Package org.biojava.nbio.structure

Class PdbId

  • All Implemented Interfaces:
    Serializable, Comparable<PdbId>
    public class PdbId
extends Object
implements Comparable<PdbId>, Serializable
    A wrapper class for the PDB identifier. It handles conversion between current (short) [1-9][0-9A-Z]{3} and upcoming (extended) PDB_\d{4}[1-9][09-A-Z] PDB ID format.
    Instances of this class are immutable.
    Creation of PdBId instance follows strict PDB ID convention. There is only one exception to this rule which is XXXX. XXXX objects are not considered equal (unless they are the one and the same object).
    Since:
    6.0.0
    Author:
    Amr ALHOSSARY
    See Also:
    Serialized Form

    • Method Detail

      • isShortCompatible

        public static boolean isShortCompatible​(String extendedId)
        Checks whether an Extended PDB ID is shortable, assuming it is a valid extended PDB ID.
        Parameters:
        extendedId - the supposedly valid extended PDB ID.
        Returns:
        true if extendedId can be shortened (ie. it matches the regular expression "(pdb|PDB)_0000[1-9][a-zA-Z0-9]{3}"), false otherwise.
        See Also:
        isValidExtendedPdbId(String)

      • getId

        public String getId()
        Get a String representation of this PdbId instance.
        By default this function will try to get the PdbId in the short (4 letters) format. If not possible, it will return the long format. N.B. This default behavior may change later;
        Returns:
        the PdbId code, preferably in short format.

      • getId

        public String getId​(boolean prefereShort)
        Get a String representation of this PdbId instance, using the passed in behavior.
        Parameters:
        prefereShort - when it is true, the class will try to produce the short ID whenever possible.
        Returns:
        The PdbId in short format if possible and prefereShort is true, the extended PDB ID form otherwise.

      • getShortId

        public String getShortId()
                  throws StructureException
        Get the PDB Id in the short format. Throws an exception if the conversion is not possible.
        Use this method only if you know that this PDB ID is shortable.
        Returns:
        the PDB ID in the short format.
        Throws:
        StructureException - if the conversion was not possible.

      • toExtendedId

        public static String toExtendedId​(String shortId)
                           throws StructureException
        Converts shortId to the PDB ID extended format. If shortId is a valid short PDB ID, it would be converted to an extended ID, if shortId is a valid extended PDB ID, it would be returned in UPPER CASE, a StructureException is thrown otherwise.
        Parameters:
        shortId - the PDB ID to convert to extended format
        Returns:
        the ID in the extended UPPER CASE format.
        Throws:
        StructureException - if the conversion was not possible.

      • toShortId

        public static String toShortId​(String extendedId)
                        throws StructureException
        Converts extendedId to the PDB ID short format. If extendedId is a valid extended PDB ID, it would be converted to a short ID, if extendedId is a valid short PDB ID, it would be returned in UPPER CASE, a StructureException is thrown otherwise.
        Parameters:
        extendedId - the PDB ID to convert to short format
        Returns:
        the ID in the short UPPER CASE format.
        Throws:
        StructureException - if the conversion was not possible.