Package ffx.potential.parsers

Class PDBFilter.Mutation

java.lang.Object
ffx.potential.parsers.PDBFilter.Mutation
Enclosing class:
PDBFilter
public static class PDBFilter.Mutation extends Object

  • Constructor Details

    • Mutation

      public Mutation(int resID, char chainChar, String newResName)

  • Method Details

    • isNonAlchemicalAtom

      public String isNonAlchemicalAtom(String atomName)
      Check to see if an atom is involved in the mutated base's glycosyl torsion. If the mutation is a switch from purine to pyrimidine or vice versa, it will return '~name', meaning the name should be replaced but to include it as an alchemical atom.
      Parameters:
      atomName - atom name to check
      Returns:
      new name to use if it is involved in glycosyl torsion, null otherwise

    • getAlchemicalAtoms

      public ArrayList<String> getAlchemicalAtoms(boolean isWriting)
      Determines what atoms should be alchemical for a purine to purine or pyrimidine to pyrimidine mutation.
      Parameters:
      isWriting - true if writing the pdb, false if reading the pdb
      Returns:
      ArrayList of alchemical atoms, null if not a pur-pur or pyr-pyr mutation

    • isMtnPurine

      public boolean isMtnPurine()
      Determine if the mutation residue is purine.
      Returns:
      true if mutation is purine

    • isMtnPyrimidine

      public boolean isMtnPyrimidine()
      Determine if the mutation residue is pyrimidine.
      Returns:
      true if mutation is pyrimidine

    • isWtPurine

      public boolean isWtPurine()
      Determine if original (wild type) residue is purine.
      Returns:
      true if original residue is purine

    • isWtPyrimidine

      public boolean isWtPyrimidine()
      Determine if original (wild type) residue is pyrimidine.
      Returns:
      true if original residue is pyrimidine