public class MMCIFFileInstallation extends java.lang.Object implements PDBInstallation
Modifier and Type | Field and Description |
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static java.util.logging.Logger |
logger |
Constructor and Description |
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MMCIFFileInstallation(java.io.File filePath) |
Modifier and Type | Method and Description |
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void |
addPDBFilter(PDBFilter filter)
add a filter for PDB files.
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void |
clearFilters()
remove all filters, next time getAll is called, it will return all available PDBs
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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
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PDBHeader |
getPDBHeader(java.lang.String pdbId)
get the PDB header for a single protein structure
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Structure |
getStructure(java.lang.String pdbId)
request a structure by its PDB identifier
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boolean |
hasNext()
return if the iteration over all structures will return another structure
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boolean |
isAutoFetch()
should the parser to fetch missing mmCif files from the RCSB FTP server automatically?
default is false
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Structure |
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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void |
setAutoFetch(boolean autoFetch)
tell the parser to fetch missing mmCif files from the RCSB FTP server automatically.
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public boolean isAutoFetch()
public void setAutoFetch(boolean autoFetch)
autoFetch
- public java.io.File downloadCIF(java.lang.String pdbId)
public void addPDBFilter(PDBFilter filter)
PDBInstallation
addPDBFilter
in interface PDBInstallation
filter
- the filter to apply when getAll is being called.PDBInstallation.getAll()
public void clearFilters()
PDBInstallation
clearFilters
in interface PDBInstallation
public java.util.List<PDBHeader> getAll()
PDBInstallation
getAll
in interface PDBInstallation
public PDBHeader getPDBHeader(java.lang.String pdbId)
PDBInstallation
getPDBHeader
in interface PDBInstallation
public Structure getStructure(java.lang.String pdbId)
PDBInstallation
getStructure
in interface PDBInstallation
public boolean hasNext()
PDBInstallation
hasNext
in interface PDBInstallation
public Structure next()
PDBInstallation
next
in interface PDBInstallation