CathDomain

java.lang.Object
- org.biojava.nbio.structure.cath.CathDomain

All Implemented Interfaces:

java.io.Serializable, StructureIdentifier
```
public class CathDomain
extends java.lang.Object
implements java.io.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
`java.lang.Integer`	`getArchitectureId()`
`java.lang.String`	`getCATH()`
`java.lang.Integer`	`getClassId()`
`java.lang.Integer`	`getClassificationId(CathCategory cathCategory)`
`java.lang.String`	`getComment()`
`java.util.Date`	`getDate()`
`java.lang.Integer`	`getDomainCounter()`
`java.lang.Integer`	`getDomainId()`
`java.lang.String`	`getDomainName()`
`java.lang.String`	`getFormat()`
`java.lang.Integer`	`getHomologyId()`
`java.lang.Integer`	`getIdenticalSequenceFamilyId()`
`java.lang.String`	`getIdentifier()` The unique identifier, using the following formal specification:
`java.lang.Integer`	`getLength()`
`java.lang.Integer`	`getLikeSequenceFamilyId()`
`java.lang.String`	`getName()`
`java.lang.Integer`	`getOrthologousSequenceFamilyId()`
`java.lang.String`	`getPdbId()` Deprecated. This method is poorly named; use `getThePdbId()` or `getPdbIdAndChain()` instead
`java.lang.String`	`getPdbIdAndChain()` Returns a string of the form `PDBID.CHAIN`.
`java.util.List<java.lang.String>`	`getRanges()` Returns a list of ranges of the form described in `StructureIdentifier.getIdentifier()`.
`java.util.List<ResidueRange>`	`getResidueRanges()` Returns the list of `ResidueRanges` that this StructureIdentifier defines.
`java.lang.Double`	`getResolution()`
`java.util.List<CathSegment>`	`getSegments()`
`java.lang.String`	`getSequence()`
`java.lang.Integer`	`getSequenceFamilyId()`
`java.lang.String`	`getSequenceHeader()`
`java.lang.String`	`getSOILD()`
`java.lang.String`	`getSource()`
`java.lang.String`	`getThePdbId()` Returns the PDB ID.
`java.lang.Integer`	`getTopologyId()`
`java.lang.String`	`getVersion()`
`void`	`setArchitectureId(java.lang.Integer architectureId)`
`void`	`setCATH(java.lang.String cathCode)`
`void`	`setClassId(java.lang.Integer classId)`
`void`	`setComment(java.lang.String comment)`
`void`	`setDate(java.util.Date date)`
`void`	`setDomainCounter(java.lang.Integer domainCounter)`
`void`	`setDomainName(java.lang.String domainName)`
`void`	`setFormat(java.lang.String format)`
`void`	`setHomologyId(java.lang.Integer homologyId)`
`void`	`setIdenticalSequenceFamilyId(java.lang.Integer identicalSequenceFamilyId)`
`void`	`setLength(java.lang.Integer length)`
`void`	`setLikeSequenceFamilyId(java.lang.Integer likeSequenceFamilyId)`
`void`	`setName(java.lang.String name)`
`void`	`setOrthologousSequenceFamilyId(java.lang.Integer orthologousSequenceFamilyId)`
`void`	`setResolution(java.lang.Double resolution)`
`void`	`setSegments(java.util.List<CathSegment> segments)`
`void`	`setSequence(java.lang.String sequence)`
`void`	`setSequenceFamilyId(java.lang.Integer sequenceFamilyId)`
`void`	`setSequenceHeader(java.lang.String sequenceHeader)`
`void`	`setSOLID(java.lang.String cathCode)`
`void`	`setSource(java.lang.String source)`
`void`	`setTopologyId(java.lang.Integer topologyId)`
`void`	`setVersion(java.lang.String version)`
`java.lang.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 java.lang.String getDomainName()

setDomainName

public void setDomainName(java.lang.String domainName)

getPdbId
```
@Deprecated
public java.lang.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 java.lang.String getThePdbId()
```
Returns the PDB ID.

getPdbIdAndChain
```
public java.lang.String getPdbIdAndChain()
```
Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.

getDomainId

public java.lang.Integer getDomainId()

getClassId
```
public java.lang.Integer getClassId()
```

setClassId

public void setClassId(java.lang.Integer classId)

getArchitectureId

public java.lang.Integer getArchitectureId()

setArchitectureId

public void setArchitectureId(java.lang.Integer architectureId)

getTopologyId

public java.lang.Integer getTopologyId()

setTopologyId

public void setTopologyId(java.lang.Integer topologyId)

getHomologyId

public java.lang.Integer getHomologyId()

setHomologyId

public void setHomologyId(java.lang.Integer homologyId)

getSequenceFamilyId

public java.lang.Integer getSequenceFamilyId()

setSequenceFamilyId

public void setSequenceFamilyId(java.lang.Integer sequenceFamilyId)

getOrthologousSequenceFamilyId

public java.lang.Integer getOrthologousSequenceFamilyId()

setOrthologousSequenceFamilyId

public void setOrthologousSequenceFamilyId(java.lang.Integer orthologousSequenceFamilyId)

getLikeSequenceFamilyId

public java.lang.Integer getLikeSequenceFamilyId()

setLikeSequenceFamilyId

public void setLikeSequenceFamilyId(java.lang.Integer likeSequenceFamilyId)

getIdenticalSequenceFamilyId

public java.lang.Integer getIdenticalSequenceFamilyId()

setIdenticalSequenceFamilyId

public void setIdenticalSequenceFamilyId(java.lang.Integer identicalSequenceFamilyId)

getDomainCounter

public java.lang.Integer getDomainCounter()

setDomainCounter

public void setDomainCounter(java.lang.Integer domainCounter)

getLength
```
public java.lang.Integer getLength()
```

setLength

public void setLength(java.lang.Integer length)

getResolution

public java.lang.Double getResolution()

setResolution

public void setResolution(java.lang.Double resolution)

setCATH

public void setCATH(java.lang.String cathCode)

getCATH
```
public java.lang.String getCATH()
```

setSOLID

public void setSOLID(java.lang.String cathCode)

getSOILD
```
public java.lang.String getSOILD()
```

getClassificationId

public java.lang.Integer getClassificationId(CathCategory cathCategory)

getFormat
```
public java.lang.String getFormat()
```

setFormat

public void setFormat(java.lang.String format)

getVersion
```
public java.lang.String getVersion()
```

setVersion

public void setVersion(java.lang.String version)

getDate
```
public java.util.Date getDate()
```

setDate

public void setDate(java.util.Date date)

getName
```
public java.lang.String getName()
```

setName

public void setName(java.lang.String name)

getSource
```
public java.lang.String getSource()
```

setSource

public void setSource(java.lang.String source)

getSequenceHeader

public java.lang.String getSequenceHeader()

setSequenceHeader

public void setSequenceHeader(java.lang.String sequenceHeader)

getSequence
```
public java.lang.String getSequence()
```

setSequence

public void setSequence(java.lang.String sequence)

getSegments

public java.util.List<CathSegment> getSegments()

setSegments

public void setSegments(java.util.List<CathSegment> segments)

getComment
```
public java.lang.String getComment()
```

setComment

public void setComment(java.lang.String comment)

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

getIdentifier

public java.lang.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 java.util.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 java.util.List<java.lang.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