Package org.jmol.modelsetbio
Class NucleicMonomer
java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.PhosphorusMonomer
org.jmol.modelsetbio.NucleicMonomer
- All Implemented Interfaces:
Structure
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Field Summary
FieldsModifier and TypeFieldDescription(package private) javajs.util.P3
private javajs.util.Lst<BasePair>
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
(package private) static final byte
private static final byte
javajs.util.P3[]
float
javajs.util.P3[]
private static final byte
private static final byte
private boolean
private static final byte[]
(package private) static final byte[]
private boolean
(package private) boolean
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte
private static final byte[]
private static final byte[]
private static final byte[]
Fields inherited from class org.jmol.modelsetbio.PhosphorusMonomer
P
Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, monomerIndex, offsets
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
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>
void
getBaseRing6Points
(javajs.util.P3[] pts) 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<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) javajs.util.P3[]
getDSSRFrame
(Viewer vwr) boolean
getEdgePoints
(javajs.util.P3[] pts) protected char
getHelixData
(int tokType, char qType, int mStep) getN0()
(package private) Atom
getN1()
(package private) Atom
getN2()
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) javajs.util.Quat
getQuaternion
(char qType) (package private) javajs.util.P3
getQuaternionFrameCenter
(char qType) void
getRiboseRing5Points
(javajs.util.P3[] pts) (package private) Atom
(package private) boolean
isConnectedAfter
(Monomer possiblyPreviousMonomer) boolean
boolean
isDna()
group ID-based definitionboolean
boolean
boolean
isPurine()
group ID-based definitionboolean
group ID-based definitionboolean
isRna()
group ID-based definitionboolean
maybeGetBaseRing5Points
(javajs.util.P3[] pts) private NucleicMonomer
set4
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets) void
setGroup1
(char g) void
void
setRingsVisible
(boolean isVisible) static Monomer
validateAndAllocate
(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes) Methods inherited from class org.jmol.modelsetbio.PhosphorusMonomer
getQuaternionP, getStructure, isCA2, isNucleic, validateAndAllocateP
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, toString, updateOffsetsForAlternativeLocations
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
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Field Details
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C6
static final byte C6- See Also:
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O2Pr
private static final byte O2Pr- See Also:
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C5
private static final byte C5- See Also:
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N1
private static final byte N1- See Also:
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C2
private static final byte C2- See Also:
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N3
private static final byte N3- See Also:
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C4
private static final byte C4- See Also:
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O2
private static final byte O2- See Also:
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N7
private static final byte N7- See Also:
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C8
private static final byte C8- See Also:
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N9
private static final byte N9- See Also:
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O4
private static final byte O4- See Also:
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O6
private static final byte O6- See Also:
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N4
private static final byte N4- See Also:
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NP
private static final byte NP- See Also:
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N6
private static final byte N6- See Also:
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N2
private static final byte N2- See Also:
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H5T
private static final byte H5T- See Also:
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O5P
private static final byte O5P- See Also:
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H3T
private static final byte H3T- See Also:
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O3P
private static final byte O3P- See Also:
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C3P
private static final byte C3P- See Also:
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O1P
private static final byte O1P- See Also:
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O2P
private static final byte O2P- See Also:
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C1P
private static final byte C1P- See Also:
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C2P
private static final byte C2P- See Also:
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C4P
private static final byte C4P- See Also:
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O4P
private static final byte O4P- See Also:
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C5P
private static final byte C5P- See Also:
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interestingNucleicAtomIDs
static final byte[] interestingNucleicAtomIDs -
isPurine
private boolean isPurine -
isPyrimidine
boolean isPyrimidine -
hasRnaO2Prime
private boolean hasRnaO2Prime -
ring6OffsetIndexes
private static final byte[] ring6OffsetIndexes -
ring5OffsetIndexes
private static final byte[] ring5OffsetIndexes -
riboseOffsetIndexes
private static final byte[] riboseOffsetIndexes -
heavyAtomIndexes
private static final byte[] heavyAtomIndexes -
baseCenter
javajs.util.P3 baseCenter -
bps
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dssrBox
public javajs.util.P3[] dssrBox -
dssrBoxHeight
public float dssrBoxHeight -
dssrFrame
public javajs.util.P3[] dssrFrame
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Constructor Details
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NucleicMonomer
private NucleicMonomer()
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Method Details
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validateAndAllocate
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set4
private NucleicMonomer set4(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets) -
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() -
getProteinStructureType
- Overrides:
getProteinStructureType
in classPhosphorusMonomer
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getP
Atom getP() -
getC1P
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getC2
Atom getC2() -
getC5
Atom getC5() -
getC6
Atom getC6() -
getC8
Atom getC8() -
getC4P
Atom getC4P() -
getN1
Atom getN1() -
getN3
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getN2
Atom getN2() -
getN4
Atom getN4() -
getN6
Atom getN6() -
getO2
Atom getO2() -
getO4
Atom getO4() -
getO6
Atom getO6() -
getTerminatorAtom
Atom getTerminatorAtom()- Overrides:
getTerminatorAtom
in classMonomer
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getBaseRing6Points
public void getBaseRing6Points(javajs.util.P3[] pts) -
getPoints
private void getPoints(byte[] a, javajs.util.P3[] pts) -
maybeGetBaseRing5Points
public boolean maybeGetBaseRing5Points(javajs.util.P3[] pts) -
getRiboseRing5Points
public void getRiboseRing5Points(javajs.util.P3[] pts) -
isConnectedAfter
- Overrides:
isConnectedAfter
in classPhosphorusMonomer
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findNearestAtomIndex
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) -
setRingsClickable
public void setRingsClickable() -
getN0
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getHelixData
- 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
- Overrides:
isCrossLinked
in classMonomer
- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(javajs.util.Lst<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) -
addBasePair
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setGroup1
public void setGroup1(char g) -
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
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