org.jmol.modelsetbio.NucleicMonomer

All Implemented Interfaces:: Structure

public class NucleicMonomer extends PhosphorusMonomer

Field Summary

Fields

Modifier and Type

Field

Description

P3[]

dssrBox

float

dssrBoxHeight

P3[]

dssrFrame

Fields inherited from class PhosphorusMonomer
P

Fields inherited from class Monomer
backboneBlockVis, bioPolymer, offsets

Fields inherited from class Group
chain, dssrNT, firstAtomIndex, group1, group3Names, groupID, groupIndex, lastAtomIndex, leadAtomIndex, selectedIndex, seqcode, shapeVisibilityFlags, specialAtomNames, standardGroupList, strutPoint
Method Summary

Modifier and Type

Method

Description

void

addBasePair(BasePair bp)

void

findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)

/////////////////////////////////////////////////////////////

Lst<BasePair>

getBasePairs()

void

getBaseRing6Points(P3[] pts)

Atom

getC1P()

boolean

getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)

P3[]

getDSSRFrame(Viewer vwr)

boolean

getEdgePoints(P3[] pts)

protected char

getGroup1b()

Object

getHelixData(int tokType, char qType, int mStep)

Atom

getN0()

Atom

getN3()

STR

getProteinStructureType()

/////////////////////////////////////////////////////////////

Quat

getQuaternion(char qType)

void

getRiboseRing5Points(P3[] pts)

boolean

isCrossLinked(Group g)

boolean

isDna()

/////////////////////////////////////////////////////////////

boolean

isGuanine()

boolean

isNucleicMonomer()

boolean

isPurine()

group ID-based definition

boolean

isPyrimidine()

group ID-based definition

boolean

isRna()

group ID-based definition

boolean

maybeGetBaseRing5Points(P3[] pts)

void

setGroup1(char g)

void

setRingsClickable()

void

setRingsVisible(boolean isVisible)

static Monomer

validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)

Methods inherited from class PhosphorusMonomer
getQuaternionP, getStructure, isCA2, isNucleic

Methods inherited from class 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, updateOffsetsForAlternativeLocations

Methods inherited from class 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, unsetStrutPoint

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details
- dssrBox
  
  public P3[] dssrBox
- dssrBoxHeight
  
  public float dssrBoxHeight
- dssrFrame
  
  public P3[] dssrFrame
Method Details
- validateAndAllocate
  
  public static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)
- isNucleicMonomer
  
  public boolean isNucleicMonomer()
  
  Overrides:
  
  isNucleicMonomer in class Group
- isDna
  
  public boolean isDna()
  
  Description copied from class: PhosphorusMonomer
  
  /////////////////////////////////////////////////////////////
  
  Overrides:
  
  isDna in class PhosphorusMonomer
  
  Returns:
  
  boolean
- isRna
  
  public boolean isRna()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isRna in class PhosphorusMonomer
  
  Returns:
  
  boolean
- isPurine
  
  public boolean isPurine()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isPurine in class PhosphorusMonomer
  
  Returns:
  
  boolean
- isPyrimidine
  
  public boolean isPyrimidine()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isPyrimidine in class PhosphorusMonomer
  
  Returns:
  
  boolean
- isGuanine
  
  public boolean isGuanine()
- getProteinStructureType
  
  public STR getProteinStructureType()
  
  Description copied from class: Monomer
  
  /////////////////////////////////////////////////////////////
  
  Overrides:
  
  getProteinStructureType in class PhosphorusMonomer
- getC1P
  
  public Atom getC1P()
- getN3
  
  public Atom getN3()
- getBaseRing6Points
  
  public void getBaseRing6Points(P3[] pts)
- maybeGetBaseRing5Points
  
  public boolean maybeGetBaseRing5Points(P3[] pts)
- getRiboseRing5Points
  
  public void getRiboseRing5Points(P3[] pts)
- findNearestAtomIndex
  
  public void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
  
  /////////////////////////////////////////////////////////////
- setRingsVisible
  
  public void setRingsVisible(boolean isVisible)
- setRingsClickable
  
  public void setRingsClickable()
- getN0
  
  public Atom getN0()
- getHelixData
  
  public Object getHelixData(int tokType, char qType, int mStep)
  
  Overrides:
  
  getHelixData in class PhosphorusMonomer
  
  Parameters:
  
  tokType -
  
  qType -
  
  mStep -
  
  Returns:
  
  helix data of some sort
- getQuaternion
  
  public Quat getQuaternion(char qType)
  
  Overrides:
  
  getQuaternion in class PhosphorusMonomer
  
  Parameters:
  
  qType -
  
  Returns:
  
  quaternion
- isCrossLinked
  
  public boolean isCrossLinked(Group g)
  
  Overrides:
  
  isCrossLinked in class Monomer
  
  Parameters:
  
  g -
  
  Returns:
  
  T/F
- getCrossLinkVector
  
  public boolean getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
  
  Overrides:
  
  getCrossLinkVector in class Monomer
  
  Parameters:
  
  vReturn -
  
  crosslinkCovalent -
  
  crosslinkHBond -
  
  Returns:
  
  T/F
- getEdgePoints
  
  public boolean getEdgePoints(P3[] pts)
- addBasePair
  
  public void addBasePair(BasePair bp)
- setGroup1
  
  public void setGroup1(char g)
- getBasePairs
  
  public Lst<BasePair> getBasePairs()
  
  Returns:
  
  list of base pairs associated with this monomer, possibly more than one if noncanonical
- getGroup1b
  
  protected char getGroup1b()
  
  Overrides:
  
  getGroup1b in class Monomer
- getDSSRFrame
  
  public P3[] getDSSRFrame(Viewer vwr)

Class NucleicMonomer

Field Summary

Fields inherited from class PhosphorusMonomer

Fields inherited from class Monomer

Fields inherited from class Group

Method Summary

Methods inherited from class PhosphorusMonomer

Methods inherited from class Monomer

Methods inherited from class Group

Methods inherited from class Object

Field Details

dssrBox

dssrBoxHeight

dssrFrame

Method Details

validateAndAllocate

isNucleicMonomer

isDna

isRna

isPurine

isPyrimidine

isGuanine

getProteinStructureType

getC1P

getN3

getBaseRing6Points

maybeGetBaseRing5Points

getRiboseRing5Points

findNearestAtomIndex

setRingsVisible

setRingsClickable

getN0

getHelixData

getQuaternion

isCrossLinked

getCrossLinkVector

getEdgePoints

addBasePair

setGroup1

getBasePairs

getGroup1b

getDSSRFrame