org.biojava.bio.structure.align.client

Class StructureName

java.lang.Object

org.biojava.bio.structure.align.client.StructureName

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<StructureName>, StructureIdentifier

public class StructureName
extends java.lang.Object
implements java.lang.Comparable<StructureName>, java.io.Serializable, StructureIdentifier

A utility class that makes working with names of structures, domains and ranges easier.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	chainId
protected java.lang.String	name
protected java.lang.String	pdbId

Constructor Summary

Constructors

Constructor and Description
StructureName(java.lang.String name)

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(StructureName o)
boolean	equals(java.lang.Object obj)
java.lang.String	getChainId()
java.lang.String	getIdentifier() The unique identifier, using the following formal specification:
java.lang.String	getName()
java.lang.String	getPdbId() PDB IDs are always returned as upper case
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.
boolean	hasChainID()
int	hashCode()
boolean	hasRanges()
boolean	isCathID()
boolean	isPdbId()
boolean	isPDPDomain()
boolean	isScopName()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

name

protected java.lang.String name

pdbId

protected java.lang.String pdbId

chainId

protected java.lang.String chainId

Constructor Detail

StructureName

public StructureName(java.lang.String name)

Method Detail

getPdbId

public java.lang.String getPdbId()

PDB IDs are always returned as upper case

Specified by:

getPdbId in interface StructureIdentifier

Returns:

upper case PDB ID

getChainId

public java.lang.String getChainId()

getName

public java.lang.String getName()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isScopName

public boolean isScopName()

hasChainID

public boolean hasChainID()

isPDPDomain

public boolean isPDPDomain()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

compareTo

public int compareTo(StructureName o)

Specified by:

compareTo in interface java.lang.Comparable<StructureName>

isCathID

public boolean isCathID()

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

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

hasRanges

public boolean hasRanges()

isPdbId

public boolean isPdbId()