Package org.biojava.nbio.structure

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 Details

    • ATOMRECORD

      static final String ATOMRECORD
      Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
      See Also:

    • SEQRESRECORD

      static final String SEQRESRECORD
      Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
      See Also:

  • Method Details

    • getN

      Atom getN()
      Get N atom.
      Returns:
      an Atom object or null if N atom does not exist

    • getCA

      Atom getCA()
      Get CA atom.
      Returns:
      an Atom object or null if CA atom does not exist

    • getC

      Atom getC()
      Get C atom.
      Returns:
      an Atom object or null if C atom does not exist

    • getO

      Atom getO()
      Get O atom.
      Returns:
      an Atom object or null if O atom does not exist

    • getCB

      Atom getCB()
      Get CB atom.
      Returns:
      an Atom object or null if CB atom does not exist

    • getAminoType

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

    • setAminoType

      void setAminoType(Character aa)
      Set the name of the AA, in single letter code .
      Parameters:
      aa - a Character object specifying the amino type value
      See Also:

    • setRecordType

      void setRecordType(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

      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: