PIP.Core
Class Residue

java.lang.Object
  PIP.Core.Residue

All Implemented Interfaces:

java.io.Serializable, MSDID, Spatial

public class Residue
extends java.lang.Object
implements Spatial, java.io.Serializable, MSDID

See Also:

Serialized Form

Constructor Summary

Residue(int id)

Method Summary

void	addAtom(Atom a)
boolean	doesResidueHaveCAAtom()
Atom	getAtomOfName(java.lang.String name)
java.util.List<Atom>	getAtoms()
Chain	getChain()
char	getCode()
float[]	getCoordinates()
int	getMSDID()
java.lang.String	getPDBOriginalCode()
int	getPDBSeq()
ResidueName	getResName() This attribute provides a code from the chem comp dictionary for standard residues.
int	getResPosInChainWithStructuralCoordinates()
int	getResPosInDomain(Domain d)
int	getResPosInDomainFromResiduesWithStructuralCoordinates(Domain d)
int	getResPosition()
char	getSecStruct()
int	getSPSerial()
boolean	hasStructuralInfo()
boolean	isBound()
boolean	isResidue()
boolean	isWater()
void	setAtoms(java.util.List<Atom> atoms)
void	setChain(Chain chain)
void	setCode(char code)
void	setMSDID(int id)
void	setPDBOriginalAltCode(java.lang.String string)
void	setPDBOriginalCode(java.lang.String PDBOriginalCode)
void	setPDBSeq(int anInt)
void	setResName(ResidueName resName) This attribute provides a code from the chem comp dictionary for standard residues.
void	setResPosition(int resPosition)
void	setSecStruct(char secStruct)
void	setSPSerial(int SPSerial)
void	setWBR(char WBRC)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Residue

public Residue(int id)

Method Detail

getMSDID

public int getMSDID()

Specified by:

getMSDID in interface MSDID

Returns:

The id of the Residue within the MSD. It can be used to link back to the MSD

setMSDID

public void setMSDID(int id)

Specified by:

setMSDID in interface MSDID

Parameters:

id - - The id of the Residue within the MSD. It can be used to link back to the MSD

getResPosition

public int getResPosition()

Returns:

the res position in the chain as per the MSD

getResPosInDomain

public int getResPosInDomain(Domain d)

Parameters:

d - - the domain that the residue is contained within

Returns:

the position of the residue within the domain passed in

getResPosInChainWithStructuralCoordinates

public int getResPosInChainWithStructuralCoordinates()

Returns:

the position of the residue within the chain to which it belongs for residues which have structural coordinates

getResPosInDomainFromResiduesWithStructuralCoordinates

public int getResPosInDomainFromResiduesWithStructuralCoordinates(Domain d)

hasStructuralInfo

public boolean hasStructuralInfo()

doesResidueHaveCAAtom

public boolean doesResidueHaveCAAtom()

setResPosition

public void setResPosition(int resPosition)

getResName

public ResidueName getResName()

This attribute provides a code from the chem comp dictionary for standard residues. This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA. All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.

Returns:

3 letter code of Residue name

setResName

public void setResName(ResidueName resName)

This attribute provides a code from the chem comp dictionary for standard residues. This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA. All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.

Parameters:

resName - - 3 letter code of Residue name

getChain

public Chain getChain()

Returns:

a link to the chain that the residue belongs to

setChain

public void setChain(Chain chain)

Parameters:

chain - - the chain that the residue belongs to

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

"Residue: ID=" + msdid

getCode

public char getCode()

Returns:

One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences

setCode

public void setCode(char code)

Parameters:

code - - One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences

getSecStruct

public char getSecStruct()

Returns:

A symbol for the secondary structure as derived by DSSP B:bulge, C:coil, E:strand, G:3-10-helix, H:alpha-helix, S:bend, I:inverse-turn, T:beta-turn

setSecStruct

public void setSecStruct(char secStruct)

Parameters:

secStruct - - A symbol for the secondary structure as derived by DSSP B:bulge, C:coil, E:strand, G:3-10-helix, H:alpha-helix, S:bend, I:inverse-turn, T:beta-turn

addAtom

public void addAtom(Atom a)

getAtomOfName

public Atom getAtomOfName(java.lang.String name)

getAtoms

public java.util.List<Atom> getAtoms()

setWBR

public void setWBR(char WBRC)

Parameters:

WBRC - - The type of the component R:residue, B:bound molecule, W:water. This normally has to correspond with the type of the chain where there residue belongs

isWater

public boolean isWater()

Returns:

true if the residue is actually a water

isResidue

public boolean isResidue()

Returns:

true if the residue is actually a residue belonging to a polypeptide chain eg a Histidine instead of a metal ion

isBound

public boolean isBound()

Returns:

true if the residue is actually a ligand rather than a residue belonging to a polypeptide chain eg a metal ion instead of a Histidine

getCoordinates

public float[] getCoordinates()

Specified by:

getCoordinates in interface Spatial

Returns:

the coordinates for the average position of all of the atoms in the residue

setAtoms

public void setAtoms(java.util.List<Atom> atoms)

Parameters:

atoms - - The atoms which belong to the residue

setSPSerial

public void setSPSerial(int SPSerial)

Parameters:

SPSerial - - the position of the residue in the chain according to swissprot

getSPSerial

public int getSPSerial()

Returns:

the position of the residue in the chain according to swissprot

setPDBOriginalCode

public void setPDBOriginalCode(java.lang.String PDBOriginalCode)

Parameters:

PDBOriginalCode - - The 3 letter residue code as seen in the original PDB file

getPDBOriginalCode

public java.lang.String getPDBOriginalCode()

Returns:

The 3 letter residue code as seen in the original PDB file.

setPDBOriginalAltCode

public void setPDBOriginalAltCode(java.lang.String string)

setPDBSeq

public void setPDBSeq(int anInt)

getPDBSeq

public int getPDBSeq()