public class SubstructureIdentifier extends java.lang.Object implements StructureIdentifier
Structure
.Constructor and Description |
---|
SubstructureIdentifier(java.lang.String id,
AtomCache cache) |
SubstructureIdentifier(java.lang.String pdbId,
java.util.List<ResidueRange> ranges) |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
getIdentifier()
The unique identifier, using the following formal specification:
|
java.lang.String |
getPdbId()
Returns the PDB identifier associated with this StructureIdentifier.
|
java.util.List<java.lang.String> |
getRanges()
Returns a list of ranges of the form described in
StructureIdentifier.getIdentifier() . |
java.util.List<? extends ResidueRange> |
getResidueRanges()
Returns the list of
ResidueRanges that this StructureIdentifier defines. |
java.lang.String |
toString() |
public SubstructureIdentifier(java.lang.String pdbId, java.util.List<ResidueRange> ranges)
public SubstructureIdentifier(java.lang.String id, AtomCache cache) throws java.io.IOException, StructureException
java.io.IOException
StructureException
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.lang.String getPdbId()
StructureIdentifier
getPdbId
in interface StructureIdentifier
public java.util.List<? extends ResidueRange> getResidueRanges()
StructureIdentifier
ResidueRanges
that this StructureIdentifier defines.
This is a unique representation.getResidueRanges
in interface StructureIdentifier
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 java.lang.String toString()
toString
in class java.lang.Object