org.jmol.modelsetbio.PhosphorusMonomer

All Implemented Interfaces:: Structure

Direct Known Subclasses:: NucleicMonomer

public class PhosphorusMonomer extends Monomer

Field Summary

Fields

Modifier and Type

Field

Description

private static float

MAX_ADJACENT_PHOSPHORUS_DISTANCE

protected static final byte

P

private static final byte[]

phosphorusOffsets

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
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

PhosphorusMonomer()
Method Summary

Modifier and Type

Method

Description

Object

getHelixData(int tokType, char qType, int mStep)

STR

getProteinStructureType()

javajs.util.Quat

getQuaternion(char qType)

(package private) javajs.util.P3

getQuaternionFrameCenter(char qType)

protected javajs.util.Quat

getQuaternionP()

Structure

getStructure()

protected boolean

isCA2(Monomer possiblyPreviousMonomer)

(package private) boolean

isConnectedAfter(Monomer possiblyPreviousMonomer)

boolean

isDna()

group ID-based definition

final boolean

isNucleic()

group ID-based definition

boolean

isPurine()

group ID-based definition

boolean

isPyrimidine()

group ID-based definition

boolean

isRna()

group ID-based definition

(package private) static Monomer

validateAndAllocateP(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)

Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, findNearestAtomIndex, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getInitiatorAtom, getLeadAtom, getMonomerIndex, getMonomerSequenceAtoms, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getTerminatorAtom, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, 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, isNucleicMonomer, isProtein, isPurineByID, isPyrimidineByID, isRnaByID, isSelected, isWithinStructure, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setProteinStructureType, setResno, setShapeVisibility

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

Field Details
- P
  
  protected static final byte P
  See Also:
  
  Constant Field Values
- phosphorusOffsets
  
  private static final byte[] phosphorusOffsets
- MAX_ADJACENT_PHOSPHORUS_DISTANCE
  
  private static float MAX_ADJACENT_PHOSPHORUS_DISTANCE
Constructor Details
- PhosphorusMonomer
  
  protected PhosphorusMonomer()
Method Details
- isNucleic
  
  public final boolean isNucleic()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isNucleic in class Group
  
  Returns:
  
  boolean
- validateAndAllocateP
  
  static Monomer validateAndAllocateP(Chain chain, String group3, int seqcode, int firstIndex, int lastIndex, int[] specialAtomIndexes)
- isDna
  
  public boolean isDna()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isDna in class Group
  
  Returns:
  
  boolean
- isRna
  
  public boolean isRna()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isRna in class Group
  
  Returns:
  
  boolean
- isPurine
  
  public boolean isPurine()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isPurine in class Group
  
  Returns:
  
  boolean
- isPyrimidine
  
  public boolean isPyrimidine()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isPyrimidine in class Group
  
  Returns:
  
  boolean
- getStructure
  
  public Structure getStructure()
  
  Overrides:
  
  getStructure in class Group
- getProteinStructureType
  
  public STR getProteinStructureType()
  
  Overrides:
  
  getProteinStructureType in class Monomer
- isConnectedAfter
  
  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
  
  Specified by:
  
  isConnectedAfter in class Monomer
- isCA2
  
  protected boolean isCA2(Monomer possiblyPreviousMonomer)
- getQuaternion
  
  public javajs.util.Quat getQuaternion(char qType)
  
  Overrides:
  
  getQuaternion in class Group
  
  Returns:
  
  quaternion
- getQuaternionP
  
  protected javajs.util.Quat getQuaternionP()
- getQuaternionFrameCenter
  
  javajs.util.P3 getQuaternionFrameCenter(char qType)
  
  Overrides:
  
  getQuaternionFrameCenter in class Monomer
  
  Returns:
  
  center
- getHelixData
  
  public Object getHelixData(int tokType, char qType, int mStep)
  
  Overrides:
  
  getHelixData in class Group
  
  Returns:
  
  helix data of some sort

Class PhosphorusMonomer

Field Summary

Fields inherited from class org.jmol.modelsetbio.Monomer

Fields inherited from class org.jmol.modelset.Group

Constructor Summary

Method Summary

Methods inherited from class org.jmol.modelsetbio.Monomer

Methods inherited from class org.jmol.modelset.Group

Methods inherited from class java.lang.Object

Field Details

P

phosphorusOffsets

MAX_ADJACENT_PHOSPHORUS_DISTANCE

Constructor Details

PhosphorusMonomer

Method Details

isNucleic

validateAndAllocateP

isDna

isRna

isPurine

isPyrimidine

getStructure

getProteinStructureType

isConnectedAfter

isCA2

getQuaternion

getQuaternionP

getQuaternionFrameCenter

getHelixData