Field Detail

• C6

  static final byte C6

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• O2Pr

  private static final byte O2Pr

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• C5

  private static final byte C5

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• N1

  private static final byte N1

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• C2

  private static final byte C2

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• N3

  private static final byte N3

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• C4

  private static final byte C4

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• O2

  private static final byte O2

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• N7

  private static final byte N7

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• C8

  private static final byte C8

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• N9

  private static final byte N9

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• O4

  private static final byte O4

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• O6

  private static final byte O6

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• N4

  private static final byte N4

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• NP

  private static final byte NP

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• N6

  private static final byte N6

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• N2

  private static final byte N2

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• H5T

  private static final byte H5T

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• O5P

  private static final byte O5P

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• H3T

  private static final byte H3T

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• O3P

  private static final byte O3P

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• C3P

  private static final byte C3P

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• O1P

  private static final byte O1P

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• O2P

  private static final byte O2P

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• C1P

  private static final byte C1P

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• C2P

  private static final byte C2P

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• C4P

  private static final byte C4P

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• O4P

  private static final byte O4P

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• C5P

  private static final byte C5P

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• interestingNucleicAtomIDs

  static final byte[] interestingNucleicAtomIDs

• isPurine

  private boolean isPurine

• isPyrimidine

  boolean isPyrimidine

• hasRnaO2Prime

  private boolean hasRnaO2Prime

• ring6OffsetIndexes

  private static final byte[] ring6OffsetIndexes

• ring5OffsetIndexes

  private static final byte[] ring5OffsetIndexes

• riboseOffsetIndexes

  private static final byte[] riboseOffsetIndexes

• heavyAtomIndexes

  private static final byte[] heavyAtomIndexes

• baseCenter

  javajs.util.P3 baseCenter

• bps

  private javajs.util.Lst<BasePair> bps

Constructor Detail

• NucleicMonomer

  private NucleicMonomer()

Method Detail

• validateAndAllocate

  public static Monomer validateAndAllocate​(Chain chain,
                                            java.lang.String group3,
                                            int seqcode,
                                            int firstAtomIndex,
                                            int lastAtomIndex,
                                            int[] specialAtomIndexes)

• set4

  private NucleicMonomer set4​(Chain chain,
                              java.lang.String group3,
                              int seqcode,
                              int firstAtomIndex,
                              int lastAtomIndex,
                              byte[] offsets)

• isNucleicMonomer

  public boolean isNucleicMonomer()

• 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

  Atom getC1P()

• getC2

  Atom getC2()

• getC4P

  Atom getC4P()

• getN1

  Atom getN1()

• getN3

  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

  Atom getN0()

• getHelixData

  public java.lang.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<java.lang.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