Class PDBHeader

Method Details

• toString

  public String toString()

  String representation

  Overrides:

  toString in class Object

• toPDB

  public String toPDB()

  Return a PDB representation of the PDB Header

  Specified by:

  toPDB in interface PDBRecord

  Returns:

  a PDB file style display

• toPDB

  public void toPDB(StringBuffer buf)

  Appends a PDB representation of the PDB header to the provided StringBuffer

  Specified by:

  toPDB in interface PDBRecord

  Parameters:

  buf -

• getId

  public Long getId()

  Get the ID used by Hibernate.

  Returns:

  the ID used by Hibernate

  See Also:

  • setId(Long)

• equals

  public boolean equals(PDBHeader other)

  Compare two PDBHeader objects

  Parameters:

  other - a PDBHeader object to compare this one to.

  Returns:

  true if they are equal or false if they are not.

• getIdCode

  public String getIdCode()

  The PDB code for this protein structure.

  Returns:

  the PDB identifier

  See Also:

  • setIdCode(String)

• setIdCode

  public void setIdCode(String idCode)

  The PDB code for this protein structure.

  Parameters:

  idCode - the PDB identifier

  See Also:

  • getIdCode()

• getClassification

  public String getClassification()

• setClassification

  public void setClassification(String classification)

• getDepDate

  public Date getDepDate()

  Return the deposition date of the structure in the PDB.

  Returns:

  the deposition date

• setDepDate

  public void setDepDate(Date depDate)

  The deposition date of the structure in the PDB

  Parameters:

  depDate - the deposition date

• getExperimentalTechniques

  public Set<ExperimentalTechnique> getExperimentalTechniques()

  Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid experimental techniques when the Set will contain 2 or more values

  Returns:

  the Set of ExperimentalTechniques or null if not set

• setExperimentalTechnique

  public boolean setExperimentalTechnique(String techniqueStr)

  Adds the experimental technique to the set of experimental techniques of this header. Note that if input is not a recognised technique string then no errors will be produced but false will be returned

  Parameters:

  techniqueStr -

  Returns:

  true if the input corresponds to a recognised technique string (see ExperimentalTechnique) and it was not already present in the current set of ExperimentalTechniques

• getCrystallographicInfo

  public PDBCrystallographicInfo getCrystallographicInfo()

• setCrystallographicInfo

  public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)

• getResolution

  public float getResolution()

• setResolution

  public void setResolution(float resolution)

• getRfree

  public float getRfree()

• setRfree

  public void setRfree(float rFree)

• getModDate

  public Date getModDate()

  Return the latest modification date of the structure.

  Returns:

  the latest modification date

• setModDate

  public void setModDate(Date modDate)

  The latest modification date of the structure.

  Parameters:

  modDate - the latest modification date

• getRelDate

  public Date getRelDate()

  Return the release date of the structure in the PDB.

  Returns:

  the release date

• setRelDate

  public void setRelDate(Date relDate)

  The release date of the structure in the PDB.

  Parameters:

  relDate - the release date

• getTitle

  public String getTitle()

• setTitle

  public void setTitle(String title)

• getDescription

  public String getDescription()

• setDescription

  public void setDescription(String description)

• getAuthors

  public String getAuthors()

  Return the names of the authors as listed in the AUTHORS section of a PDB file. Not necessarily the same authors as listed in the AUTH section of the primary citation!

  Returns:

  Authors as a string

• setAuthors

  public void setAuthors(String authors)

• hasJournalArticle

  public boolean hasJournalArticle()

  Return whether or not the entry has an associated journal article or publication. The JRNL section is not mandatory and thus may not be present.

  Returns:

  flag if a JournalArticle could be found.

• getJournalArticle

  public JournalArticle getJournalArticle()

  Get the associated publication as defined by the JRNL records in a PDB file.

  Returns:

  a JournalArticle

• setJournalArticle

  public void setJournalArticle(JournalArticle journalArticle)

  Set the associated publication as defined by the JRNL records in a PDB file.

  Parameters:

  journalArticle - the article

• getBioAssemblies

  public Map<Integer,BioAssemblyInfo> getBioAssemblies()

  Return the map of biological assemblies. The keys are the biological assembly identifiers (starting at 1). Non-numerical identifiers such as PAU or XAU are not supported.

  Returns:

• setBioAssemblies

  public void setBioAssemblies(Map<Integer,BioAssemblyInfo> bioAssemblies)

• getNrBioAssemblies

  public int getNrBioAssemblies()

  Get the number of biological assemblies available in the PDB header

  Returns:

• getRevisionRecords

  public List<DatabasePdbrevRecord> getRevisionRecords()

• setRevisionRecords

  public void setRevisionRecords(List<DatabasePdbrevRecord> revisionRecords)

• getRwork

  public float getRwork()

  Returns:

  the R-work for this structure.

• setRwork

  public void setRwork(float rWork)

  Parameters:

  rWork - the R-work for this structure.