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)