Class DBRef

Method Details

• 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()

• getParent

  public Structure getParent()

  Get the structure object that this DBRef relates to.

  Returns:

  s a structure object

  See Also:

  • setParent(Structure)

• 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.

• toString

  public String toString()

  String representation of a DBRef.

  Overrides:

  toString in class Object

  Returns:

  a String

• getIdCode

  public String getIdCode()

  get the idCode for this entry

  Returns:

  the idCode

  See Also:

  • setIdCode(String)

• setIdCode

  public void setIdCode(String idCode)

  Set the idCode for this entry.

  Parameters:

  idCode - the idCode for this entry

  See Also:

  • getIdCode()

• getChainId

  public String getChainId()

  The chain ID of the corresponding chain.

  Returns:

  chainId the ID of the corresponding chain.

• setChainId

  public void setChainId(String chainId)

  The chain ID of the corresponding chain.

  Parameters:

  chainId - the ID of the corresponding chain

  See Also:

  • getChainId()

• 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()

• getDbAccession

  public String getDbAccession()

  Sequence database accession code.

  Returns:

  the dbAccession

  See Also:

  • setDbAccession(String)

• setDbAccession

  public void setDbAccession(String dbAccession)

  Sequence database accession code.

  Parameters:

  dbAccession - the dbAccession

  See Also:

  • getDbAccession()

• getDbIdCode

  public String getDbIdCode()

  Sequence database identification code.

  Returns:

  the dbIdCode

  See Also:

  • setDbIdCode(String)

• setDbIdCode

  public void setDbIdCode(String dbIdCode)

  Sequence database identification code.

  Parameters:

  dbIdCode - identification code

  See Also:

  • getDbIdCode()

• getDbSeqBegin

  public int getDbSeqBegin()

  Initial sequence number of the database seqment.

  Returns:

  position

  See Also:

  • setDbSeqBegin(int)

• 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)

• getInsertBegin

  public char getInsertBegin()

  Initial insertion code of the PDB sequence segment.

  Returns:

  insertBegin

  See Also:

  • setInsertBegin(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)