Atom[] atoms, javajs.util.BS bsSelected)
final void getMonomerSequenceAtoms(javajs.util.BS bsInclude,
javajs.util.BS bsResult)
protected static final boolean checkOptional(byte[] offsets,
byte atom,
int firstAtomIndex,
int index)
javajs.util.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 Grouppublic boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond)
getCrossLinkVector in class Groupprotected boolean getCrossLinkGroup(int i,
javajs.util.Lst<java.lang.Integer> vReturn,
Group group,
boolean crosslinkCovalent,
boolean crosslinkHBond,
boolean isNotCheck)
i - vReturn - null implies just checking for a specific groupgroup - specific group to check or null to indicate just PREVIOUS group (carbohydrates)crosslinkCovalent - (S-S)crosslinkHBond - (hbond)isNotCheck - TODOpublic boolean isConnectedPrevious()
isConnectedPrevious in class Groupvoid setGroupParameter(int tok,
float f)
public float getGroupParameter(int tok)
GroupgetGroupParameter in class Groupprotected char getGroup1b()
public void setGroupID(java.lang.String group3)
setGroupID in class Group