CathDomain (biojava 4.2.1 API)

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 and Description

static long serialVersionUID

Fields
Modifier and Type	Field and Description
`static long`	`serialVersionUID`

Constructor Summary

Constructors
Constructor and Description

CathDomain()

Constructors
Constructor and Description
`CathDomain()`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and 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`	`getPdbId()` Deprecated. This method is poorly named; use `getThePdbId()` or `getPdbIdAndChain()` instead
`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 Detail
  - serialVersionUID
```
public static final long serialVersionUID
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - CathDomain
```
public CathDomain()
```
- Method Detail
  - getDomainName
```
public String getDomainName()
```
  - setDomainName
```
public void setDomainName(String domainName)
```
  - getPdbId
```
@Deprecated
public String getPdbId()
```
    Deprecated. This method is poorly named; use getThePdbId() or getPdbIdAndChain() instead
    
    Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.
  - 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()
```
    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
  - 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
    
    See Also:
    
    StructureTools.getReducedStructure(Structure, String)
  - 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
    
    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

Class CathDomain

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

Constructor Detail

CathDomain

Method Detail

getDomainName

setDomainName

getPdbId

getThePdbId

getPdbIdAndChain

getDomainId

getClassId

setClassId

getArchitectureId

setArchitectureId

getTopologyId

setTopologyId

getHomologyId

setHomologyId

getSequenceFamilyId

setSequenceFamilyId

getOrthologousSequenceFamilyId

setOrthologousSequenceFamilyId

getLikeSequenceFamilyId

setLikeSequenceFamilyId

getIdenticalSequenceFamilyId

setIdenticalSequenceFamilyId

getDomainCounter

setDomainCounter

getLength

setLength

getResolution

setResolution

setCATH

getCATH

setSOLID

getSOILD

getClassificationId

getFormat

setFormat

getVersion

setVersion

getDate

setDate

getName

setName

getSource

setSource

getSequenceHeader

setSequenceHeader

getSequence

setSequence

getSegments

setSegments

getComment

setComment

toString

getChains

getIdentifier

toCanonical

reduce

loadStructure