org.simtk.molecularstructure
Class ResidueClass

java.lang.Object
  org.simtk.molecularstructure.MolecularClass
      org.simtk.molecularstructure.ResidueClass

All Implemented Interfaces:

MassBody, Chemical, Molecular, Residue, ResidueType

public class ResidueClass
extends MolecularClass
implements Residue

Field Summary

static java.util.List<java.lang.String>	knownHetatms
static java.util.List<java.lang.String>	modifiedAdenylates
static java.util.List<java.lang.String>	modifiedCytidylates
static java.util.List<java.lang.String>	modifiedGuanylates
static java.util.List<java.lang.String>	modifiedInositates
static java.util.List<java.lang.String>	modifiedThymidylates
static java.util.List<java.lang.String>	modifiedUridylates
protected Residue	nextResidue
protected Residue	previousResidue
java.lang.Integer	residueNumber

Constructor Summary

ResidueClass(ResidueType type)

ResidueClass(java.lang.String PdbLine)

Method Summary

java.util.Set<Atom>	atoms() Override atoms() method to use a class that can index by atom name
java.util.Map<java.lang.String,java.util.Set<java.lang.String>>	genericBonds()
Molecular	get(FunctionalGroup fg)
Atom	getAtom(java.lang.String atomName) Get the atom with the given name.
Vector3D	getBackbonePosition() Return preferred location of backbone trace in molecular representations
java.lang.String	getGlycosyl()
java.util.Set<java.lang.String>	getHydrogenBondAcceptorAtomNames()
java.util.Set<Atom>	getHydrogenBondAcceptors()
java.util.Set<java.lang.String>	getHydrogenBondDonorAtomNames()
java.util.Set<Atom>	getHydrogenBondDonors()
Residue	getNextResidue()
char	getOneLetterCode() Create an empty Residue object with no atoms.
char	getPdbInsertionCode()
Residue	getPreviousResidue()
java.lang.String	getPucker()
java.lang.String	getResidueName()
int	getResidueNumber()
ResidueType	getResidueType()
Vector3D	getSideChainPosition()
java.lang.String	getThreeLetterCode()
boolean	isAlphaHelix()
static boolean	isDNA(java.lang.String residueName)
boolean	isHelix()
static boolean	isKnownHetatm(java.lang.String residueName)
static boolean	isNucleicAcid(java.lang.String residueName)
static boolean	isProtein(java.lang.String residueName)
static boolean	isRNA(java.lang.String residueName)
static boolean	isSolvent(java.lang.String residueName)
boolean	isStrand()
boolean	matchesPdbLine(java.lang.String PdbLine)
java.util.Collection<SecondaryStructure>	secondaryStructures()
void	setGlycosyl(java.lang.String glycosyl)
void	setNextResidue(Residue r)
void	setPdbInsertionCode(char insertionCode)
void	setPreviousResidue(Residue r)
void	setPucker(java.lang.String pucker)
void	setResidueNumber(int residueNumber)
void	updateAtomPosition(Atom atom)

Methods inherited from class org.simtk.molecularstructure.MolecularClass

bestPlane3D, getCenterOfMass, getMass

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.simtk.molecularstructure.Molecular

bestPlane3D

Methods inherited from interface org.simtk.geometry3d.MassBody

getCenterOfMass, getMass

Field Detail

modifiedAdenylates

public static java.util.List<java.lang.String> modifiedAdenylates

modifiedCytidylates

public static java.util.List<java.lang.String> modifiedCytidylates

modifiedGuanylates

public static java.util.List<java.lang.String> modifiedGuanylates

modifiedInositates

public static java.util.List<java.lang.String> modifiedInositates

modifiedThymidylates

public static java.util.List<java.lang.String> modifiedThymidylates

modifiedUridylates

public static java.util.List<java.lang.String> modifiedUridylates

knownHetatms

public static java.util.List<java.lang.String> knownHetatms

residueNumber

public java.lang.Integer residueNumber

nextResidue

protected Residue nextResidue

previousResidue

protected Residue previousResidue

Constructor Detail

ResidueClass

public ResidueClass(ResidueType type)

ResidueClass

public ResidueClass(java.lang.String PdbLine)
             throws java.text.ParseException

Throws:

java.text.ParseException

Method Detail

getGlycosyl

public java.lang.String getGlycosyl()

setGlycosyl

public void setGlycosyl(java.lang.String glycosyl)

getPucker

public java.lang.String getPucker()

setPucker

public void setPucker(java.lang.String pucker)

matchesPdbLine

public boolean matchesPdbLine(java.lang.String PdbLine)
                       throws java.text.ParseException

