Class PDBHeader

  • All Implemented Interfaces:
    java.io.Serializable, PDBRecord

    public class PDBHeader
    extends java.lang.Object
    implements PDBRecord, java.io.Serializable
    A class that contains PDB Header information.
    Since:
    1.6
    Author:
    Andreas Prlic
    See Also:
    Serialized Form
    • Field Detail

      • newline

        public static final java.lang.String newline
    • Constructor Detail

      • PDBHeader

        public PDBHeader()
    • Method Detail

      • toString

        public java.lang.String toString()
        String representation
        Overrides:
        toString in class java.lang.Object
      • toPDB

        public java.lang.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​(java.lang.StringBuffer buf)
        Appends a PDB representation of the PDB header to the provided StringBuffer
        Specified by:
        toPDB in interface PDBRecord
        Parameters:
        buf -
      • getId

        public java.lang.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 java.lang.String getIdCode()
        The PDB code for this protein structure.
        Returns:
        the PDB identifier
        See Also:
        setIdCode(String)
      • setIdCode

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

        public java.lang.String getClassification()
      • setClassification

        public void setClassification​(java.lang.String classification)
      • getDepDate

        public java.util.Date getDepDate()
      • setDepDate

        public void setDepDate​(java.util.Date depDate)
      • getExperimentalTechniques

        public java.util.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​(java.lang.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()
      • setResolution

        public void setResolution​(float resolution)
      • getRfree

        public float getRfree()
      • setRfree

        public void setRfree​(float rFree)
      • getModDate

        public java.util.Date getModDate()
      • setModDate

        public void setModDate​(java.util.Date modDate)
      • getTitle

        public java.lang.String getTitle()
      • setTitle

        public void setTitle​(java.lang.String title)
      • getDescription

        public java.lang.String getDescription()
      • setDescription

        public void setDescription​(java.lang.String description)
      • getAuthors

        public java.lang.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​(java.lang.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 java.util.Map<java.lang.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​(java.util.Map<java.lang.Integer,​BioAssemblyInfo> bioAssemblies)
      • getNrBioAssemblies

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

        public void setRevisionRecords​(java.util.List<DatabasePdbrevRecord> revisionRecords)