org.jmol.modelsetbio.AlphaMonomer

All Implemented Interfaces:: Structure

Direct Known Subclasses:: AminoMonomer

public class AlphaMonomer extends Monomer

Field Summary

Fields

Modifier and Type

Field

Description

protected P3

nitrogenHydrogenPoint

ProteinStructure

proteinStructure

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, strutPoint
Constructor Summary

Constructors

Modifier

Constructor

Description

protected

AlphaMonomer()
Method Summary

Modifier and Type

Method

Description

final Atom

getAtom(byte specialAtomID)

final P3

getAtomPoint(byte specialAtomID)

Object

getHelixData(int tokType, char qType, int mStep)

STR

getProteinStructureSubType()

STR

getProteinStructureType()

Quat

getQuaternion(char qType)

protected Quat

getQuaternionAlpha(char qType)

protected P3

getQuaternionFrameCenterAlpha(char qType)

int

getStrucNo()

Structure

getStructure()

boolean

isHelix()

boolean

isProtein()

group ID-based definition

boolean

isSheet()

boolean

isWithinStructure(STR type)

int

setProteinStructureType(STR type, int monomerIndexCurrent)

void

setStrucNo(int n)

Methods inherited from class org.jmol.modelsetbio.Monomer
checkOptional, getAtomFromOffsetIndex, getAtomIndex, getBioPolymerIndexInModel, getBioPolymerLength, getCrossLinkGroup, getCrossLinkVector, getGroup1, getGroup1b, getGroupParameter, getHelixData2, getLeadAtom, getMonomerIndex, getMyInfo, getSelectedMonomerCount, getSelectedMonomerIndex, getSpecialAtom, getSpecialAtomPoint, getStructureId, getUniqueID, getWingAtom, have, isConnectedPrevious, isCrossLinked, isLeadAtom, scanForOffsets, set2, setGroupID, setLeadAtomIndex, toString, updateOffsetsForAlternativeLocations

Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getBSSideChain, getCarbonylOxygenAtom, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, getNitrogenAtom, getProteinStructureTag, getQuaternionFrame, getResno, getSeqcodeFor, getSeqcodeString, getSeqcodeStringFor, getSeqNumberFor, haveSequenceNumber, isAdded, isCarbohydrate, isCursorOnTopOf, isDna, isDnaByID, isNucleic, isNucleicMonomer, isPurine, isPurineByID, isPyrimidine, isPyrimidineByID, isRna, isRnaByID, isSelected, scaleToScreen, setAtomBits, setAtomBitsAndClear, setGroup, setResno, setShapeVisibility, unsetStrutPoint

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

Field Details
- proteinStructure
  
  public ProteinStructure proteinStructure
- nitrogenHydrogenPoint
  
  protected P3 nitrogenHydrogenPoint
Constructor Details
- AlphaMonomer
  
  protected AlphaMonomer()
Method Details
- isProtein
  
  public boolean isProtein()
  
  Description copied from class: Group
  
  group ID-based definition
  
  Overrides:
  
  isProtein in class Group
  
  Returns:
  
  boolean
- getStructure
  
  public Structure getStructure()
  
  Overrides:
  
  getStructure in class Group
- setStrucNo
  
  public void setStrucNo(int n)
  
  Overrides:
  
  setStrucNo in class Monomer
  
  Parameters:
  
  n -
- getProteinStructureType
  
  public STR getProteinStructureType()
  
  Overrides:
  
  getProteinStructureType in class Monomer
- getProteinStructureSubType
  
  public STR getProteinStructureSubType()
  
  Overrides:
  
  getProteinStructureSubType in class Group
- getStrucNo
  
  public int getStrucNo()
  
  Overrides:
  
  getStrucNo in class Group
- isHelix
  
  public boolean isHelix()
  
  Overrides:
  
  isHelix in class Monomer
- isSheet
  
  public boolean isSheet()
  
  Overrides:
  
  isSheet in class Monomer
- setProteinStructureType
  
  public int setProteinStructureType(STR type, int monomerIndexCurrent)
  
  Overrides:
  
  setProteinStructureType in class Group
  
  Parameters:
  
  type -
  
  monomerIndexCurrent - a pointer to the current ProteinStructure
  
  Returns:
  
  a pointer to this ProteinStructure
- getAtom
  
  public final Atom getAtom(byte specialAtomID)
- getAtomPoint
  
  public final P3 getAtomPoint(byte specialAtomID)
- isWithinStructure
  
  public boolean isWithinStructure(STR type)
  
  Overrides:
  
  isWithinStructure in class Group
  
  Parameters:
  
  type -
  
  Returns:
  
  T/F
- getQuaternionFrameCenterAlpha
  
  protected P3 getQuaternionFrameCenterAlpha(char qType)
- getHelixData
  
  public Object getHelixData(int tokType, char qType, int mStep)
  
  Overrides:
  
  getHelixData in class Group
  
  Parameters:
  
  tokType -
  
  qType -
  
  mStep -
  
  Returns:
  
  helix data of some sort
- getQuaternion
  
  public Quat getQuaternion(char qType)
  
  Overrides:
  
  getQuaternion in class Group
  
  Parameters:
  
  qType -
  
  Returns:
  
  quaternion
- getQuaternionAlpha
  
  protected Quat getQuaternionAlpha(char qType)

Class AlphaMonomer

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

proteinStructure

nitrogenHydrogenPoint

Constructor Details

AlphaMonomer

Method Details

isProtein

getStructure

setStrucNo

getProteinStructureType

getProteinStructureSubType

getStrucNo

isHelix

isSheet

setProteinStructureType

getAtom

getAtomPoint

isWithinStructure

getQuaternionFrameCenterAlpha

getHelixData

getQuaternion

getQuaternionAlpha