Package org.biojava.nbio.structure.scop
Class ScopDomain
- java.lang.Object
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- org.biojava.nbio.structure.scop.ScopDomain
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- 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 usingScopDatabase.getDomainByScopID(String)
- Author:
- Andreas Prlic
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description ScopDomain()
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Method Summary
All Methods Instance Methods Concrete 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.String
getPdbId()
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)
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()
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Constructor Detail
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ScopDomain
public ScopDomain()
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Method Detail
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getClassificationId
public String getClassificationId()
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setClassificationId
public void setClassificationId(String classificationId)
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getClassId
public int getClassId()
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setClassId
public void setClassId(int classId)
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getFoldId
public int getFoldId()
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setFoldId
public void setFoldId(int foldId)
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getSuperfamilyId
public int getSuperfamilyId()
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setSuperfamilyId
public void setSuperfamilyId(int superfamilyId)
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getFamilyId
public int getFamilyId()
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setFamilyId
public void setFamilyId(int familyId)
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getDomainId
public int getDomainId()
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setDomainId
public void setDomainId(int domainId)
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getSpeciesId
public int getSpeciesId()
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setSpeciesId
public void setSpeciesId(int speciesId)
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getPx
public int getPx()
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setPx
public void setPx(int px)
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clone
protected Object clone() throws CloneNotSupportedException
- Overrides:
clone
in classObject
- Throws:
CloneNotSupportedException
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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.
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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 interfaceStructureIdentifier
- Returns:
- The String form of this identifier
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getResidueRanges
public List<ResidueRange> getResidueRanges()
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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 interfaceStructureIdentifier
- Returns:
- A SubstructureIdentifier equivalent to this
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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 interfaceStructureIdentifier
- 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)
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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 toStructureIdentifier.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 interfaceStructureIdentifier
- 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 structureIOException
- Errors reading the structure from disk
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