org.simtk.molecularstructure.nucleicacid
Class Pyrimidine

java.lang.Object
  org.simtk.molecularstructure.ResidueTypeClass
      org.simtk.molecularstructure.nucleicacid.Nucleotide
          org.simtk.molecularstructure.nucleicacid.Pyrimidine

All Implemented Interfaces:

ResidueType

Direct Known Subclasses:

Cytidylate, Thymidylate, Uridylate

public class Pyrimidine
extends Nucleotide

Author:

Christopher Bruns

Field Summary

Fields inherited from class org.simtk.molecularstructure.nucleicacid.Nucleotide

baseGroup, phosphateGroup, sugarGroup

Fields inherited from class org.simtk.molecularstructure.ResidueTypeClass

genericBonds, oneLetterCode, residueName, threeLetterCode, UNKNOWN_RESIDUE_TYPE

Constructor Summary

Pyrimidine(char olc, java.lang.String tlc, java.lang.String name)

Method Summary

protected void	addGenericBonds()
java.util.Set<java.lang.String>	getHydrogenBondAcceptorAtomNames()

Methods inherited from class org.simtk.molecularstructure.nucleicacid.Nucleotide

getHydrogenBondDonorAtomNames

Methods inherited from class org.simtk.molecularstructure.ResidueTypeClass

addGenericBond, genericBonds, getOneLetterCode, getResidueName, getThreeLetterCode, getType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Pyrimidine

public Pyrimidine(char olc,
                  java.lang.String tlc,
                  java.lang.String name)

Method Detail

addGenericBonds

protected void addGenericBonds()

Overrides:

addGenericBonds in class Nucleotide

getHydrogenBondAcceptorAtomNames

public java.util.Set<java.lang.String> getHydrogenBondAcceptorAtomNames()

Specified by:

getHydrogenBondAcceptorAtomNames in interface ResidueType

Overrides:

getHydrogenBondAcceptorAtomNames in class Nucleotide