Throws:

java.text.ParseException

atoms

public java.util.Set<Atom> atoms()

Override atoms() method to use a class that can index by atom name

Specified by:

atoms in interface Molecular

Overrides:

atoms in class MolecularClass

setNextResidue

public void setNextResidue(Residue r)

Specified by:

setNextResidue in interface Residue

setPreviousResidue

public void setPreviousResidue(Residue r)

Specified by:

setPreviousResidue in interface Residue

getNextResidue

public Residue getNextResidue()

Specified by:

getNextResidue in interface Residue

getPreviousResidue

public Residue getPreviousResidue()

Specified by:

getPreviousResidue in interface Residue

getResidueType

public ResidueType getResidueType()

Specified by:

getResidueType in interface Residue

secondaryStructures

public java.util.Collection<SecondaryStructure> secondaryStructures()

Specified by:

secondaryStructures in interface Residue

getHydrogenBondDonors

public java.util.Set<Atom> getHydrogenBondDonors()

Specified by:

getHydrogenBondDonors in interface Residue

getHydrogenBondAcceptors

public java.util.Set<Atom> getHydrogenBondAcceptors()

Specified by:

getHydrogenBondAcceptors in interface Residue

getHydrogenBondDonorAtomNames

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

Specified by:

getHydrogenBondDonorAtomNames in interface ResidueType

getHydrogenBondAcceptorAtomNames

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

Specified by:

getHydrogenBondAcceptorAtomNames in interface ResidueType

getBackbonePosition

public Vector3D getBackbonePosition()
                             throws InsufficientAtomsException

Return preferred location of backbone trace in molecular representations

Specified by:

getBackbonePosition in interface Residue

Throws:

InsufficientAtomsException

getSideChainPosition

public Vector3D getSideChainPosition()
                              throws InsufficientAtomsException

Specified by:

getSideChainPosition in interface Residue

Throws:

InsufficientAtomsException

getOneLetterCode

public final char getOneLetterCode()

Create an empty Residue object with no atoms.

Specified by:

getOneLetterCode in interface ResidueType

getResidueName

public final java.lang.String getResidueName()

Specified by:

getResidueName in interface ResidueType

genericBonds

public java.util.Map<java.lang.String,java.util.Set<java.lang.String>> genericBonds()

Specified by:

genericBonds in interface ResidueType

getThreeLetterCode

public final java.lang.String getThreeLetterCode()

Specified by:

getThreeLetterCode in interface ResidueType

get

public Molecular get(FunctionalGroup fg)
              throws InsufficientAtomsException

Specified by:

get in interface Residue

Throws:

InsufficientAtomsException

getPdbInsertionCode

public char getPdbInsertionCode()

Specified by:

getPdbInsertionCode in interface Residue

Returns:

Returns the insertionCode.

setPdbInsertionCode

public void setPdbInsertionCode(char insertionCode)

Parameters:

insertionCode - The insertionCode to set.

getResidueNumber

public int getResidueNumber()

Specified by:

getResidueNumber in interface Residue

Returns:

Returns the residueNumber.

setResidueNumber

public void setResidueNumber(int residueNumber)

Specified by:

setResidueNumber in interface Residue

Parameters:

residueNumber - The residueNumber to set.

getAtom

public Atom getAtom(java.lang.String atomName)

Get the atom with the given name. If there are atoms with alternate locations, the first such atom is returned. If the atom name argument includes an alternate location character, the atom at that particular location is returned.

Specified by:

getAtom in interface Residue

Parameters:

atomName -

Returns:

the first atom found with the given name, or null if there is no such atom

isSolvent

public static boolean isSolvent(java.lang.String residueName)

isProtein

public static boolean isProtein(java.lang.String residueName)

isNucleicAcid

public static boolean isNucleicAcid(java.lang.String residueName)

isKnownHetatm

public static boolean isKnownHetatm(java.lang.String residueName)

isDNA

public static boolean isDNA(java.lang.String residueName)

isRNA

public static boolean isRNA(java.lang.String residueName)

isStrand

public boolean isStrand()

Specified by:

isStrand in interface Residue

isHelix

public boolean isHelix()

Specified by:

isHelix in interface Residue

isAlphaHelix

public boolean isAlphaHelix()

Specified by:

isAlphaHelix in interface Residue

updateAtomPosition

public void updateAtomPosition(Atom atom)

Specified by:

updateAtomPosition in interface Residue