org.biojava.bio.structure.server

Interface PDBInstallation

All Known Implementing Classes:

FlatFileInstallation, MMCIFFileInstallation

Deprecated.

public interface PDBInstallation

an interface that defines different access methods to PDB installations. Installations can be Flat file based ones, database ones, Installations that download all files from the net, etc.

Author:

Andreas Prlic

Method Summary

Methods

Modifier and Type	Method and Description
void	addPDBFilter(PDBFilter filter) Deprecated. add a filter for PDB files.
void	clearFilters() Deprecated. remove all filters, next time getAll is called, it will return all available PDBs
List<PDBHeader>	getAll() Deprecated. get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs
PDBHeader	getPDBHeader(String pdbId) Deprecated. get the PDB header for a single protein structure
Structure	getStructure(String pdbId) Deprecated. request a structure by its PDB identifier
boolean	hasNext() Deprecated. return if the iteration over all structures will return another structure
Structure	next() Deprecated. iterate over all structures in this Installation that pass the provided filters and return the next one in the list.

Method Detail

getAll

List<PDBHeader> getAll()

Deprecated.

get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs

Returns:

a list of PDBHeader objects

getPDBHeader

PDBHeader getPDBHeader(String pdbId)

Deprecated.

get the PDB header for a single protein structure

Parameters:

pdbId -

Returns:

the PDB header object

addPDBFilter

void addPDBFilter(PDBFilter filter)

Deprecated.

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.

Parameters:

filter - the filter to apply when getAll is being called.

See Also:

getAll()

clearFilters

void clearFilters()

Deprecated.

remove all filters, next time getAll is called, it will return all available PDBs

getStructure

Structure getStructure(String pdbId)

Deprecated.

request a structure by its PDB identifier

Parameters:

pdbId -

Returns:

the structure for the pdbId

next

Structure next()

Deprecated.

iterate over all structures in this Installation that pass the provided filters and return the next one in the list.

Returns:

the next structure

hasNext

boolean hasNext()

Deprecated.

return if the iteration over all structures will return another structure

Returns:

true if there is another structure that has not been iterated over yet