Class PDBHeader

    • Method Detail

      • 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.
      • setIdCode

        public void setIdCode​(String idCode)
        The PDB code for this protein structure.
        Parameters:
        idCode - the PDB identifier
        See Also:
        getIdCode()
      • 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<ExperimentalTechniquegetExperimentalTechniques()
        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
      • setResolution

        public void setResolution​(float resolution)
      • 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
      • 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
      • 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,​BioAssemblyInfogetBioAssemblies()
        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:
      • getNrBioAssemblies

        public int getNrBioAssemblies()
        Get the number of biological assemblies available in the PDB header
        Returns:
      • 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.