org.biojava.bio.structure.server

Class MMCIFFileInstallation

java.lang.Object

org.biojava.bio.structure.server.MMCIFFileInstallation

All Implemented Interfaces:

PDBInstallation

public class MMCIFFileInstallation
extends java.lang.Object
implements PDBInstallation

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.logging.Logger	logger

Constructor Summary

Constructors

Constructor and Description
MMCIFFileInstallation(java.io.File filePath)

Method Summary

Methods

Modifier and Type	Method and Description
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
java.io.File	downloadCIF(java.lang.String pdbId)
java.util.List<PDBHeader>	getAll() get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
PDBHeader	getPDBHeader(java.lang.String pdbId) get the PDB header for a single protein structure
Structure	getStructure(java.lang.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 java.util.logging.Logger logger

Constructor Detail

MMCIFFileInstallation

public MMCIFFileInstallation(java.io.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 java.io.File downloadCIF(java.lang.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 java.util.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(java.lang.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(java.lang.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