Package pl.poznan.put.atom

Enum AtomName

java.lang.Object
java.lang.Enum<AtomName>
pl.poznan.put.atom.AtomName
All Implemented Interfaces:
Serializable, Comparable<AtomName>, java.lang.constant.Constable
public enum AtomName extends Enum<AtomName>
A unified atom name found in PDB and mmCIF files with a list of alternative names.

  • Enum Constant Details

  • Method Details

    • values

      public static AtomName[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      Returns:
      an array containing the constants of this enum type, in the order they are declared

    • valueOf

      public static AtomName valueOf(String name)
      Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum type has no constant with the specified name
      NullPointerException - if the argument is null

    • fromString

      public static AtomName fromString(String pdbName)
      Creates an instance from String. For null or unknown atom names, a special constant UNKNOWN is used.
      Parameters:
      pdbName - String representation of the atom name.
      Returns:
      An instance of this enum.

    • matchesName

      public boolean matchesName(String pdbName)
      Checks if this constant matches a name found in PDB or mmCIF file. Certain atom names have more than one matching PDB names e.g. O2P/OP2.
      Parameters:
      pdbName - Name found in PDB or mmCIF file.
      Returns:
      True if this constant matches pdbName.

    • getName

      public String getName()
      Gets the default atom name (if more than one is configured).
      Returns:
      The default name for this constant.

    • isHeavy

      public boolean isHeavy()
      Checks if atom is heavy (i.e. not a hydrogen).
      Returns:
      True if this constant describes an atom which is not a hydrogen.

    • getType

      public AtomType getType()
      Gets enum describing the type of atom that this constant represents.
      Returns:
      {AtomType} object representing the atom type.