Class NucleicMonomer

All Implemented Interfaces:
Structure

public class NucleicMonomer extends PhosphorusMonomer
  • Field Details

  • Constructor Details

    • NucleicMonomer

      private NucleicMonomer()
  • Method Details

    • validateAndAllocate

      public static Monomer validateAndAllocate(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes)
    • set4

      private NucleicMonomer set4(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] offsets)
    • isNucleicMonomer

      public boolean isNucleicMonomer()
      Overrides:
      isNucleicMonomer in class Group
    • isDna

      public boolean isDna()
      Description copied from class: Group
      group ID-based definition
      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()
      Overrides:
      getProteinStructureType in class PhosphorusMonomer
    • getP

      Atom getP()
    • getC1P

      public Atom getC1P()
    • getC2

      Atom getC2()
    • getC5

      Atom getC5()
    • getC6

      Atom getC6()
    • getC8

      Atom getC8()
    • getC4P

      Atom getC4P()
    • getN1

      Atom getN1()
    • getN3

      public Atom getN3()
    • getN2

      Atom getN2()
    • getN4

      Atom getN4()
    • getN6

      Atom getN6()
    • getO2

      Atom getO2()
    • getO4

      Atom getO4()
    • getO6

      Atom getO6()
    • getTerminatorAtom

      Atom getTerminatorAtom()
      Overrides:
      getTerminatorAtom in class Monomer
    • getBaseRing6Points

      public void getBaseRing6Points(javajs.util.P3[] pts)
    • getPoints

      private void getPoints(byte[] a, javajs.util.P3[] pts)
    • maybeGetBaseRing5Points

      public boolean maybeGetBaseRing5Points(javajs.util.P3[] pts)
    • getRiboseRing5Points

      public void getRiboseRing5Points(javajs.util.P3[] pts)
    • isConnectedAfter

      boolean isConnectedAfter(Monomer possiblyPreviousMonomer)
      Overrides:
      isConnectedAfter in class PhosphorusMonomer
    • findNearestAtomIndex

      public 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
      Parameters:
      x -
      y -
      closest -
      madBegin -
      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
    • getQuaternionFrameCenter

      javajs.util.P3 getQuaternionFrameCenter(char qType)
      Overrides:
      getQuaternionFrameCenter in class PhosphorusMonomer
      Parameters:
      qType -
      Returns:
      center
    • getQuaternion

      public javajs.util.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(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
      Overrides:
      getCrossLinkVector in class Monomer
      Parameters:
      vReturn -
      crosslinkCovalent -
      crosslinkHBond -
      Returns:
      T/F
    • getEdgePoints

      public boolean getEdgePoints(javajs.util.P3[] pts)
    • addBasePair

      public void addBasePair(BasePair bp)
    • setGroup1

      public void setGroup1(char g)
    • getBasePairs

      public javajs.util.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 javajs.util.P3[] getDSSRFrame(Viewer vwr)