Package org.biojava.nbio.structure

Class 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:
    Serialized Form

    • 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.

      • 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:
        getPdbId()

      • 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

      • 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)

      • 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,​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:

      • 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.

      • 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