Class AminoAcidImpl

  • All Implemented Interfaces:
    java.io.Serializable, AminoAcid, Group

    public class AminoAcidImpl
    extends HetatomImpl
    implements AminoAcid
    AminoAcid inherits most from Hetatom. Adds a few AminoAcid specific methods.
    Since:
    1.4
    Version:
    %I% %G%
    Author:
    Andreas Prlic, Jules Jacobsen
    See Also:
    Serialized Form
    • Field Detail

      • type

        public static final GroupType type
        this is an Amino acid. type is "amino".
    • Constructor Detail

      • AminoAcidImpl

        public AminoAcidImpl()
        inherits most from Hetero and has just a few extensions.
    • Method Detail

      • getN

        public Atom getN()
        Get N atom.
        Specified by:
        getN in interface AminoAcid
        Returns:
        an Atom object or null if N atom does not exist
      • getCA

        public Atom getCA()
        Get CA atom.
        Specified by:
        getCA in interface AminoAcid
        Returns:
        an Atom object or null if CA atom does not exist
      • getC

        public Atom getC()
        Get C atom.
        Specified by:
        getC in interface AminoAcid
        Returns:
        an Atom object or null if C atom does not exist
      • getO

        public Atom getO()
        Get O atom.
        Specified by:
        getO in interface AminoAcid
        Returns:
        an Atom object or null if O atom does not exist
      • getCB

        public Atom getCB()
        Get CB atom.
        Specified by:
        getCB in interface AminoAcid
        Returns:
        an Atom object or null if CB atom does not exist
      • setAminoType

        public void setAminoType​(java.lang.Character aa)
        Set the name of the AA, in single letter code .
        Specified by:
        setAminoType in interface AminoAcid
        Parameters:
        aa - a Character object specifying the amino type value
        See Also:
        AminoAcid.getAminoType()
      • setRecordType

        public void setRecordType​(java.lang.String recordName)
        Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
        Specified by:
        setRecordType in interface AminoAcid
        Parameters:
        recordName - either ATOMRECORD or SEQRESRECORD
        See Also:
        AminoAcid.getRecordType()
      • getRecordType

        public java.lang.String getRecordType()
        Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
        Specified by:
        getRecordType in interface AminoAcid
        Returns:
        the origin of this amino acid (ATOM or SEQRES records)
        See Also:
        AminoAcid.setRecordType(String)
      • toString

        public java.lang.String toString()
        string representation.
        Overrides:
        toString in class HetatomImpl
      • clone

        public java.lang.Object clone()
        returns and identical copy of this Group object .
        Specified by:
        clone in interface Group
        Overrides:
        clone in class HetatomImpl
        Returns:
        and identical copy of this Group object