public class ScopDomain extends java.lang.Object implements java.io.Serializable, java.lang.Cloneable, StructureIdentifier
Constructor and Description |
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ScopDomain() |
Modifier and Type | Method and Description |
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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()
The unique identifier, using the following formal specification:
|
java.lang.String |
getPdbId()
Returns the PDB identifier associated with this StructureIdentifier.
|
int |
getPx() |
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.String |
getScopId() |
int |
getSpeciesId() |
java.lang.Integer |
getSunid() |
int |
getSuperfamilyId() |
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) |
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()
StructureIdentifier
getPdbId
in interface StructureIdentifier
public void setPdbId(java.lang.String pdbId)
public java.util.List<java.lang.String> getRanges()
StructureIdentifier
StructureIdentifier.getIdentifier()
. For example:
getRanges().get(0): 'A' getRanges().get(1): 'B_5-100'This is a unique representation.
getRanges
in interface StructureIdentifier
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
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 partsMore options may be added to the specification at a future time.
getIdentifier
in interface StructureIdentifier
public java.util.List<ResidueRange> getResidueRanges()
StructureIdentifier
ResidueRanges
that this StructureIdentifier defines.
This is a unique representation.getResidueRanges
in interface StructureIdentifier