Package org.biojava.bio.structure.server
Interface PDBInstallation
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- All Known Implementing Classes:
FlatFileInstallation
,MMCIFFileInstallation
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
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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 PDBsjava.util.List<PDBHeader>
getAll()
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBsPDBHeader
getPDBHeader(java.lang.String pdbId)
get the PDB header for a single protein structureStructure
getStructure(java.lang.String pdbId)
request a structure by its PDB identifierboolean
hasNext()
return if the iteration over all structures will return another structureStructure
next()
iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
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Method Detail
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getAll
java.util.List<PDBHeader> getAll()
get all PDBHeaders that pass the added Filters, if no filters have been added returns all available PDBs- Returns:
- a list of PDBHeader objects
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getPDBHeader
PDBHeader getPDBHeader(java.lang.String pdbId)
get the PDB header for a single protein structure- Parameters:
pdbId
-- Returns:
- the PDB header object
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addPDBFilter
void addPDBFilter(PDBFilter filter)
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()
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clearFilters
void clearFilters()
remove all filters, next time getAll is called, it will return all available PDBs
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getStructure
Structure getStructure(java.lang.String pdbId)
request a structure by its PDB identifier- Parameters:
pdbId
-- Returns:
- the structure for the pdbId
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next
Structure next()
iterate over all structures in this Installation that pass the provided filters and return the next one in the list.- Returns:
- the next structure
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hasNext
boolean hasNext()
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
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