Package org.biojava.spark.utils

Class CanonNames

  • public class CanonNames
extends java.lang.Object
    A class of static methods to find the canonical names of AtomContact interactions.
    Author:
    Anthony Bradley

    • Constructor Summary

      Constructors 
      Constructor Description
      CanonNames()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String getCanonAtomNames​(org.biojava.nbio.structure.contact.AtomContact atomContact)
      Canonically represent atom name pairs as strings.
      static java.lang.String getCanonChains​(org.biojava.nbio.structure.contact.AtomContact atomContact)
      Get the canonical names of two chains from an AtomContact
      static java.lang.String getCanonElementNames​(org.biojava.nbio.structure.contact.AtomContact atomContact)
      Canonically represent element name pairs as strings.
      static java.lang.String getCanonGroups​(org.biojava.nbio.structure.contact.AtomContact atomContact)
      Canonically represent group pairs as strings.
      static java.lang.String getCanonResidueNumbers​(org.biojava.nbio.structure.contact.AtomContact atomContact)
      Get the canonical names of two residues from an AtomContact

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • CanonNames

        public CanonNames()

    • Method Detail

      • getCanonGroups

        public static java.lang.String getCanonGroups​(org.biojava.nbio.structure.contact.AtomContact atomContact)
        Canonically represent group pairs as strings.
        Parameters:
        atomContact - the input AtomContact object
        Returns:
        the canonicalised representation of the groups involved

      • getCanonAtomNames

        public static java.lang.String getCanonAtomNames​(org.biojava.nbio.structure.contact.AtomContact atomContact)
        Canonically represent atom name pairs as strings.
        Parameters:
        atomContact - the input AtomContact object
        Returns:
        the canonicalised representation of the atom names involved

      • getCanonElementNames

        public static java.lang.String getCanonElementNames​(org.biojava.nbio.structure.contact.AtomContact atomContact)
        Canonically represent element name pairs as strings.
        Parameters:
        atomContact - the input AtomContact object
        Returns:
        the canonicalised representation of the atom names involved

      • getCanonChains

        public static java.lang.String getCanonChains​(org.biojava.nbio.structure.contact.AtomContact atomContact)
        Get the canonical names of two chains from an AtomContact
        Parameters:
        atomContact - the input AtomContact
        Returns:
        the canonical name of the chains

      • getCanonResidueNumbers

        public static java.lang.String getCanonResidueNumbers​(org.biojava.nbio.structure.contact.AtomContact atomContact)
        Get the canonical names of two residues from an AtomContact
        Parameters:
        atomContact - the input AtomContact
        Returns:
        the canonical name of the residues