CathDomain (biojava-structure 4.0.0 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

Methods
Modifier and Type	Method and Description
`Integer`	`getArchitectureId()`
`String`	`getCATH()`
`Integer`	`getClassId()`
`Integer`	`getClassificationId(CathCategory cathCategory)`
`String`	`getComment()`
`Date`	`getDate()`
`Integer`	`getDomainCounter()`
`Integer`	`getDomainId()`
`String`	`getDomainName()`
`String`	`getFormat()`
`Integer`	`getHomologyId()`
`Integer`	`getIdenticalSequenceFamilyId()`
`String`	`getIdentifier()` The unique identifier, using the following formal specification:
`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`.
`List<String>`	`getRanges()` Returns a list of ranges of the form described in `StructureIdentifier.getIdentifier()`.
`List<ResidueRange>`	`getResidueRanges()` Returns the list of `ResidueRanges` that this StructureIdentifier defines.
`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()`
`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)`
`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.

Specified by:

getPdbId in interface StructureIdentifier

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

getIdentifier

public String getIdentifier()

Description copied from interface: StructureIdentifier

The unique identifier, using the following formal specification:

                name     := pdbID
                               | pdbID '.' chainID
                               | pdbID '.' range
                               | scopID
                range         := '('? range (',' range)? ')'?
                               | chainID
                               | chainID '_' resNum '-' resNum
                pdbID         := [0-9][a-zA-Z0-9]{3}
                chainID       := [a-zA-Z0-9]
                scopID        := 'd' pdbID [a-z_][0-9_]
                cathID        := pdbID [A-Z][0-9]{2}
                resNum        := [-+]?[0-9]+[A-Za-z]?

For example:

                1TIM                            #whole structure
                1tim                            #same as above
                4HHB.C                          #single chain
                3AA0.A,B                        #two chains
                d2bq6a1                         #SCOP domain
      1cukA01                         #CATH domain
                4GCR.A_1-40                     #substructure
      3iek.A_17-28,A_56-294,A_320-377 #substructure of 3 disjoint parts

More options may be added to the specification at a future time.

Specified by:: getIdentifier in interface StructureIdentifier

getResidueRanges
```
public List<ResidueRange> getResidueRanges()
```
Description copied from interface: StructureIdentifier

Returns the list of ResidueRanges that this StructureIdentifier defines. This is a unique representation.

Specified by:

getResidueRanges in interface StructureIdentifier

getRanges
```
public List<String> getRanges()
```
Description copied from interface: StructureIdentifier
Returns a list of ranges of the form described in StructureIdentifier.getIdentifier(). For example:
```
 getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
 
```
This is a unique representation.
Specified by:

getRanges in interface StructureIdentifier

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

getIdentifier

getResidueRanges

getRanges