Package pl.poznan.put.pdb.analysis

Class DefaultPdbResidue

java.lang.Object

pl.poznan.put.pdb.analysis.DefaultPdbResidue

All Implemented Interfaces:

Serializable, Comparable<ChainNumberICode>, PdbResidue, ChainNumberICode

Direct Known Subclasses:

ImmutableDefaultPdbResidue

@Immutable
public abstract class DefaultPdbResidue
extends Object
implements PdbResidue

A default implementation of a residue (nucleotide or amino acid).

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DefaultPdbResidue()

Method Summary

Modifier and Type	Method	Description
Set<AtomName>	atomNames()
abstract List<PdbAtomLine>	atoms()
static PdbResidue	fromBioJavaGroup(org.biojava.nbio.structure.Group group)	Creates an instance of this class from Group object defined in BioJava.
boolean	hasAllHeavyAtoms()	Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
abstract PdbResidueIdentifier	identifier()
abstract String	modifiedResidueName()
ResidueInformationProvider	residueInformationProvider()	Detects the type of residue by its name and atom content.
abstract String	standardResidueName()
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

Methods inherited from interface pl.poznan.put.pdb.analysis.PdbResidue

chainIdentifier, findAtom, hasAnyHydrogen, hasAtom, insertionCode, isConnectedTo, isMissing, isModified, namedResidueIdentifier, nucleobasePlane, oneLetterName, residueNumber, toCif, toPdb

Constructor Detail

DefaultPdbResidue

public DefaultPdbResidue()

Method Detail

fromBioJavaGroup

public static PdbResidue fromBioJavaGroup(org.biojava.nbio.structure.Group group)

Creates an instance of this class from Group object defined in BioJava.

Parameters:

group - A BioJava counterpart.

Returns:

An instance of this class with contents equal to those from the BioJava counterpart.

identifier

@Parameter(order=1)
public abstract PdbResidueIdentifier identifier()

Specified by:

identifier in interface PdbResidue

Returns:

The identifier of a residue.

standardResidueName

@Parameter(order=2)
public abstract String standardResidueName()

Specified by:

standardResidueName in interface PdbResidue

Returns:

The usual name of the residue. For example, a pseudouridine will be seen as uracil here.

modifiedResidueName

@Parameter(order=3)
public abstract String modifiedResidueName()

Specified by:

modifiedResidueName in interface PdbResidue

Returns:

The name of the residue as read from PDB or mmCIF file.

atoms

@Parameter(order=4)
public abstract List<PdbAtomLine> atoms()

Specified by:

atoms in interface PdbResidue

Returns:

The list of atoms.

residueInformationProvider

@Lazy
public ResidueInformationProvider residueInformationProvider()

Description copied from interface: PdbResidue

Detects the type of residue by its name and atom content.

Specified by:

residueInformationProvider in interface PdbResidue

Returns:

An instance with details about what this reside represents.

atomNames

@Lazy
public Set<AtomName> atomNames()

Specified by:

atomNames in interface PdbResidue

Returns:

The set of all atom names available in this residue.

hasAllHeavyAtoms

@Lazy
public boolean hasAllHeavyAtoms()

Description copied from interface: PdbResidue

Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.

Specified by:

hasAllHeavyAtoms in interface PdbResidue

Returns:

True if all expected heavy atoms (non-hydrogen) for this residue type are present in this residue.

toString

public final String toString()

Overrides:

toString in class Object