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 |
javajs.util.P3[] |
dssrBox |
float |
dssrBoxHeight |
javajs.util.P3[] |
dssrFrame |
private static byte |
H3T |
private static byte |
H5T |
private boolean |
hasRnaO2Prime |
private static byte[] |
heavyAtomIndexes |
(package private) static byte[] |
interestingNucleicAtomIDs |
private boolean |
isPurine |
(package private) boolean |
isPyrimidine |
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 |
PbackboneBlockVis, bioPolymer, monomerIndex, offsetschain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, 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) |
Atom |
getC1P() |
(package private) Atom |
getC2() |
(package private) Atom |
getC4P() |
(package private) Atom |
getC5() |
(package private) Atom |
getC6() |
(package private) Atom |
getC8() |
boolean |
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond) |
javajs.util.P3[] |
getDSSRFrame(Viewer vwr) |
boolean |
getEdgePoints(javajs.util.P3[] pts) |
protected char |
getGroup1b() |
java.lang.Object |
getHelixData(int tokType,
char qType,
int mStep) |
Atom |
getN0() |
(package private) Atom |
getN1() |
(package private) Atom |
getN2() |
Atom |
getN3() |
(package private) Atom |
getN4() |
(package private) Atom |
getN6() |
(package private) Atom |
getO2() |
(package private) Atom |
getO4() |
(package private) Atom |
getO6() |
(package private) Atom |
getP() |
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()
group ID-based definition
|
boolean |
isGuanine() |
boolean |
isNucleicMonomer() |
boolean |
isPurine()
group ID-based definition
|
boolean |
isPyrimidine()
group ID-based definition
|
boolean |
isRna()
group ID-based definition
|
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) |
getQuaternionP, getStructure, isCA2, isNucleic, validateAndAllocatePcheckOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getGroup1, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, have, isConnectedPrevious, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setBioPolymer, setGroupID, setGroupParameter, setLeadAtomIndex, setStrucNo, updateOffsetsForAlternativeLocationsaddAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureSubType, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, getStrucNo, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDnaByID, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility, toStringstatic 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 isPurine
boolean isPyrimidine
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 javajs.util.P3[] dssrBox
public float dssrBoxHeight
public javajs.util.P3[] dssrFrame
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()
isNucleicMonomer in class Grouppublic boolean isDna()
GroupisDna in class PhosphorusMonomerpublic boolean isRna()
GroupisRna in class PhosphorusMonomerpublic boolean isPurine()
GroupisPurine in class PhosphorusMonomerpublic boolean isPyrimidine()
GroupisPyrimidine in class PhosphorusMonomerpublic boolean isGuanine()
public STR getProteinStructureType()
getProteinStructureType in class PhosphorusMonomerAtom getP()
public Atom getC1P()
Atom getC2()
Atom getC5()
Atom getC6()
Atom getC8()
Atom getC4P()
Atom getN1()
public Atom getN3()
Atom getN2()
Atom getN4()
Atom getN6()
Atom getO2()
Atom getO4()
Atom getO6()
Atom getTerminatorAtom()
getTerminatorAtom in class Monomerpublic 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 PhosphorusMonomerpublic void findNearestAtomIndex(int x,
int y,
Atom[] closest,
short madBegin,
short madEnd)
MonomerfindNearestAtomIndex in class Monomerpublic void setRingsVisible(boolean isVisible)
public void setRingsClickable()
public Atom getN0()
public java.lang.Object getHelixData(int tokType,
char qType,
int mStep)
getHelixData in class PhosphorusMonomerjavajs.util.P3 getQuaternionFrameCenter(char qType)
getQuaternionFrameCenter in class PhosphorusMonomerpublic javajs.util.Quat getQuaternion(char qType)
getQuaternion in class PhosphorusMonomerpublic boolean isCrossLinked(Group g)
isCrossLinked in class Monomerpublic boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond)
getCrossLinkVector in class Monomerpublic 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 Monomerpublic javajs.util.P3[] getDSSRFrame(Viewer vwr)