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 Details

    • 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.