public class NucleicMonomer extends PhosphorusMonomer
Modifier and Type | Field and Description |
---|---|
(package private) javajs.util.P3 |
baseCenter |
private javajs.util.Lst<BasePair> |
bps |
private static byte |
C1P |
private static byte |
C2 |
private static byte |
C2P |
private static byte |
C3P |
private static byte |
C4 |
private static byte |
C4P |
private static byte |
C5 |
private static byte |
C5P |
(package private) static byte |
C6 |
private static byte |
C8 |
private static byte |
H3T |
private static byte |
H5T |
private boolean |
hasRnaO2Prime |
private static byte[] |
heavyAtomIndexes |
(package private) static byte[] |
interestingNucleicAtomIDs |
private static byte |
N1 |
private static byte |
N2 |
private static byte |
N3 |
private static byte |
N4 |
private static byte |
N6 |
private static byte |
N7 |
private static byte |
N9 |
private static byte |
NP |
private static byte |
O1P |
private static byte |
O2 |
private static byte |
O2P |
private static byte |
O2Pr |
private static byte |
O3P |
private static byte |
O4 |
private static byte |
O4P |
private static byte |
O5P |
private static byte |
O6 |
private static byte[] |
riboseOffsetIndexes |
private static byte[] |
ring5OffsetIndexes |
private static byte[] |
ring6OffsetIndexes |
isPurine, isPyrimidine, P
bioPolymer, monomerIndex, offsets
chain, firstAtomIndex, group1, group3Names, groupID, groupIndex, htGroup, lastAtomIndex, leadAtomIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
Modifier | Constructor and Description |
---|---|
private |
NucleicMonomer() |
Modifier and Type | Method and Description |
---|---|
void |
addBasePair(BasePair bp) |
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.
|
javajs.util.Lst<BasePair> |
getBasePairs() |
void |
getBaseRing6Points(javajs.util.P3[] pts) |
(package private) Atom |
getC1P() |
(package private) Atom |
getC2() |
(package private) Atom |
getC4P() |
boolean |
getCrossLinkLead(javajs.util.Lst<java.lang.Integer> vReturn) |
boolean |
getEdgePoints(javajs.util.P3[] pts) |
protected char |
getGroup1b() |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
(package private) Atom |
getN0() |
(package private) Atom |
getN1() |
(package private) Atom |
getN2() |
(package private) Atom |
getN3() |
(package private) Atom |
getN4() |
(package private) Atom |
getN6() |
(package private) Atom |
getO2() |
(package private) Atom |
getO4() |
(package private) Atom |
getO6() |
private void |
getPoints(byte[] a,
javajs.util.P3[] pts) |
STR |
getProteinStructureType() |
javajs.util.Quat |
getQuaternion(char qType) |
(package private) javajs.util.P3 |
getQuaternionFrameCenter(char qType) |
void |
getRiboseRing5Points(javajs.util.P3[] pts) |
(package private) Atom |
getTerminatorAtom() |
(package private) boolean |
isConnectedAfter(Monomer possiblyPreviousMonomer) |
boolean |
isCrossLinked(Group g) |
boolean |
isDna() |
boolean |
isGuanine() |
boolean |
isNucleicMonomer() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
isRna() |
boolean |
maybeGetBaseRing5Points(javajs.util.P3[] pts) |
private NucleicMonomer |
set4(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
byte[] offsets) |
void |
setGroup1(char g) |
void |
setRingsClickable() |
void |
setRingsVisible(boolean isVisible) |
static Monomer |
validateAndAllocate(Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int lastAtomIndex,
int[] specialAtomIndexes) |
getP, getQuaternionP, getStructure, isCA2, isNucleic, isPhosphorusMonomer, set3, validateAndAllocateP
calcBioParameters, checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getConformation, getCrossLinkGroup, getGroup1, getGroupParameter, getGroups, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, have, haveParameters, isConnectedPrevious, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setStrucNo, updateOffsetsForAlternativeLocations
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getModelIndex, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSelectedGroupIndex, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isProtein, isSelected, isWithinStructure, scaleToScreen, selectAtoms, setGroup, setProteinStructureType, setShapeVisibility, toString
static final byte C6
private static final byte O2Pr
private static final byte C5
private static final byte N1
private static final byte C2
private static final byte N3
private static final byte C4
private static final byte O2
private static final byte N7
private static final byte C8
private static final byte N9
private static final byte O4
private static final byte O6
private static final byte N4
private static final byte NP
private static final byte N6
private static final byte N2
private static final byte H5T
private static final byte O5P
private static final byte H3T
private static final byte O3P
private static final byte C3P
private static final byte O1P
private static final byte O2P
private static final byte C1P
private static final byte C2P
private static final byte C4P
private static final byte O4P
private static final byte C5P
static final byte[] interestingNucleicAtomIDs
private boolean hasRnaO2Prime
private static final byte[] ring6OffsetIndexes
private static final byte[] ring5OffsetIndexes
private static final byte[] riboseOffsetIndexes
private static final byte[] heavyAtomIndexes
javajs.util.P3 baseCenter
private javajs.util.Lst<BasePair> bps
public static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)
private NucleicMonomer set4(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
public boolean isNucleicMonomer()
public boolean isDna()
isDna
in class PhosphorusMonomer
public boolean isRna()
isRna
in class PhosphorusMonomer
public boolean isPurine()
isPurine
in class PhosphorusMonomer
public boolean isPyrimidine()
isPyrimidine
in class PhosphorusMonomer
public boolean isGuanine()
public STR getProteinStructureType()
getProteinStructureType
in class PhosphorusMonomer
Atom getC1P()
Atom getC2()
Atom getC4P()
Atom getN1()
Atom getN3()
Atom getN2()
Atom getN4()
Atom getN6()
Atom getO2()
Atom getO4()
Atom getO6()
Atom getTerminatorAtom()
getTerminatorAtom
in class Monomer
public void getBaseRing6Points(javajs.util.P3[] pts)
private void getPoints(byte[] a, javajs.util.P3[] pts)
public boolean maybeGetBaseRing5Points(javajs.util.P3[] pts)
public void getRiboseRing5Points(javajs.util.P3[] pts)
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
isConnectedAfter
in class PhosphorusMonomer
public void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Monomer
findNearestAtomIndex
in class Monomer
public void setRingsVisible(boolean isVisible)
public void setRingsClickable()
Atom getN0()
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
getHelixData
in class PhosphorusMonomer
javajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter
in class PhosphorusMonomer
public javajs.util.Quat getQuaternion(char qType)
getQuaternion
in class PhosphorusMonomer
public boolean isCrossLinked(Group g)
isCrossLinked
in class Monomer
public boolean getCrossLinkLead(javajs.util.Lst<java.lang.Integer> vReturn)
getCrossLinkLead
in class Monomer
public boolean getEdgePoints(javajs.util.P3[] pts)
public void addBasePair(BasePair bp)
public void setGroup1(char g)
public javajs.util.Lst<BasePair> getBasePairs()
protected char getGroup1b()
getGroup1b
in class Monomer