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:

  • Constructor Details

    • DefaultPdbModel

      public DefaultPdbModel()

  • Method Details

    • 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.

    • normalize

      @Check protected DefaultPdbModel normalize()