Interface AminoAcid

  • All Superinterfaces:
    Group
    All Known Implementing Classes:
    AminoAcidImpl

    public interface AminoAcid
    extends Group

    A Group that represents an AminoAcid.

    In PDB files information on AminoAcids can be observed in the SEQRES and in the ATOM records. Since frequently coordinates for some of the amino acids are missing, during parsing of the PDB files the SEQRES and the ATOM records are aligned and a whenever possible the AminoAcid objects are combined. Access to the SEQRES and ATOM sequence is possible through the Chain object. It is possible to distinguish between SEQRES and ATOM derived AminoAcids by getRecordType().

    AminoAcid inherits most from HetatomImpl. Adds a few AminoAcid specific methods.

    Since:
    1.4
    Version:
    %I% %G%
    Author:
    Andreas Prlic
    • Field Detail

      • ATOMRECORD

        static final java.lang.String ATOMRECORD
        Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
        See Also:
        Constant Field Values
      • SEQRESRECORD

        static final java.lang.String SEQRESRECORD
        Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
        See Also:
        Constant Field Values
    • Method Detail

      • setSecStruc

        void setSecStruc​(java.util.Map<java.lang.String,​java.lang.String> secstr)
        Specifies the secondary structure as a Map.
        Parameters:
        secstr - a Map object specifying the sec struc
        See Also:
        getSecStruc()
      • getAminoType

        java.lang.Character getAminoType()
        returns the name of the AA, in single letter code.
        Returns:
        a Character object representing the amino type value
        See Also:
        setAminoType(java.lang.Character)
      • setAminoType

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

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

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

        java.lang.String toString()
        string representation.
        Overrides:
        toString in class java.lang.Object