Package org.biojava.nbio.protmod

Class Component

java.lang.Object
org.biojava.nbio.protmod.Component
public final class Component extends Object
contains information about a certain Component. The Component class uses the extensible enum pattern. You can't instantiate Component directly, instead you have to use one of the register and of(java.lang.String) methods.
Since:
3.0
Author:
Jianjiong Gao

  • Method Details

    • getPdbccIds

      public Set<String> getPdbccIds()
      Returns:
      Protein Data Bank ID.

    • isNTerminal

      public boolean isNTerminal()
      Returns:
      true if occurring on N terminal; false, otherwise.

    • isCTerminal

      public boolean isCTerminal()
      Returns:
      true if occurring on C terminal; false, other wise.

    • of

      public static Component of(String pdbccId)
      Get a Component that does not have to occur at terminals. If the corresponding component has already been registered, return that one.
      Parameters:
      pdbccIds - possible Protein Data Bank ID.
      Returns:
      a component.
      Throws:
      IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type.

    • of

      public static Component of(String pdbccId, boolean isNTerminal, boolean isCTerminal)
      Get or create a Component.
      Parameters:
      pdbccId - Protein Data Bank ID.
      isNTerminal - true if occurring at N-terminal. false, otherwise.
      isCTerminal - true if occurring at C-terminal. false, otherwise.
      Returns:
      a component.
      Throws:
      IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type, or terminal condition is indicated for non-amino-acid component, or both N-terminal and C-terminal are true.

    • of

      public static Component of(Set<String> pdbccIds)
      Get a Component that does not have to occur at terminals. If the corresponding component has already been registered, return that one.
      Parameters:
      pdbccIds - a set of possible Protein Data Bank ID.
      Returns:
      a component.
      Throws:
      IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type.

    • of

      public static Component of(Set<String> pdbccIds, boolean isNTerminal, boolean isCTerminal)
      Get or create a Component.
      Parameters:
      pdbccIds - a set of possible Protein Data Bank ID.
      isNTerminal - true if occurring at N-terminal. false, otherwise.
      isCTerminal - true if occurring at C-terminal. false, otherwise.
      Returns:
      a component.
      Throws:
      IllegalArgumentException - if pdbccId or type is null, or the pdbccId has been registered as a different type, or terminal condition is indicated for non-amino-acid component, or both N-terminal and C-terminal are true.

    • allComponents

      public static Set<Component> allComponents()

    • toString

      public String toString()
      Overrides:
      toString in class Object
      Returns:
      informative description.