Package org.biojava.nbio.structure.scop

Class ScopDomain

java.lang.Object

org.biojava.nbio.structure.scop.ScopDomain

All Implemented Interfaces:

Serializable, Cloneable, StructureIdentifier

public class ScopDomain
extends Object
implements Serializable, Cloneable, StructureIdentifier

Container for the information for a domain. Contains a line in the file dir.cla.scop.txt_1.75 e.g d1dlwa_ 1dlw A: a.1.1.1 14982 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46461,px=14982 Instantiated using ScopDatabase.getDomainByScopID(String)

Author:

Andreas Prlic

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
ScopDomain()

Method Summary

Modifier and Type	Method	Description
protected Object	clone()
Set<String>	getChains()	Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
int	getClassId()
String	getClassificationId()
int	getDomainId()
int	getFamilyId()
int	getFoldId()
String	getIdentifier()	Get the String form of this identifier.
PdbId	getPdbId()	Gets the PDB identifier for this protein structure.
int	getPx()
List<String>	getRanges()
List<ResidueRange>	getResidueRanges()
String	getScopId()
int	getSpeciesId()
Integer	getSunid()
int	getSuperfamilyId()
Structure	loadStructure(AtomCache cache)	Loads a structure encompassing the structure identified.
Structure	reduce(Structure input)	Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
void	setClassId(int classId)
void	setClassificationId(String classificationId)
void	setDomainId(int domainId)
void	setFamilyId(int familyId)
void	setFoldId(int foldId)
void	setPdbId(String pdbId)	Deprecated. use setPdbId(PdbId)
void	setPdbId(PdbId pdbId)
void	setPx(int px)
void	setRanges(List<String> ranges)
void	setScopId(String scopId)
void	setSpeciesId(int speciesId)
void	setSunid(Integer sunid)
void	setSuperfamilyId(int superfamilyId)
SubstructureIdentifier	toCanonical()	Convert to a canonical SubstructureIdentifier.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

ScopDomain

public ScopDomain()

Method Details

toString

public String toString()

Overrides:

toString in class Object

getScopId

public String getScopId()

setScopId

public void setScopId(String scopId)

getPdbId

public PdbId getPdbId()

Gets the PDB identifier for this protein structure. Before BioJava 6.0.0, this method used to return a String.

Returns:

the PdbId PDB identifier

Since:

6.0.0

See Also:

• setPdbId(PdbId)

setPdbId

@Deprecated
public void setPdbId(String pdbId)

Deprecated.

use setPdbId(PdbId)

Parameters:

pdbId -

setPdbId

public void setPdbId(PdbId pdbId)

Parameters:

pdbId -

Since:

6.0.0

getRanges

public List<String> getRanges()

setRanges

public void setRanges(List<String> ranges)

getClassificationId

public String getClassificationId()

setClassificationId

public void setClassificationId(String classificationId)

getSunid

public Integer getSunid()

setSunid

public void setSunid(Integer sunid)

getClassId

public int getClassId()

setClassId

public void setClassId(int classId)

getFoldId

public int getFoldId()

setFoldId

public void setFoldId(int foldId)

getSuperfamilyId

public int getSuperfamilyId()

setSuperfamilyId

public void setSuperfamilyId(int superfamilyId)

getFamilyId

public int getFamilyId()

setFamilyId

public void setFamilyId(int familyId)

getDomainId

public int getDomainId()

setDomainId

public void setDomainId(int domainId)

getSpeciesId

public int getSpeciesId()

setSpeciesId

public void setSpeciesId(int speciesId)

getPx

public int getPx()

setPx

public void setPx(int px)

clone

protected Object clone()
                throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

getChains

public Set<String> getChains()

Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.

getIdentifier

public String getIdentifier()

Description copied from interface: StructureIdentifier

Get the String form of this identifier. It is recommended that the toString() method also return the identifier, for consistency during serialization.

Specified by:

getIdentifier in interface StructureIdentifier

Returns:

The String form of this identifier

getResidueRanges

public List<ResidueRange> getResidueRanges()

toCanonical

public SubstructureIdentifier toCanonical()

Description copied from interface: StructureIdentifier

Convert to a canonical SubstructureIdentifier.

This allows all domains to be converted to a standard format String.

Specified by:

toCanonical in interface StructureIdentifier

Returns:

A SubstructureIdentifier equivalent to this

reduce

public Structure reduce(Structure input)
                 throws StructureException

Description copied from interface: StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

Specified by:

reduce in interface StructureIdentifier

Parameters:

input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.

Returns:

Throws:

StructureException

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws StructureException,
IOException

Description copied from interface: StructureIdentifier

Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure).

It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.

Specified by:

loadStructure in interface StructureIdentifier

Parameters:

cache - A potential sources of structures

Returns:

A Structure containing at least the atoms identified by this, or null if Structures are not applicable.

Throws:

StructureException - For errors loading and parsing the structure

IOException - Errors reading the structure from disk