org.simtk.molecularstructure
Interface Residue

All Superinterfaces:

Chemical, MassBody, Molecular, ResidueType

All Known Implementing Classes:

ResidueClass

public interface Residue
extends ResidueType, Molecular

Method Summary

Molecular	get(FunctionalGroup fg)
Atom	getAtom(java.lang.String atomName)
Vector3D	getBackbonePosition()
java.util.Set<Atom>	getHydrogenBondAcceptors()
java.util.Set<Atom>	getHydrogenBondDonors()
Residue	getNextResidue()
char	getPdbInsertionCode()
Residue	getPreviousResidue()
int	getResidueNumber()
ResidueType	getResidueType()
Vector3D	getSideChainPosition()
boolean	isAlphaHelix()
boolean	isHelix()
boolean	isStrand()
java.util.Collection<SecondaryStructure>	secondaryStructures()
void	setNextResidue(Residue r)
void	setPreviousResidue(Residue r)
void	setResidueNumber(int residueNumber)
void	updateAtomPosition(Atom atom)

Methods inherited from interface org.simtk.molecularstructure.ResidueType

genericBonds, getHydrogenBondAcceptorAtomNames, getHydrogenBondDonorAtomNames, getOneLetterCode, getResidueName, getThreeLetterCode

Methods inherited from interface org.simtk.molecularstructure.Molecular

atoms, bestPlane3D

Methods inherited from interface org.simtk.geometry3d.MassBody

getCenterOfMass, getMass

Method Detail

getPreviousResidue

Residue getPreviousResidue()

getNextResidue

Residue getNextResidue()

getResidueNumber

int getResidueNumber()

getResidueType

ResidueType getResidueType()

getAtom

Atom getAtom(java.lang.String atomName)

getPdbInsertionCode

char getPdbInsertionCode()

secondaryStructures

java.util.Collection<SecondaryStructure> secondaryStructures()

setPreviousResidue

void setPreviousResidue(Residue r)

setNextResidue

void setNextResidue(Residue r)

setResidueNumber

void setResidueNumber(int residueNumber)

getHydrogenBondDonors

java.util.Set<Atom> getHydrogenBondDonors()

getHydrogenBondAcceptors

java.util.Set<Atom> getHydrogenBondAcceptors()

getBackbonePosition

Vector3D getBackbonePosition()
                             throws InsufficientAtomsException

Throws:

InsufficientAtomsException

getSideChainPosition

Vector3D getSideChainPosition()
                              throws InsufficientAtomsException

Throws:

InsufficientAtomsException

get

Molecular get(FunctionalGroup fg)
              throws InsufficientAtomsException

Throws:

InsufficientAtomsException

isStrand

boolean isStrand()

isHelix

boolean isHelix()

isAlphaHelix

boolean isAlphaHelix()

updateAtomPosition

void updateAtomPosition(Atom atom)