Package pl.poznan.put.pdb.analysis

Interface PdbResidue

All Superinterfaces:
ChainNumberICode, Comparable<ChainNumberICode>, Serializable
All Known Implementing Classes:
DefaultPdbResidue, ImmutableDefaultPdbResidue
public interface PdbResidue extends ChainNumberICode
A residue (nucleotide or amino acid).

  • Method Details

    • identifier

      PdbResidueIdentifier identifier()
      Returns:
      The identifier of a residue.

    • standardResidueName

      String standardResidueName()
      Returns:
      The usual name of the residue. For example, a pseudouridine will be seen as uracil here.

    • modifiedResidueName

      String modifiedResidueName()
      Returns:
      The name of the residue as read from PDB or mmCIF file.

    • atoms

      List<PdbAtomLine> atoms()
      Returns:
      The list of atoms.

    • toPdb

      default String toPdb()
      Returns:
      A text representation of this residue in PDB format.

    • toCif

      default String toCif() throws IOException
      Returns:
      A text representation of this residue in mmCIF format.
      Throws:
      IOException

    • isMissing

      default boolean isMissing()
      Returns:
      True if the list of atoms is empty.

    • residueInformationProvider

      default ResidueInformationProvider residueInformationProvider()
      Detects the type of residue by its name and atom content.
      Returns:
      An instance with details about what this reside represents.

    • oneLetterName

      default char oneLetterName()
      Returns:
      A one letter name which is lowercase for modified residues and uppercase otherwise.

    • isConnectedTo

      default boolean isConnectedTo(PdbResidue other)
      Checks if this residue is connected with another one (see MoleculeType.areConnected(PdbResidue, PdbResidue)).
      Parameters:
      other - The other residue.
      Returns:
      True if this residue and the other one are connected.

    • chainIdentifier

      default String chainIdentifier()
      Specified by:
      chainIdentifier in interface ChainNumberICode
      Returns:
      The identifier of the chain a residue belongs to.

    • residueNumber

      default int residueNumber()
      Specified by:
      residueNumber in interface ChainNumberICode
      Returns:
      The number of a residue in the chain.

    • insertionCode

      default Optional<String> insertionCode()
      Specified by:
      insertionCode in interface ChainNumberICode
      Returns:
      Optional insertion code, used in some PDB and mmCIF files to represent "inserted" residues while maintaining the original numbering.

    • findAtom

      default PdbAtomLine findAtom(AtomName atomName)
      Finds an atom of a given name.
      Parameters:
      atomName - An atom name.
      Returns:
      An instance of atom (with coordinates) of the given type.

    • nucleobasePlane

      default org.apache.commons.math3.geometry.euclidean.threed.Plane nucleobasePlane()
      Calculates the plane equation of the nucleobase in this residue. This method works only for nucleotides and will throw an IllegalArgumentException for amino acids. The plane for purines (A or G) is based on N9, C2 and C6 atoms. The plane for pyrimidines (C, U or T) is based on N1, N3 and C5 atoms.
      Returns:
      The plane of the nucleobase.

    • namedResidueIdentifier

      default PdbNamedResidueIdentifier namedResidueIdentifier()
      Returns:
      The instance of named identifier.

    • atomNames

      default Set<AtomName> atomNames()
      Returns:
      The set of all atom names available in this residue.

    • hasAtom

      default boolean hasAtom(AtomName atomName)
      Checks whether this residue has atom of the given name.
      Parameters:
      atomName - The atom name.
      Returns:
      True if this residue has an atom of the given name.

    • hasAnyHydrogen

      default boolean hasAnyHydrogen()
      Returns:
      True if there is any hydrogen atom available in this residue.

    • hasAllHeavyAtoms

      default boolean hasAllHeavyAtoms()
      Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
      Returns:
      True if all expected heavy atoms (non-hydrogen) for this residue type are present in this residue.

    • isModified

      default boolean isModified()
      Returns:
      True if the standard and modified residue names differ or if there are some atoms in the residue, but they do not match the expected set of atoms.