Package org.biojava.nbio.structure

Class DBRef

  • All Implemented Interfaces:
    Serializable, PDBRecord
    public class DBRef
extends Object
implements PDBRecord
    A class to represent database cross references. This is just a simple bean that contains the infor from one DBREF line
    Since:
    4:56:14 PM
    Version:
    %I% %G%
    Author:
    Andreas Prlic
    See Also:
    Serialized Form

    • Constructor Detail

    • Method Detail

      • getId

        public Long getId()
        Get the ID used by Hibernate.
        Returns:
        the ID used by Hibernate
        See Also:
        setId(Long)

      • setId

        public void setId​(Long id)
        Set the ID used by Hibernate.
        Parameters:
        id - the id assigned by Hibernate
        See Also:
        getId()

      • setParent

        public void setParent​(Structure s)
        Set the structure object that this DBRef relates to.
        Parameters:
        s - a structure object
        See Also:
        getParent()

      • toPDB

        public String toPDB()
        Convert the DBRef object to a DBREF record as it is used in PDB files
        Specified by:
        toPDB in interface PDBRecord
        Returns:
        a PDB - DBREF formatted line

      • toPDB

        public void toPDB​(StringBuffer buf)
        Append the PDB representation of this DBRef to the provided StringBuffer
        Specified by:
        toPDB in interface PDBRecord
        Parameters:
        buf - the StringBuffer to write to.

      • setIdCode

        public void setIdCode​(String idCode)
        Set the idCode for this entry.
        Parameters:
        idCode - the idCode for this entry
        See Also:
        getIdCode()

      • getChainName

        public String getChainName()
        The name of the corresponding chain.
        Returns:
        chainName the name of the corresponding chain.

      • setChainName

        public void setChainName​(String chainName)
        The name of the corresponding chain.
        Parameters:
        chainName - the name of the corresponding chain
        See Also:
        getChainName()

      • getDatabase

        public String getDatabase()
        The database of the db-ref. uses the abbreviation as provided in the PDB files: 
           Database name                         database
                                                                         (code in columns 27 - 32)
        ----------------------------------------------------------
        GenBank                               GB
        Protein Data Bank                     PDB
        Protein Identification Resource       PIR
        SWISS-PROT                            SWS
        TREMBL                                TREMBL
        UNIPROT                               UNP
        Returns:
        name of database of this DBRef
        See Also:
        setDatabase(String)

      • setDatabase

        public void setDatabase​(String database)
        Specifies the database value.
        Parameters:
        database - the database
        See Also:
        getDatabase()

      • setDbIdCode

        public void setDbIdCode​(String dbIdCode)
        Sequence database identification code.
        Parameters:
        dbIdCode - identification code
        See Also:
        getDbIdCode()

      • setDbSeqBegin

        public void setDbSeqBegin​(int dbSeqBegin)
        Initial sequence number of the database seqment.
        Parameters:
        dbSeqBegin - a sequence position
        See Also:
        getDbSeqBegin()

      • getDbSeqEnd

        public int getDbSeqEnd()
        Ending sequence position of the database segment.
        Returns:
        dbSeqEnd
        See Also:
        setDbSeqEnd(int)

      • setDbSeqEnd

        public void setDbSeqEnd​(int dbSeqEnd)
        The begin of the sequence position in the database
        Parameters:
        dbSeqEnd - sequence position
        See Also:
        getDbSeqEnd()

      • getIdbnsBegin

        public char getIdbnsBegin()
        Insertion code of initial residue of the segment, if PDB is the reference.
        Returns:
        idbnsBegin isnertion code
        See Also:
        setIdbnsBegin(char)

      • setIdbnsBegin

        public void setIdbnsBegin​(char idbnsBegin)
        Insertion code of initial residue of the segment, if PDB is the reference.
        Parameters:
        idbnsBegin - insertion code
        See Also:
        getIdbnsBegin()

      • getIdbnsEnd

        public char getIdbnsEnd()
        Insertion code of the ending residue of the segment, if PDB is the reference.
        Returns:
        idbnsEnd insertion code
        See Also:
        setIdbnsEnd(char)

      • setIdbnsEnd

        public void setIdbnsEnd​(char idbnsEnd)
        Insertion code of the ending residue of the segment, if PDB is the reference.
        Parameters:
        idbnsEnd - the insertion code
        See Also:
        setIdbnsEnd(char)

      • setInsertBegin

        public void setInsertBegin​(char insertBegin)
        Initial insertion code of the PDB sequence segment.
        Parameters:
        insertBegin -
        See Also:
        getInsertBegin()

      • getInsertEnd

        public char getInsertEnd()
        Ending insertion code of the PDB sequence segment.
        Returns:
        insertEnd insertion code
        See Also:
        setInsertEnd(char)

      • setInsertEnd

        public void setInsertEnd​(char insertEnd)
        Ending insertion code of the PDB sequence segment.
        Parameters:
        insertEnd - insertEnd
        See Also:
        getInsertEnd()

      • getSeqBegin

        public int getSeqBegin()
        Initial sequence number of the PDB sequence segment.
        Returns:
        start seq. position
        See Also:
        setSeqBegin(int)

      • setSeqBegin

        public void setSeqBegin​(int seqbegin)
        Initial sequence number of the PDB sequence segment.
        Parameters:
        seqbegin - start seq. position
        See Also:
        getSeqBegin()

      • getSeqEnd

        public int getSeqEnd()
        Ending sequence number of the PDB sequence segment.
        Returns:
        sequence end position
        See Also:
        getSeqEnd()

      • setSeqEnd

        public void setSeqEnd​(int seqEnd)
        Ending sequence number of the PDB sequence segment.
        Parameters:
        seqEnd - sequence end position
        See Also:
        setSeqEnd(int)