org.jmol.modelsetbio.AminoMonomer

All Implemented Interfaces:: Structure

public class AminoMonomer extends AlphaMonomer

Field Summary

Fields

Modifier and Type

Field

Description

private static final float

beta

private static final byte

C

private static final byte

CA

(package private) static final byte[]

interestingAminoAtomIDs

private static final byte

N

(package private) boolean

nhChecked

private static final byte

O

private static final byte

OT

private javajs.util.P3

ptTemp

Fields inherited from class org.jmol.modelsetbio.AlphaMonomer
alphaOffsets, nitrogenHydrogenPoint, proteinStructure

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

AminoMonomer()
Method Summary

Modifier and Type

Method

Description

private void

clear(javajs.util.BS bs, Atom a, boolean andH)

(package private) 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.BS

getBSSideChain()

Atom

getCarbonylCarbonAtom()

Atom

getCarbonylOxygenAtom()

Atom

getExplicitNH()

(package private) Atom

getInitiatorAtom()

boolean

getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)

Atom

getNitrogenAtom()

(package private) javajs.util.P3

getNitrogenHydrogenPoint()

String

getProteinStructureTag()

javajs.util.Quat

getQuaternion(char qType)

(package private) javajs.util.P3

getQuaternionFrameCenter(char qType)

String

getStructureId()

(package private) Atom

getTerminatorAtom()

(package private) boolean

hasOAtom()

(package private) boolean

isAminoMonomer()

private static boolean

isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)

private static boolean

isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)

(package private) boolean

isConnectedAfter(Monomer possiblyPreviousMonomer)

void

resetHydrogenPoint()

(package private) static Monomer

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

Methods inherited from class org.jmol.modelsetbio.AlphaMonomer
getAtom, getAtomPoint, getHelixData, getProteinStructureSubType, getProteinStructureType, getQuaternionAlpha, getQuaternionFrameCenterAlpha, getStrucNo, getStructure, isAlphaMonomer, isHelix, isProtein, isSheet, isWithinStructure, setProteinStructureType, setStrucNo, setStructure, validateAndAllocateA

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

Methods inherited from class org.jmol.modelset.Group
addAtoms, fixIndices, getGroup3, getGroupInfo, getInsCode, getInsertionCode, getInsertionCodeChar, getInsertionCodeFor, getLeadAtomOr, getMinZ, getModel, 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

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

Field Details
- CA
  
  private static final byte CA
  See Also:
  
  Constant Field Values
- O
  
  private static final byte O
  See Also:
  
  Constant Field Values
- N
  
  private static final byte N
  See Also:
  
  Constant Field Values
- C
  
  private static final byte C
  See Also:
  
  Constant Field Values
- OT
  
  private static final byte OT
  See Also:
  
  Constant Field Values
- interestingAminoAtomIDs
  
  static final byte[] interestingAminoAtomIDs
- nhChecked
  
  boolean nhChecked
- beta
  
  private static final float beta
  See Also:
  
  Constant Field Values
- ptTemp
  
  private javajs.util.P3 ptTemp
Constructor Details
- AminoMonomer
  
  protected AminoMonomer()
Method Details
- validateAndAllocate
  
  static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)
- isBondedCorrectlyRange
  
  private static boolean isBondedCorrectlyRange(int offset1, int offset2, int firstAtomIndex, byte[] offsets, Atom[] atoms)
- isBondedCorrectly
  
  private static boolean isBondedCorrectly(int firstAtomIndex, byte[] offsets, Atom[] atoms)
- isAminoMonomer
  
  boolean isAminoMonomer()
- getNitrogenAtom
  
  public Atom getNitrogenAtom()
  
  Overrides:
  
  getNitrogenAtom in class Group
- getCarbonylCarbonAtom
  
  public Atom getCarbonylCarbonAtom()
- getCarbonylOxygenAtom
  
  public Atom getCarbonylOxygenAtom()
  
  Overrides:
  
  getCarbonylOxygenAtom in class Group
- getInitiatorAtom
  
  Atom getInitiatorAtom()
  
  Overrides:
  
  getInitiatorAtom in class Monomer
- getTerminatorAtom
  
  Atom getTerminatorAtom()
  
  Overrides:
  
  getTerminatorAtom in class Monomer
- hasOAtom
  
  boolean hasOAtom()
- isConnectedAfter
  
  boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
  
  Overrides:
  
  isConnectedAfter in class AlphaMonomer
- findNearestAtomIndex
  
  void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
  
  Description copied from class: Monomer
  
  Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
  
  Overrides:
  
  findNearestAtomIndex in class Monomer
- resetHydrogenPoint
  
  public void resetHydrogenPoint()
- getNitrogenHydrogenPoint
  
  javajs.util.P3 getNitrogenHydrogenPoint()
- getExplicitNH
  
  public Atom getExplicitNH()
- getNHPoint
  
  public boolean getNHPoint(javajs.util.P3 aminoHydrogenPoint, javajs.util.V3 vNH, boolean jmolHPoint, boolean dsspIgnoreHydrogens)
- getQuaternionFrameCenter
  
  javajs.util.P3 getQuaternionFrameCenter(char qType)
  
  Overrides:
  
  getQuaternionFrameCenter in class AlphaMonomer
  
  Returns:
  
  center
- getQuaternion
  
  public javajs.util.Quat getQuaternion(char qType)
  
  Overrides:
  
  getQuaternion in class AlphaMonomer
  
  Returns:
  
  quaternion
- getStructureId
  
  public String getStructureId()
  
  Overrides:
  
  getStructureId in class Monomer
- getProteinStructureTag
  
  public String getProteinStructureTag()
  
  Overrides:
  
  getProteinStructureTag in class Group
- getBSSideChain
  
  public javajs.util.BS getBSSideChain()
  
  Overrides:
  
  getBSSideChain in class Group
- clear
  
  private void clear(javajs.util.BS bs, Atom a, boolean andH)

Class AminoMonomer

Field Summary

Fields inherited from class org.jmol.modelsetbio.AlphaMonomer

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.AlphaMonomer

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

CA

O

N

C

OT

interestingAminoAtomIDs

nhChecked

beta

ptTemp

Constructor Details

AminoMonomer

Method Details

validateAndAllocate

isBondedCorrectlyRange

isBondedCorrectly

isAminoMonomer

getNitrogenAtom

getCarbonylCarbonAtom

getCarbonylOxygenAtom

getInitiatorAtom

getTerminatorAtom

hasOAtom

isConnectedAfter

findNearestAtomIndex

resetHydrogenPoint

getNitrogenHydrogenPoint

getExplicitNH

getNHPoint

getQuaternionFrameCenter

getQuaternion

getStructureId

getProteinStructureTag

getBSSideChain

clear