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
FieldsFields inherited from class org.jmol.modelsetbio.PhosphorusMonomer
P
Fields inherited from class org.jmol.modelsetbio.Monomer
backboneBlockVis, bioPolymer, 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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Method Summary
Modifier and TypeMethodDescriptionvoid
addBasePair
(BasePair bp) void
findNearestAtomIndex
(int x, int y, Atom[] closest, short madBegin, short madEnd) void
getBaseRing6Points
(P3[] pts) getC1P()
boolean
getCrossLinkVector
(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) P3[]
getDSSRFrame
(Viewer vwr) boolean
getEdgePoints
(P3[] pts) protected char
getHelixData
(int tokType, char qType, int mStep) getN0()
getN3()
getQuaternion
(char qType) void
getRiboseRing5Points
(P3[] pts) boolean
boolean
isDna()
group ID-based definitionboolean
boolean
boolean
isPurine()
group ID-based definitionboolean
group ID-based definitionboolean
isRna()
group ID-based definitionboolean
maybeGetBaseRing5Points
(P3[] pts) 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
Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getGroup1, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, have, isConnectedPrevious, isHelix, isLeadAtom, isSheet, scanForOffsets, set2, setGroupID, setLeadAtomIndex, setStrucNo, toString
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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dssrBox
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dssrBoxHeight
public float dssrBoxHeight -
dssrFrame
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Method Details
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validateAndAllocate
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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() -
getProteinStructureType
- Overrides:
getProteinStructureType
in classPhosphorusMonomer
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getC1P
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getN3
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getBaseRing6Points
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maybeGetBaseRing5Points
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getRiboseRing5Points
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findNearestAtomIndex
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setRingsVisible
public void setRingsVisible(boolean isVisible) -
setRingsClickable
public void setRingsClickable() -
getN0
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getHelixData
- Overrides:
getHelixData
in classPhosphorusMonomer
- Parameters:
tokType
-qType
-mStep
-- Returns:
- helix data of some sort
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getQuaternion
- Overrides:
getQuaternion
in classPhosphorusMonomer
- Parameters:
qType
-- Returns:
- quaternion
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isCrossLinked
- Overrides:
isCrossLinked
in classMonomer
- Parameters:
g
-- Returns:
- T/F
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getCrossLinkVector
public boolean getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) - Overrides:
getCrossLinkVector
in classMonomer
- Parameters:
vReturn
-crosslinkCovalent
-crosslinkHBond
-- Returns:
- T/F
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getEdgePoints
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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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