Class NucleicMonomer

All Implemented Interfaces:
Structure

public class NucleicMonomer extends PhosphorusMonomer
  • 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: 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
    • 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
      Returns:
      helix data of some sort
    • getQuaternion

      public Quat getQuaternion(char qType)
      Overrides:
      getQuaternion in class PhosphorusMonomer
      Returns:
      quaternion
    • isCrossLinked

      public boolean isCrossLinked(Group g)
      Overrides:
      isCrossLinked in class Monomer
      Returns:
      T/F
    • getCrossLinkVector

      public boolean getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
      Overrides:
      getCrossLinkVector in class Monomer
      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)