Package org.jmol.modelsetbio

Class NucleicMonomer

java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
org.jmol.modelsetbio.PhosphorusMonomer
org.jmol.modelsetbio.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

    • 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

    • getQuaternionFrameCenter

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

    • getQuaternion

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