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

All Methods Instance Methods Concrete Methods Deprecated Methods
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 Detail
  - ScopDomain
```
public ScopDomain()
```
- Method Detail
  - 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
    
    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 ScopDomain

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ScopDomain

Method Detail

toString

getScopId

setScopId

getPdbId

setPdbId

setPdbId

getRanges

setRanges

getClassificationId

setClassificationId

getSunid

setSunid

getClassId

setClassId

getFoldId

setFoldId

getSuperfamilyId

setSuperfamilyId

getFamilyId

setFamilyId

getDomainId

setDomainId

getSpeciesId

setSpeciesId

getPx

setPx

clone

getChains

getIdentifier

getResidueRanges

toCanonical

reduce

loadStructure