Package org.biojava.nbio.structure.cath

Class CathDomain

java.lang.Object

org.biojava.nbio.structure.cath.CathDomain

All Implemented Interfaces:

Serializable, StructureIdentifier

public class CathDomain
extends Object
implements Serializable, StructureIdentifier

A class which represents a single CATH domain.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final long	serialVersionUID

Constructor Summary

Constructors

Constructor	Description
CathDomain()

Method Summary

Modifier and Type	Method	Description
Integer	getArchitectureId()
String	getCATH()
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.
Integer	getClassId()
Integer	getClassificationId(CathCategory cathCategory)
String	getComment()
Date	getDate()
Integer	getDomainCounter()
Integer	getDomainId()
String	getDomainName()
String	getFormat()
Integer	getHomologyId()
Integer	getIdenticalSequenceFamilyId()
String	getIdentifier()	Get the String form of this identifier.
Integer	getLength()
Integer	getLikeSequenceFamilyId()
String	getName()
Integer	getOrthologousSequenceFamilyId()
String	getPdbIdAndChain()	Returns a string of the form PDBID.CHAIN.
Double	getResolution()
List<CathSegment>	getSegments()
String	getSequence()
Integer	getSequenceFamilyId()
String	getSequenceHeader()
String	getSOILD()
String	getSource()
String	getThePdbId()	Returns the PDB ID.
Integer	getTopologyId()
String	getVersion()
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	setArchitectureId(Integer architectureId)
void	setCATH(String cathCode)
void	setClassId(Integer classId)
void	setComment(String comment)
void	setDate(Date date)
void	setDomainCounter(Integer domainCounter)
void	setDomainName(String domainName)
void	setFormat(String format)
void	setHomologyId(Integer homologyId)
void	setIdenticalSequenceFamilyId(Integer identicalSequenceFamilyId)
void	setLength(Integer length)
void	setLikeSequenceFamilyId(Integer likeSequenceFamilyId)
void	setName(String name)
void	setOrthologousSequenceFamilyId(Integer orthologousSequenceFamilyId)
void	setResolution(Double resolution)
void	setSegments(List<CathSegment> segments)
void	setSequence(String sequence)
void	setSequenceFamilyId(Integer sequenceFamilyId)
void	setSequenceHeader(String sequenceHeader)
void	setSOLID(String cathCode)
void	setSource(String source)
void	setTopologyId(Integer topologyId)
void	setVersion(String version)
SubstructureIdentifier	toCanonical()	Convert to a canonical SubstructureIdentifier.
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

serialVersionUID

public static final long serialVersionUID

See Also:

• Constant Field Values

Constructor Details

CathDomain

public CathDomain()

Method Details

getDomainName

public String getDomainName()

setDomainName

public void setDomainName(String domainName)

getThePdbId

public String getThePdbId()

Returns the PDB ID.

getPdbIdAndChain

public String getPdbIdAndChain()

Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.

getDomainId

public Integer getDomainId()

getClassId

public Integer getClassId()

setClassId

public void setClassId(Integer classId)

getArchitectureId

public Integer getArchitectureId()

setArchitectureId

public void setArchitectureId(Integer architectureId)

getTopologyId

public Integer getTopologyId()

setTopologyId

public void setTopologyId(Integer topologyId)

getHomologyId

public Integer getHomologyId()

setHomologyId

public void setHomologyId(Integer homologyId)

getSequenceFamilyId

public Integer getSequenceFamilyId()

setSequenceFamilyId

public void setSequenceFamilyId(Integer sequenceFamilyId)

getOrthologousSequenceFamilyId

public Integer getOrthologousSequenceFamilyId()

setOrthologousSequenceFamilyId

public void setOrthologousSequenceFamilyId(Integer orthologousSequenceFamilyId)

getLikeSequenceFamilyId

public Integer getLikeSequenceFamilyId()

setLikeSequenceFamilyId

public void setLikeSequenceFamilyId(Integer likeSequenceFamilyId)

getIdenticalSequenceFamilyId

public Integer getIdenticalSequenceFamilyId()

setIdenticalSequenceFamilyId

public void setIdenticalSequenceFamilyId(Integer identicalSequenceFamilyId)

getDomainCounter

public Integer getDomainCounter()

setDomainCounter

public void setDomainCounter(Integer domainCounter)

getLength

public Integer getLength()

setLength

public void setLength(Integer length)

getResolution

public Double getResolution()

setResolution

public void setResolution(Double resolution)

setCATH

public void setCATH(String cathCode)

getCATH

public String getCATH()

setSOLID

public void setSOLID(String cathCode)

getSOILD

public String getSOILD()

getClassificationId

public Integer getClassificationId(CathCategory cathCategory)

getFormat

public String getFormat()

setFormat

public void setFormat(String format)

getVersion

public String getVersion()

setVersion

public void setVersion(String version)

getDate

public Date getDate()

setDate

public void setDate(Date date)

getName

public String getName()

setName

public void setName(String name)

getSource

public String getSource()

setSource

public void setSource(String source)

getSequenceHeader

public String getSequenceHeader()

setSequenceHeader

public void setSequenceHeader(String sequenceHeader)

getSequence

public String getSequence()

setSequence

public void setSequence(String sequence)

getSegments

public List<CathSegment> getSegments()

setSegments

public void setSegments(List<CathSegment> segments)

getComment

public String getComment()

setComment

public void setComment(String comment)

toString

public String toString()

Overrides:

toString in class Object

getChains

public Set<String> getChains()
                      throws StructureException

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

Throws:

StructureException

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

toCanonical

public SubstructureIdentifier toCanonical()
                                   throws StructureException

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

Throws:

StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

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