Package pl.poznan.put.pdb.analysis

Class AbstractPdbModel

java.lang.Object

pl.poznan.put.pdb.analysis.AbstractPdbModel

All Implemented Interfaces:

Serializable, PdbModel, ResidueCollection

Direct Known Subclasses:

DefaultCifModel, DefaultPdbModel

public abstract class AbstractPdbModel
extends Object
implements PdbModel

A structure which detects residues from atoms alone and then chains from residues.

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
AbstractPdbModel()

Method Summary

Modifier and Type	Method	Description
List<PdbChain>	chains()	Groups together residues in the same chain and repeat that for every chain.
List<PdbResidue>	residues()	Groups together atoms from the same residue and repeat that for every residue.

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

atoms, chainTerminatedAfter, containsAny, experimentalData, filteredMissing, filteredNewInstance, findChainContainingResidue, header, idCode, isModified, missingResidues, modelNumber, modificationDetails, modifiedResidues, resolution, title

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

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

Constructor Details

AbstractPdbModel

public AbstractPdbModel()

Method Details

chains

public List<PdbChain> chains()

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

Specified by:

chains in interface PdbModel

Returns:

A list of chains in the structure.

residues

public List<PdbResidue> residues()

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

Specified by:

residues in interface ResidueCollection

Returns:

A list of residues in the structure.