Package org.jmol.modelsetbio
Class NucleicMonomer
- java.lang.Object
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- org.jmol.modelset.Group
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- org.jmol.modelsetbio.Monomer
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- org.jmol.modelsetbio.PhosphorusMonomer
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- org.jmol.modelsetbio.NucleicMonomer
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- All Implemented Interfaces:
Structure
public class NucleicMonomer extends PhosphorusMonomer
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Field Summary
Fields Modifier and Type Field 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
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Fields inherited from class org.jmol.modelsetbio.PhosphorusMonomer
P
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Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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Fields inherited from class org.jmol.modelset.Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList
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Constructor Summary
Constructors Modifier Constructor Description private
NucleicMonomer()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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 definitionboolean
isGuanine()
boolean
isNucleicMonomer()
boolean
isPurine()
group ID-based definitionboolean
isPyrimidine()
group ID-based definitionboolean
isRna()
group ID-based definitionboolean
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)
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Methods inherited from class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionP, getStructure, isCA2, isNucleic, validateAndAllocateP
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Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, 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, updateOffsetsForAlternativeLocations
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Methods inherited from class org.jmol.modelset.Group
addAtoms, 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, toString
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Field Detail
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C6
static final byte C6
- See Also:
- Constant Field Values
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O2Pr
private static final byte O2Pr
- See Also:
- Constant Field Values
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C5
private static final byte C5
- See Also:
- Constant Field Values
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N1
private static final byte N1
- See Also:
- Constant Field Values
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C2
private static final byte C2
- See Also:
- Constant Field Values
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N3
private static final byte N3
- See Also:
- Constant Field Values
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C4
private static final byte C4
- See Also:
- Constant Field Values
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O2
private static final byte O2
- See Also:
- Constant Field Values
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N7
private static final byte N7
- See Also:
- Constant Field Values
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C8
private static final byte C8
- See Also:
- Constant Field Values
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N9
private static final byte N9
- See Also:
- Constant Field Values
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O4
private static final byte O4
- See Also:
- Constant Field Values
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O6
private static final byte O6
- See Also:
- Constant Field Values
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N4
private static final byte N4
- See Also:
- Constant Field Values
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NP
private static final byte NP
- See Also:
- Constant Field Values
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N6
private static final byte N6
- See Also:
- Constant Field Values
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N2
private static final byte N2
- See Also:
- Constant Field Values
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H5T
private static final byte H5T
- See Also:
- Constant Field Values
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O5P
private static final byte O5P
- See Also:
- Constant Field Values
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H3T
private static final byte H3T
- See Also:
- Constant Field Values
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O3P
private static final byte O3P
- See Also:
- Constant Field Values
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C3P
private static final byte C3P
- See Also:
- Constant Field Values
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O1P
private static final byte O1P
- See Also:
- Constant Field Values
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O2P
private static final byte O2P
- See Also:
- Constant Field Values
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C1P
private static final byte C1P
- See Also:
- Constant Field Values
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C2P
private static final byte C2P
- See Also:
- Constant Field Values
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C4P
private static final byte C4P
- See Also:
- Constant Field Values
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O4P
private static final byte O4P
- See Also:
- Constant Field Values
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C5P
private static final byte C5P
- See Also:
- Constant Field Values
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interestingNucleicAtomIDs
static final byte[] interestingNucleicAtomIDs
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isPurine
private boolean isPurine
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isPyrimidine
boolean isPyrimidine
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hasRnaO2Prime
private boolean hasRnaO2Prime
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ring6OffsetIndexes
private static final byte[] ring6OffsetIndexes
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ring5OffsetIndexes
private static final byte[] ring5OffsetIndexes
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riboseOffsetIndexes
private static final byte[] riboseOffsetIndexes
