Package org.biojava.bio.structure.server
Class MMCIFFileInstallation
- java.lang.Object
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- org.biojava.bio.structure.server.MMCIFFileInstallation
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- All Implemented Interfaces:
PDBInstallation
public class MMCIFFileInstallation extends java.lang.Object implements PDBInstallation
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Field Summary
Fields Modifier and Type Field Description static java.util.logging.Logger
logger
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Constructor Summary
Constructors Constructor Description MMCIFFileInstallation(java.io.File filePath)
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Method Summary
All Methods Instance Methods Concrete 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.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 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 structureboolean
isAutoFetch()
should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is falseStructure
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.
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Method Detail
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isAutoFetch
public boolean isAutoFetch()
should the parser to fetch missing mmCif files from the RCSB FTP server automatically? default is false- Returns:
- flag
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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
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downloadCIF
public java.io.File downloadCIF(java.lang.String pdbId)
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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 interfacePDBInstallation
- Parameters:
filter
- the filter to apply when getAll is being called.- See Also:
PDBInstallation.getAll()
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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 interfacePDBInstallation
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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 interfacePDBInstallation
- Returns:
- a list of PDBHeader objects
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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 interfacePDBInstallation
- Returns:
- the PDB header object
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getStructure
public Structure getStructure(java.lang.String pdbId)
Description copied from interface:PDBInstallation
request a structure by its PDB identifier- Specified by:
getStructure
in interfacePDBInstallation
- Returns:
- the structure for the pdbId
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hasNext
public boolean hasNext()
Description copied from interface:PDBInstallation
return if the iteration over all structures will return another structure- Specified by:
hasNext
in interfacePDBInstallation
- Returns:
- true if there is another structure that has not been iterated over yet
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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 interfacePDBInstallation
- Returns:
- the next structure
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