java.io.Serializable
, java.lang.Cloneable
, StructureIdentifier
public class ScopDomain extends java.lang.Object implements java.io.Serializable, java.lang.Cloneable, StructureIdentifier
ScopDatabase.getDomainByScopID(String)
Constructor | Description |
---|---|
ScopDomain() |
Modifier and Type | Method | Description |
---|---|---|
protected java.lang.Object |
clone() |
|
java.util.Set<java.lang.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() |
|
java.lang.String |
getClassificationId() |
|
int |
getDomainId() |
|
int |
getFamilyId() |
|
int |
getFoldId() |
|
java.lang.String |
getIdentifier() |
Get the String form of this identifier.
|
java.lang.String |
getPdbId() |
|
int |
getPx() |
|
java.util.List<java.lang.String> |
getRanges() |
|
java.util.List<ResidueRange> |
getResidueRanges() |
|
java.lang.String |
getScopId() |
|
int |
getSpeciesId() |
|
java.lang.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(java.lang.String classificationId) |
|
void |
setDomainId(int domainId) |
|
void |
setFamilyId(int familyId) |
|
void |
setFoldId(int foldId) |
|
void |
setPdbId(java.lang.String pdbId) |
|
void |
setPx(int px) |
|
void |
setRanges(java.util.List<java.lang.String> ranges) |
|
void |
setScopId(java.lang.String scopId) |
|
void |
setSpeciesId(int speciesId) |
|
void |
setSunid(java.lang.Integer sunid) |
|
void |
setSuperfamilyId(int superfamilyId) |
|
SubstructureIdentifier |
toCanonical() |
Convert to a canonical SubstructureIdentifier.
|
java.lang.String |
toString() |
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getScopId()
public void setScopId(java.lang.String scopId)
public java.lang.String getPdbId()
public void setPdbId(java.lang.String pdbId)
public java.util.List<java.lang.String> getRanges()
public void setRanges(java.util.List<java.lang.String> ranges)
public java.lang.String getClassificationId()
public void setClassificationId(java.lang.String classificationId)
public java.lang.Integer getSunid()
public void setSunid(java.lang.Integer sunid)
public int getClassId()
public void setClassId(int classId)
public int getFoldId()
public void setFoldId(int foldId)
public int getSuperfamilyId()
public void setSuperfamilyId(int superfamilyId)
public int getFamilyId()
public void setFamilyId(int familyId)
public int getDomainId()
public void setDomainId(int domainId)
public int getSpeciesId()
public void setSpeciesId(int speciesId)
public int getPx()
public void setPx(int px)
protected java.lang.Object clone() throws java.lang.CloneNotSupportedException
clone
in class java.lang.Object
java.lang.CloneNotSupportedException
public java.util.Set<java.lang.String> getChains()
public java.lang.String getIdentifier()
StructureIdentifier
#toString()
method also return the
identifier, for consistency during serialization.getIdentifier
in interface StructureIdentifier
public java.util.List<ResidueRange> getResidueRanges()
public SubstructureIdentifier toCanonical()
StructureIdentifier
This allows all domains to be converted to a standard format String.
toCanonical
in interface StructureIdentifier
public Structure reduce(Structure input) throws StructureException
StructureIdentifier
The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
reduce
in interface StructureIdentifier
input
- A full structure, e.g. as loaded from the PDB. The structure
ID should match that returned by getPdbId(), if applicable.StructureException
StructureTools.getReducedStructure(Structure, String)
public Structure loadStructure(AtomCache cache) throws StructureException, java.io.IOException
StructureIdentifier
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.loadStructure
in interface StructureIdentifier
StructureException
- For errors loading and parsing the structurejava.io.IOException
- Errors reading the structure from disk