Package pl.poznan.put.pdb.analysis

Class DefaultPdbModel

java.lang.Object

pl.poznan.put.pdb.analysis.AbstractPdbModel

pl.poznan.put.pdb.analysis.DefaultPdbModel

All Implemented Interfaces:

Serializable, PdbModel, ResidueCollection

Direct Known Subclasses:

ImmutableDefaultPdbModel

@Immutable
public abstract class DefaultPdbModel
extends AbstractPdbModel

A default implementation of a structure parsed from a PDB file.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DefaultPdbModel()

Method Summary

Modifier and Type	Method	Description
abstract List<PdbAtomLine>	atoms()
List<PdbChain>	chains()	Groups together residues in the same chain and repeat that for every chain.
abstract Set<PdbResidueIdentifier>	chainTerminatedAfter()
protected void	check()
abstract PdbExpdtaLine	experimentalData()
PdbModel	filteredNewInstance(MoleculeType moleculeType)	Filters out residues of a given molecule type (RNA or protein) and creates a new instance of this class.
abstract PdbHeaderLine	header()
abstract List<PdbRemark465Line>	missingResidues()
abstract int	modelNumber()
abstract List<PdbModresLine>	modifiedResidues()
static PdbModel	of(Iterable<PdbAtomLine> atoms)	Creates an instance of this class with just a list of atoms and all other fields set to default values or empty.
List<PdbResidue>	residues()	Groups together atoms from the same residue and repeat that for every residue.
abstract PdbRemark2Line	resolution()
abstract String	title()

Methods inherited from class java.lang.Object

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

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

containsAny, filteredMissing, findChainContainingResidue, idCode, isModified, modificationDetails

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

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

Constructor Detail

DefaultPdbModel

public DefaultPdbModel()

Method Detail

of

public static PdbModel of(Iterable<PdbAtomLine> atoms)

Creates an instance of this class with just a list of atoms and all other fields set to default values or empty.

Parameters:

atoms - A list of atoms.

Returns:

An instance of a PdbModel without a header, experimental data information, missing or modified residues.

header

@Parameter(order=1)
@Auxiliary
public abstract PdbHeaderLine header()

Returns:

The structure header.

experimentalData

@Parameter(order=2)
@Auxiliary
public abstract PdbExpdtaLine experimentalData()

Returns:

Details about experiment used to solve the structure.

resolution

@Parameter(order=3)
@Auxiliary
public abstract PdbRemark2Line resolution()

Returns:

Information about the experimental resolution.

modelNumber

@Parameter(order=4)
@Auxiliary
public abstract int modelNumber()

Returns:

Model number as stated in the PDB or mmCIF file.

atoms

@Parameter(order=5)
public abstract List<PdbAtomLine> atoms()

Returns:

The list of atoms present in the structure.

modifiedResidues

@Parameter(order=6)
@Auxiliary
public abstract List<PdbModresLine> modifiedResidues()

Returns:

The list of modified residues as parsed from the PDB or mmCIF file.

missingResidues

@Parameter(order=7)
@Auxiliary
public abstract List<PdbRemark465Line> missingResidues()

Returns:

The list of missing residues as parsed from the PDB or mmCIF file.

title

@Parameter(order=8)
@Auxiliary
public abstract String title()

Returns:

Structure title.

chainTerminatedAfter

@Parameter(order=9)
@Auxiliary
public abstract Set<PdbResidueIdentifier> chainTerminatedAfter()

Returns:

The set of residues, after which the chain was terminated.

filteredNewInstance

public PdbModel filteredNewInstance(MoleculeType moleculeType)

Description copied from interface: PdbModel

Filters out residues of a given molecule type (RNA or protein) and creates a new instance of this class.

Parameters:

moleculeType - Type of molecule.

Returns:

An instance of this class with residues only of a desired type.

chains

@Lazy
public List<PdbChain> chains()

Description copied from class: AbstractPdbModel

Groups together residues in the same chain and repeat that for every chain.

Specified by:

chains in interface PdbModel

Overrides:

chains in class AbstractPdbModel

Returns:

A list of chains in the structure.

residues

@Lazy
public List<PdbResidue> residues()

Description copied from class: AbstractPdbModel

Groups together atoms from the same residue and repeat that for every residue.

Specified by:

residues in interface ResidueCollection

Overrides:

residues in class AbstractPdbModel

Returns:

A list of residues in the structure.

check

@Check
protected void check()