org.biojava.bio.structure.server
Class MMCIFFileInstallation

java.lang.Object
  extended by org.biojava.bio.structure.server.MMCIFFileInstallation
All Implemented Interfaces:
PDBInstallation

public class MMCIFFileInstallation
extends Object
implements PDBInstallation


Field Summary
static Logger logger
           
 
Constructor Summary
MMCIFFileInstallation(File filePath)
           
 
Method Summary
 void addPDBFilter(PDBFilter filter)
          add a filter for PDB files.
 void clearFilters()
          remove all filters, next time getAll is called, it will return all available PDBs
 File downloadCIF(String pdbId)
           
 List<PDBHeader> getAll()
          get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
 PDBHeader getPDBHeader(String pdbId)
          get the PDB header for a single protein structure
 Structure getStructure(String pdbId)
          request a structure by its PDB identifier
 boolean hasNext()
          return if the iteration over all structures will return another structure
 boolean isAutoFetch()
          should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false
 Structure next()
          iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
 void setAutoFetch(boolean autoFetch)
          tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger

public static final Logger logger
Constructor Detail

MMCIFFileInstallation

public MMCIFFileInstallation(File filePath)
Method Detail

isAutoFetch

public boolean isAutoFetch()
should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false

Returns:
flag

setAutoFetch

public void setAutoFetch(boolean autoFetch)
tell the parser to fetch missing mmCif files from the RCSB FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.

Parameters:
autoFetch -

downloadCIF

public File downloadCIF(String pdbId)

addPDBFilter

public void addPDBFilter(PDBFilter filter)
Description copied from interface: PDBInstallation
add a filter for PDB files. THis can be used to request, e.g. all X-ray structures, or all structures with a given resolution, all proteins with a certain function, etc.

Specified by:
addPDBFilter in interface PDBInstallation
Parameters:
filter - the filter to apply when getAll is being called.
See Also:
PDBInstallation.getAll()

clearFilters

public void clearFilters()
Description copied from interface: PDBInstallation
remove all filters, next time getAll is called, it will return all available PDBs

Specified by:
clearFilters in interface PDBInstallation

getAll

public List<PDBHeader> getAll()
Description copied from interface: PDBInstallation
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs

Specified by:
getAll in interface PDBInstallation
Returns:
a list of PDBHeader objects

getPDBHeader

public PDBHeader getPDBHeader(String pdbId)
Description copied from interface: PDBInstallation
get the PDB header for a single protein structure

Specified by:
getPDBHeader in interface PDBInstallation
Returns:
the PDB header object

getStructure

public Structure getStructure(String pdbId)
Description copied from interface: PDBInstallation
request a structure by its PDB identifier

Specified by:
getStructure in interface PDBInstallation
Returns:
the structure for the pdbId

hasNext

public boolean hasNext()
Description copied from interface: PDBInstallation
return if the iteration over all structures will return another structure

Specified by:
hasNext in interface PDBInstallation
Returns:
true if there is another structure that has not been iterated over yet

next

public Structure next()
Description copied from interface: PDBInstallation
iterate over all structures in this Installation that pass the provided filters and return the next one in the list.

Specified by:
next in interface PDBInstallation
Returns:
the next structure