Package org.biojava.nbio.structure

Class PDBHeader

java.lang.Object
org.biojava.nbio.structure.PDBHeader
All Implemented Interfaces:
Serializable, PDBRecord
public class PDBHeader extends Object implements PDBRecord
A class that contains PDB Header information. In contrast to what the name suggests, this class does not represent a direct mapping of the Header section of the PDB legacy file format. Instead, it holds the information that is not directly related to the structure data. Such information may exist in some cases and may not exist in other cases.
Since:
1.6
Author:
Andreas Prlic
See Also:

  • Field Details

  • Constructor Details

  • 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

      @Deprecated public String getIdCode()
      Deprecated.
      use getPdbId()
      The PDB code for this protein structure.
      Returns:
      the PDB identifier
      See Also:

    • setIdCode

      @Deprecated public void setIdCode(String idCode)
      Deprecated.
      use setPdbId(PdbId)
      The PDB code for this protein structure.
      Parameters:
      idCode - the PDB identifier
      See Also:

    • getPdbId

      public PdbId getPdbId()
      Gets the PDB identifier for this protein structure.
      Returns:
      the PdbId PDB identifier
      Since:
      6.0.0
      See Also:

    • setPdbId

      public void setPdbId(PdbId pdbId)
      Sets the PDB identifier code for this protein structure.
      Parameters:
      pdbId - the PDB identifier
      Since:
      6.0.0
      See Also:

    • 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()
      Returns the resolution (or effective resolution) of the experiment. This is related to _refine.ls_d_res_high (DIFFRACTION) or _em_3d_reconstruction.resolution (ELECTRON MICROSCOPY) for mmCif format, or to REMARK 2 or REMARK 3 for PDB legacy format. If more than one value is available (in rare cases), the last one is reported. If no value is available, it defaults to DEFAULT_RESOLUTION (99.0f).
      Returns:
      The reported experiment resolution, DEFAULT_RESOLUTION (99.0f) if no value is available.

    • 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

      @Deprecated public String getDescription()
      Deprecated.
      will be removed later. Use getKeywords() if you use description to keep the keywords.
      Returns:

    • setDescription

      @Deprecated public void setDescription(String description)
      Deprecated.
      will be removed later. Use getKeywords() if you use description to keep the keywords.
      Parameters:
      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.

    • getKeywords

      public List<String> getKeywords()
      Gets the keywords (KEYWODS) record of the structure
      Returns:
      The keywords in a List<String>
      Since:
      6.0.0

    • setKeywords

      public void setKeywords(List<String> keywords)
      Sets the KEYWODS record of the structure.
      Parameters:
      keywords - The keywords in a List<String> to set.
      Since:
      6.0.0