PDBHeader (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.structure.PDBHeader

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

Field Summary

Fields
Modifier and Type Field and Description

static float DEFAULT_RESOLUTION

static float DEFAULT_RFREE

static String newline

Fields
Modifier and Type	Field and Description
`static float`	`DEFAULT_RESOLUTION`
`static float`	`DEFAULT_RFREE`
`static String`	`newline`

Constructor Summary

Constructors
Constructor and Description

PDBHeader()

Constructors
Constructor and Description
`PDBHeader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(PDBHeader other)` Compare two PDBHeader objects
`String`	`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 values
`Long`	`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 header
`Date`	`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 PDB
`void`	`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 Header
`void`	`toPDB(StringBuffer buf)` Appends a PDB representation of the PDB header to the provided StringBuffer
`String`	`toString()` String representation

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - DEFAULT_RESOLUTION
```
public static final float DEFAULT_RESOLUTION
```
    See Also:
    
    Constant Field Values
  - DEFAULT_RFREE
```
public static final float DEFAULT_RFREE
```
    See Also:
    
    Constant Field Values
  - newline
```
public static final String newline
```
- Constructor Detail
  - PDBHeader
```
public PDBHeader()
```
- Method Detail
  - 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(String)
  - setIdCode
```
public void setIdCode(String idCode)
```
    The PDB code for this protein structure.
    
    Parameters:
    
    idCode - the PDB identifier
    
    See Also:
    
    getIdCode()
  - getClassification
```
public String getClassification()
```
  - setClassification
```
public void setClassification(String classification)
```
  - 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
  - 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()
```
    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
  - 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 (starting at 1). Non-numerical identifiers such as PAU or XAU are not supported.
    
    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)
```
  - 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.

Class PDBHeader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_RESOLUTION

DEFAULT_RFREE

newline

Constructor Detail

PDBHeader

Method Detail

toString

toPDB

toPDB

getId

equals

getIdCode

setIdCode

getClassification

setClassification

getDepDate

setDepDate

getExperimentalTechniques

setExperimentalTechnique

getCrystallographicInfo

setCrystallographicInfo

getResolution

setResolution

getRfree

setRfree

getModDate

setModDate

getRelDate

setRelDate

getTitle

setTitle

getDescription

setDescription

getAuthors

setAuthors

hasJournalArticle

getJournalArticle

setJournalArticle

getBioAssemblies

setBioAssemblies

getNrBioAssemblies

getRevisionRecords

setRevisionRecords

getRwork

setRwork