org.biojava.nbio.structure.scop

Class ScopDomain

java.lang.Object

org.biojava.nbio.structure.scop.ScopDomain

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, StructureIdentifier

public class ScopDomain
extends java.lang.Object
implements java.io.Serializable, java.lang.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

Author:

Andreas Prlic

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ScopDomain()

Method Summary

Methods

Modifier and Type	Method and 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() 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()

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 java.lang.String toString()

Overrides:

toString in class java.lang.Object

getScopId

public java.lang.String getScopId()

setScopId

public void setScopId(java.lang.String scopId)

getPdbId

public java.lang.String getPdbId()

Description copied from interface: StructureIdentifier

Returns the PDB identifier associated with this StructureIdentifier.

Specified by:

getPdbId in interface StructureIdentifier

setPdbId

public void setPdbId(java.lang.String pdbId)

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

setRanges

public void setRanges(java.util.List<java.lang.String> ranges)

getClassificationId

public java.lang.String getClassificationId()

setClassificationId

public void setClassificationId(java.lang.String classificationId)

getSunid

public java.lang.Integer getSunid()

setSunid

public void setSunid(java.lang.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 java.lang.Object clone()
                          throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

getChains

public 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.

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