org.simtk.molecularstructure.nucleicacid
Class Nucleotide

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

All Implemented Interfaces:

ResidueType

Direct Known Subclasses:

Purine, Pyrimidine

public class Nucleotide
extends ResidueTypeClass

Field Summary

static FunctionalGroup	baseGroup
static FunctionalGroup	phosphateGroup
static FunctionalGroup	sugarGroup

Fields inherited from class org.simtk.molecularstructure.ResidueTypeClass

genericBonds, oneLetterCode, residueName, threeLetterCode, UNKNOWN_RESIDUE_TYPE

Constructor Summary

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

Method Summary

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

Field Detail

baseGroup

public static FunctionalGroup baseGroup

sugarGroup

public static FunctionalGroup sugarGroup

phosphateGroup

public static FunctionalGroup phosphateGroup

Constructor Detail

Nucleotide

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

Method Detail

getHydrogenBondDonorAtomNames

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

Specified by:

getHydrogenBondDonorAtomNames in interface ResidueType

Overrides:

getHydrogenBondDonorAtomNames in class ResidueTypeClass

getHydrogenBondAcceptorAtomNames

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

Specified by:

getHydrogenBondAcceptorAtomNames in interface ResidueType

Overrides:

getHydrogenBondAcceptorAtomNames in class ResidueTypeClass

addGenericBonds

protected void addGenericBonds()

Overrides:

addGenericBonds in class ResidueTypeClass