Package pl.poznan.put.pdb.analysis

Interface PdbModel

All Superinterfaces:

ResidueCollection, Serializable

All Known Subinterfaces:

CifModel

All Known Implementing Classes:

AbstractPdbModel, DefaultCifModel, DefaultPdbModel, ImmutableDefaultCifModel, ImmutableDefaultPdbModel

public interface PdbModel
extends ResidueCollection

A structure parsed from a PDB file.

Method Summary

Modifier and Type	Method	Description
List<PdbAtomLine>	atoms()
List<PdbChain>	chains()
Set<PdbResidueIdentifier>	chainTerminatedAfter()
default boolean	containsAny(MoleculeType moleculeType)	Checks if any chain is of a given type.
PdbExpdtaLine	experimentalData()
default List<PdbRemark465Line>	filteredMissing(MoleculeType moleculeType)	Finds all missing residues of the given type.
PdbModel	filteredNewInstance(MoleculeType moleculeType)	Filters out residues of a given molecule type (RNA or protein) and creates a new instance of this class.
default SingleTypedResidueCollection	findChainContainingResidue(ChainNumberICode query)	Finds a chain which has a given residue.
PdbHeaderLine	header()
default String	idCode()
default boolean	isModified(PdbResidueIdentifier query)	Checks if a given residue is modified (as stated in the PDB or mmCIF headers).
List<PdbRemark465Line>	missingResidues()
int	modelNumber()
default PdbModresLine	modificationDetails(PdbResidueIdentifier query)	Provides details about modification of the residue.
List<PdbModresLine>	modifiedResidues()
PdbRemark2Line	resolution()
String	title()

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

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

Method Detail

header

PdbHeaderLine header()

Returns:

The structure header.

experimentalData

PdbExpdtaLine experimentalData()

Returns:

Details about experiment used to solve the structure.

resolution

PdbRemark2Line resolution()

Returns:

Information about the experimental resolution.

modelNumber

int modelNumber()

Returns:

Model number as stated in the PDB or mmCIF file.

atoms

List<PdbAtomLine> atoms()

Returns:

The list of atoms present in the structure.

modifiedResidues

List<PdbModresLine> modifiedResidues()

Returns:

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

missingResidues

List<PdbRemark465Line> missingResidues()

Returns:

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

title

String title()

Returns:

Structure title.

chainTerminatedAfter

Set<PdbResidueIdentifier> chainTerminatedAfter()

Returns:

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

chains

List<PdbChain> chains()

Returns:

The list of chains in the structure.

filteredNewInstance

PdbModel filteredNewInstance(MoleculeType moleculeType)

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.

idCode

default String idCode()

Returns:

PDB id of the structure.

containsAny

default boolean containsAny(MoleculeType moleculeType)

Checks if any chain is of a given type.

Parameters:

moleculeType - The type of molecule to check.

Returns:

True if at least one chain is of given type.

findChainContainingResidue

default SingleTypedResidueCollection findChainContainingResidue(ChainNumberICode query)

Finds a chain which has a given residue.

Parameters:

query - A triplet of (chain, number, icode) to look for.

Returns:

A chain with desired residue.

filteredMissing

default List<PdbRemark465Line> filteredMissing(MoleculeType moleculeType)

Finds all missing residues of the given type.

Parameters:

moleculeType - The type of molecule to look for.

Returns:

A list of missing residues.

isModified

default boolean isModified(PdbResidueIdentifier query)

Checks if a given residue is modified (as stated in the PDB or mmCIF headers).

Parameters:

query - An identifier of a residue.

Returns:

True if the residue is modified.

modificationDetails

default PdbModresLine modificationDetails(PdbResidueIdentifier query)

Provides details about modification of the residue.

Parameters:

query - An identifier of a residue.

Returns:

An object containing details about residue modification.