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heavyAtomIndexes
private static final byte[] heavyAtomIndexes
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baseCenter
javajs.util.P3 baseCenter
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bps
private javajs.util.Lst<BasePair> bps
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dssrBox
public javajs.util.P3[] dssrBox
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dssrBoxHeight
public float dssrBoxHeight
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dssrFrame
public javajs.util.P3[] dssrFrame
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Method Detail
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validateAndAllocate
public static Monomer validateAndAllocate(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)
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set4
private NucleicMonomer set4(Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
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isNucleicMonomer
public boolean isNucleicMonomer()
- Overrides:
isNucleicMonomer
in classGroup
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isDna
public boolean isDna()
Description copied from class:Group
group ID-based definition- Overrides:
isDna
in classPhosphorusMonomer
- Returns:
- boolean
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isRna
public boolean isRna()
Description copied from class:Group
group ID-based definition- Overrides:
isRna
in classPhosphorusMonomer
- Returns:
- boolean
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isPurine
public boolean isPurine()
Description copied from class:Group
group ID-based definition- Overrides:
isPurine
in classPhosphorusMonomer
- Returns:
- boolean
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isPyrimidine
public boolean isPyrimidine()
Description copied from class:Group
group ID-based definition- Overrides:
isPyrimidine
in classPhosphorusMonomer
- Returns:
- boolean
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isGuanine
public boolean isGuanine()
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getProteinStructureType
public STR getProteinStructureType()
- Overrides:
getProteinStructureType
in classPhosphorusMonomer
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getP
Atom getP()
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getC1P
public Atom getC1P()
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getC2
Atom getC2()
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getC5
Atom getC5()
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getC6
Atom getC6()
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getC8
Atom getC8()
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getC4P
Atom getC4P()
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getN1
Atom getN1()
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getN3
public Atom getN3()
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getN2
Atom getN2()
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getN4
Atom getN4()
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getN6
Atom getN6()
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getO2
Atom getO2()
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getO4
Atom getO4()
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getO6
Atom getO6()
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getTerminatorAtom
Atom getTerminatorAtom()
- Overrides:
getTerminatorAtom
in classMonomer
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getBaseRing6Points
public void getBaseRing6Points(javajs.util.P3[] pts)
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getPoints
private void getPoints(byte[] a, javajs.util.P3[] pts)
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maybeGetBaseRing5Points
public boolean maybeGetBaseRing5Points(javajs.util.P3[] pts)
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getRiboseRing5Points
public void getRiboseRing5Points(javajs.util.P3[] pts)
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isConnectedAfter
boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
- Overrides:
isConnectedAfter
in classPhosphorusMonomer
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findNearestAtomIndex
public void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
Description copied from class:Monomer
Selects LeadAtom when this Monomer is clicked iff it is closer to the user.- Overrides:
findNearestAtomIndex
in classMonomer
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setRingsVisible
public void setRingsVisible(boolean isVisible)
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setRingsClickable
public void setRingsClickable()
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getN0
public Atom getN0()
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getHelixData
public java.lang.Object getHelixData(int tokType, char qType, int mStep)
- Overrides:
getHelixData
in classPhosphorusMonomer
- Returns:
- helix data of some sort
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getQuaternionFrameCenter
javajs.util.P3 getQuaternionFrameCenter(char qType)
- Overrides:
getQuaternionFrameCenter
in classPhosphorusMonomer
- Returns:
- center
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getQuaternion
public javajs.util.Quat getQuaternion(char qType)
- Overrides:
getQuaternion
in classPhosphorusMonomer
- Returns:
- quaternion
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isCrossLinked
public boolean isCrossLinked(Group g)
- Overrides:
isCrossLinked
in classMonomer
- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
- Overrides:
getCrossLinkVector
in classMonomer
- Returns:
- T/F
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getEdgePoints
public boolean getEdgePoints(javajs.util.P3[] pts)
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addBasePair
public void addBasePair(BasePair bp)
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setGroup1
public void setGroup1(char g)
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getBasePairs
public javajs.util.Lst<BasePair> getBasePairs()
- Returns:
- list of base pairs associated with this monomer, possibly more than one if noncanonical
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getGroup1b
protected char getGroup1b()
- Overrides:
getGroup1b
in classMonomer
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getDSSRFrame
public javajs.util.P3[] getDSSRFrame(Viewer vwr)
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