Package pl.poznan.put.pdb

Class PdbNamedResidueIdentifier

java.lang.Object

pl.poznan.put.pdb.PdbNamedResidueIdentifier

All Implemented Interfaces:

Serializable, Comparable<ChainNumberICode>, ChainNumberICode

Direct Known Subclasses:

ImmutablePdbNamedResidueIdentifier

@Immutable
public abstract class PdbNamedResidueIdentifier
extends Object
implements ChainNumberICode, Serializable

Class that represents a residue identifier with a known name. In some cases, the name is known only after post-processing e.g. when finding out the name of a residue based on the atom content.

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
PdbNamedResidueIdentifier()

Method Summary

Modifier and Type	Method	Description
abstract String	chainIdentifier()
abstract Optional<String>	insertionCode()
abstract char	oneLetterName()
abstract int	residueNumber()
final PdbResidueIdentifier	toResidueIdentifier()
final String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface pl.poznan.put.pdb.ChainNumberICode

compareTo

Constructor Details

PdbNamedResidueIdentifier

public PdbNamedResidueIdentifier()

Method Details

chainIdentifier

@Parameter(order=1)
public abstract String chainIdentifier()

Specified by:

chainIdentifier in interface ChainNumberICode

Returns:

The identifier of the chain a residue belongs to.

residueNumber

@Parameter(order=2)
public abstract int residueNumber()

Specified by:

residueNumber in interface ChainNumberICode

Returns:

The number of a residue in the chain.

insertionCode

@Parameter(order=3)
public abstract Optional<String> insertionCode()

Specified by:

insertionCode in interface ChainNumberICode

Returns:

Optional insertion code, used in some PDB and mmCIF files to represent "inserted" residues while maintaining the original numbering.

oneLetterName

@Parameter(order=4)
public abstract char oneLetterName()

Returns:

The one letter name of the residue.

toResidueIdentifier

public final PdbResidueIdentifier toResidueIdentifier()

Returns:

An instance of identifier without the oneLetterName field.

toString

public final String toString()

Overrides:

toString in class Object