Class PDPDomain
- java.lang.Object
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- org.biojava.nbio.structure.domain.PDPDomain
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- All Implemented Interfaces:
java.io.Serializable
,StructureIdentifier
public class PDPDomain extends java.lang.Object implements StructureIdentifier
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static java.util.regex.Pattern
PDP_NAME_PATTERN
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Constructor Summary
Constructors Constructor Description PDPDomain(java.lang.String pdpDomainName, java.util.List<ResidueRange> ranges)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getIdentifier()
Get the String form of this identifier.java.lang.String
getPdbId()
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.SubstructureIdentifier
toCanonical()
Convert to a canonical SubstructureIdentifier.java.lang.String
toString()
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Constructor Detail
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PDPDomain
public PDPDomain(java.lang.String pdpDomainName, java.util.List<ResidueRange> ranges)
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Method Detail
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getIdentifier
public java.lang.String getIdentifier()
Description copied from interface:StructureIdentifier
Get the String form of this identifier. It is recommended that the#toString()
method also return the identifier, for consistency during serialization.- Specified by:
getIdentifier
in interfaceStructureIdentifier
- Returns:
- The String form of this identifier
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getPdbId
public java.lang.String getPdbId()
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toCanonical
public SubstructureIdentifier toCanonical()
Description copied from interface:StructureIdentifier
Convert to a canonical SubstructureIdentifier.This allows all domains to be converted to a standard format String.
- Specified by:
toCanonical
in interfaceStructureIdentifier
- Returns:
- A SubstructureIdentifier equivalent to this
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reduce
public Structure reduce(Structure input) throws StructureException
Description copied from interface:StructureIdentifier
Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
- Specified by:
reduce
in interfaceStructureIdentifier
- Parameters:
input
- A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.- Returns:
- Throws:
StructureException
- See Also:
StructureTools.getReducedStructure(Structure, String)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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loadStructure
public Structure loadStructure(AtomCache cache) throws StructureException, java.io.IOException
Description copied from interface:StructureIdentifier
Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input toStructureIdentifier.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.- Specified by:
loadStructure
in interfaceStructureIdentifier
- Returns:
- A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
- Throws:
StructureException
- For errors loading and parsing the structurejava.io.IOException
- Errors reading the structure from disk
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