Package pl.poznan.put.pdb.analysis

Class PdbCompactFragment

java.lang.Object

pl.poznan.put.pdb.analysis.PdbCompactFragment

All Implemented Interfaces:

Serializable, ResidueCollection, SingleTypedResidueCollection

Direct Known Subclasses:

ImmutablePdbCompactFragment

@Immutable
public abstract class PdbCompactFragment
extends Object
implements SingleTypedResidueCollection

A collection of residues such that (i, i+1) are connected.

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pl.poznan.put.pdb.analysis.ResidueCollection

ResidueCollection.CifBuilder, ResidueCollection.PdbBuilder

Constructor Summary

Constructors

Constructor	Description
PdbCompactFragment()

Method Summary

Modifier and Type	Method	Description
protected Set<TorsionAngleType>	angleTypes()
protected List<ResidueTorsionAngles>	angleValues()
String	name()
abstract List<PdbResidue>	residues()
final PdbCompactFragment	shifted(int shift, int size)	Creates a new instance from this one which starts from a shifted position and has a limited size.
final ResidueTorsionAngles	torsionAngles(PdbResidueIdentifier identifier)	Computes torsion angles' values for a given residue.
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.analysis.ResidueCollection

filteredAtoms, findBondLengthViolations, findResidue, hasResidue, indexOf, namedResidueIdentifiers, residueIdentifiers, sequence, toCif, toPdb, withoutAlternateLocations

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

moleculeType

Constructor Details

PdbCompactFragment

public PdbCompactFragment()

Method Details

residues

@Parameter(order=1)
public abstract List<PdbResidue> residues()

Specified by:

residues in interface ResidueCollection

Returns:

The list of residues.

name

@Default
public String name()

Returns:

The name of this compact fragment.

shifted

public final PdbCompactFragment shifted(int shift,
 int size)

Creates a new instance from this one which starts from a shifted position and has a limited size.

Parameters:

shift - Starting position.

size - Length of the new compact fragment.

Returns:

An instance of this class created by taking a sublist of the residues.

torsionAngles

public final ResidueTorsionAngles torsionAngles(PdbResidueIdentifier identifier)

Computes torsion angles' values for a given residue.

Parameters:

identifier - A residue identifier.

Returns:

An object containing values of torsion angles in the given residue.

toString

public final String toString()

Overrides:

toString in class Object

angleTypes

@Lazy
protected Set<TorsionAngleType> angleTypes()

angleValues

@Lazy
protected List<ResidueTorsionAngles> angleValues()