Package org.biojava.nbio.structure
Class PDBHeader
- java.lang.Object
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- org.biojava.nbio.structure.PDBHeader
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- All Implemented Interfaces:
Serializable
,PDBRecord
public class PDBHeader extends Object implements PDBRecord
A class that contains PDB Header information.- Since:
- 1.6
- Author:
- Andreas Prlic
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static float
DEFAULT_RESOLUTION
static float
DEFAULT_RFREE
static String
newline
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Constructor Summary
Constructors Constructor Description PDBHeader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
equals(PDBHeader other)
Compare two PDBHeader objectsString
getAuthors()
Return the names of the authors as listed in the AUTHORS section of a PDB file.Map<Integer,BioAssemblyInfo>
getBioAssemblies()
Return the map of biological assemblies.String
getClassification()
PDBCrystallographicInfo
getCrystallographicInfo()
Date
getDepDate()
Return the deposition date of the structure in the PDB.String
getDescription()
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 valuesLong
getId()
Get the ID used by Hibernate.String
getIdCode()
The PDB code for this protein structure.JournalArticle
getJournalArticle()
Get the associated publication as defined by the JRNL records in a PDB file.Date
getModDate()
Return the latest modification date of the structure.int
getNrBioAssemblies()
Get the number of biological assemblies available in the PDB headerDate
getRelDate()
Return the release date of the structure in the PDB.float
getResolution()
List<DatabasePdbrevRecord>
getRevisionRecords()
float
getRfree()
float
getRwork()
String
getTitle()
boolean
hasJournalArticle()
Return whether or not the entry has an associated journal article or publication.void
setAuthors(String authors)
void
setBioAssemblies(Map<Integer,BioAssemblyInfo> bioAssemblies)
void
setClassification(String classification)
void
setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)
void
setDepDate(Date depDate)
The deposition date of the structure in the PDBvoid
setDescription(String description)
boolean
setExperimentalTechnique(String techniqueStr)
Adds the experimental technique to the set of experimental techniques of this header.void
setIdCode(String idCode)
The PDB code for this protein structure.void
setJournalArticle(JournalArticle journalArticle)
Set the associated publication as defined by the JRNL records in a PDB file.void
setModDate(Date modDate)
The latest modification date of the structure.void
setRelDate(Date relDate)
The release date of the structure in the PDB.void
setResolution(float resolution)
void
setRevisionRecords(List<DatabasePdbrevRecord> revisionRecords)
void
setRfree(float rFree)
void
setRwork(float rWork)
void
setTitle(String title)
String
toPDB()
Return a PDB representation of the PDB Headervoid
toPDB(StringBuffer buf)
Appends a PDB representation of the PDB header to the provided StringBufferString
toString()
String representation
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Field Detail
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DEFAULT_RESOLUTION
public static final float DEFAULT_RESOLUTION
- See Also:
- Constant Field Values
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DEFAULT_RFREE
public static final float DEFAULT_RFREE
- See Also:
- Constant Field Values
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Constructor Detail
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PDBHeader
public PDBHeader()
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Method Detail
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toPDB
public void toPDB(StringBuffer buf)
Appends a PDB representation of the PDB header to the provided StringBuffer
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getId
public Long getId()
Get the ID used by Hibernate.- Returns:
- the ID used by Hibernate
- See Also:
setId(Long)
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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.
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getIdCode
public String getIdCode()
The PDB code for this protein structure.- Returns:
- the PDB identifier
- See Also:
setIdCode(String)
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setIdCode
public void setIdCode(String idCode)
The PDB code for this protein structure.- Parameters:
idCode
- the PDB identifier- See Also:
getIdCode()
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getClassification
public String getClassification()
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setClassification
public void setClassification(String classification)
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getDepDate
public Date getDepDate()
Return the deposition date of the structure in the PDB.- Returns:
- the deposition date
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setDepDate
public void setDepDate(Date depDate)
The deposition date of the structure in the PDB- Parameters:
depDate
- the deposition date
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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
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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
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getCrystallographicInfo
public PDBCrystallographicInfo getCrystallographicInfo()
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setCrystallographicInfo
public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)
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getResolution
public float getResolution()
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setResolution
public void setResolution(float resolution)
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getRfree
public float getRfree()
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setRfree
public void setRfree(float rFree)
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getModDate
public Date getModDate()
Return the latest modification date of the structure.- Returns:
- the latest modification date
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setModDate
public void setModDate(Date modDate)
The latest modification date of the structure.- Parameters:
modDate
- the latest modification date
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getRelDate
public Date getRelDate()
Return the release date of the structure in the PDB.- Returns:
- the release date
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setRelDate
public void setRelDate(Date relDate)
The release date of the structure in the PDB.- Parameters:
relDate
- the release date
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getDescription
public String getDescription()
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setDescription
public void setDescription(String description)
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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
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setAuthors
public void setAuthors(String authors)
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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.
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getJournalArticle
public JournalArticle getJournalArticle()
Get the associated publication as defined by the JRNL records in a PDB file.- Returns:
- a JournalArticle
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setJournalArticle
public void setJournalArticle(JournalArticle journalArticle)
Set the associated publication as defined by the JRNL records in a PDB file.- Parameters:
journalArticle
- the article
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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:
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setBioAssemblies
public void setBioAssemblies(Map<Integer,BioAssemblyInfo> bioAssemblies)
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getNrBioAssemblies
public int getNrBioAssemblies()
Get the number of biological assemblies available in the PDB header- Returns:
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getRevisionRecords
public List<DatabasePdbrevRecord> getRevisionRecords()
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setRevisionRecords
public void setRevisionRecords(List<DatabasePdbrevRecord> revisionRecords)
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getRwork
public float getRwork()
- Returns:
- the R-work for this structure.
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setRwork
public void setRwork(float rWork)
- Parameters:
rWork
- the R-work for this structure.
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