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:

  • Constructor Details

    • DefaultCifModel

      public DefaultCifModel()

  • Method Details

    • 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.

    • normalize

      @Check public DefaultCifModel normalize()