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, Serializable
A class that contains PDB Header information.
Since:
1.6
Author:
Andreas Prlic
See Also:

  • Field Details

  • Constructor Details

    • PDBHeader

      public 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

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

    • getClassification

      public String getClassification()

    • setClassification

      public void setClassification(String classification)

    • getDepDate

      public Date getDepDate()

    • setDepDate

      public void setDepDate(Date depDate)

    • 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()

    • setModDate

      public void setModDate(Date modDate)

    • 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, usually numerical from "1" to "n", but can also be "PAU" and "XAU"
      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)