Package org.biojava.nbio.structure

Class PdbId

java.lang.Object
org.biojava.nbio.structure.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:

  • Field Details

    • PATTERN_SHORT_PDBID

      public static final Pattern PATTERN_SHORT_PDBID
      A regular expression that matches a PDB ID in the short format.

    • PATTERN_EXTENDED_PDBID

      public static final Pattern PATTERN_EXTENDED_PDBID
      A regular expression that matches a PDB ID in the extended format.

    • PATTERN_SHORTABLE_EXTENDED_PDBID

      public static final Pattern PATTERN_SHORTABLE_EXTENDED_PDBID
      / * A regular expression that matches an extended PDB ID that is compatible with the short format.

  • Constructor Details

  • Method Details

    • isValidShortPdbId

      public static boolean isValidShortPdbId(String id)
      Check whether id represents a valid PDB ID in the short format.
      Parameters:
      id - Prospect ID
      Returns:
      true if id is a valid short PDB ID, false otherwise.
      Throws:
      NullPointerException - if id is null.
      See Also:

    • isValidExtendedPdbId

      public static boolean isValidExtendedPdbId(String id)
      Check whether id represents a valid PDB ID in the extended format.
      Parameters:
      id - Prospect ID
      Returns:
      true if id is a valid extended PDB ID, false otherwise.
      Throws:
      NullPointerException - if id is null.
      See Also:

    • 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:

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • clone

      protected Object clone() throws CloneNotSupportedException
      Overrides:
      clone in class Object
      Throws:
      CloneNotSupportedException

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • 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.

    • compareTo

      public int compareTo(PdbId o)
      Specified by:
      compareTo in interface Comparable<PdbId>