Package pl.poznan.put.pdb.analysis

Class DefaultCifModel

java.lang.Object

pl.poznan.put.pdb.analysis.AbstractPdbModel

pl.poznan.put.pdb.analysis.DefaultCifModel

All Implemented Interfaces:

Serializable, CifModel, PdbModel, ResidueCollection

Direct Known Subclasses:

ImmutableDefaultCifModel

@Immutable
public abstract class DefaultCifModel
extends AbstractPdbModel
implements CifModel

A default implementation of a structure parsed from an mmCIF file.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DefaultCifModel()

Method Summary

Modifier and Type	Method	Description
abstract List<PdbAtomLine>	atoms()
abstract List<QuantifiedBasePair>	basePairs()
List<PdbChain>	chains()	Groups together residues in the same chain and repeat that for every chain.
abstract Set<PdbResidueIdentifier>	chainTerminatedAfter()
abstract PdbExpdtaLine	experimentalData()
CifModel	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()
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

DefaultCifModel

public DefaultCifModel()

Method Detail

header

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

Specified by:

header in interface PdbModel

Returns:

The structure header.

experimentalData

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

Specified by:

experimentalData in interface PdbModel

Returns:

Details about experiment used to solve the structure.

resolution

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

Specified by:

resolution in interface PdbModel

Returns:

Information about the experimental resolution.

modelNumber

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

Specified by:

modelNumber in interface PdbModel

Returns:

Model number as stated in the PDB or mmCIF file.

atoms

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

Specified by:

atoms in interface PdbModel

Returns:

The list of atoms present in the structure.

modifiedResidues

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

Specified by:

modifiedResidues in interface PdbModel

Returns:

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

missingResidues

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

Specified by:

missingResidues in interface PdbModel

Returns:

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

title

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

Specified by:

title in interface PdbModel

Returns:

Structure title.

chainTerminatedAfter

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

Specified by:

chainTerminatedAfter in interface PdbModel

Returns:

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

filteredNewInstance

public final CifModel 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.

Specified by:

filteredNewInstance in interface PdbModel

Parameters:

moleculeType - Type of molecule.

Returns:

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

basePairs

@Parameter(order=10)
@Auxiliary
public abstract List<QuantifiedBasePair> basePairs()

Specified by:

basePairs in interface CifModel

Returns:

The list of base pairs as parsed from mmCIF file.

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.