Package org.biojava.nbio.structure.io
Class MMCIFFileReader
- java.lang.Object
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- org.biojava.nbio.structure.io.LocalPDBDirectory
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- org.biojava.nbio.structure.io.MMCIFFileReader
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- All Implemented Interfaces:
StructureIOFile
,StructureProvider
public class MMCIFFileReader extends LocalPDBDirectory
How to parse an mmCif file:public static void main(String[] args) throws Exception { String filename = "/path/to/something.cif.gz" ; StructureIOFile reader = new MMCIFFileReader(); Structure struc = reader.getStructure(filename); System.out.println(struc); }
- Since:
- 1.7
- Author:
- Andreas Prlic
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Nested Class Summary
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Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
MMCIF_OBSOLETE_DIR
static java.lang.String[]
MMCIF_SPLIT_DIR
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Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, MIN_PDB_FILE_SIZE, PDB_FILE_SERVER_PROPERTY
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Constructor Summary
Constructors Constructor Description MMCIFFileReader()
Constructs a new MMCIFFileReader, initializing the extensions member variable.MMCIFFileReader(java.lang.String path)
Constructs a new PDBFileReader, initializing the extensions member variable.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected java.lang.String
getFilename(java.lang.String pdbId)
Converts a PDB ID into a filename with the proper extensionSimpleMMcifConsumer
getMMcifConsumer()
protected java.lang.String[]
getObsoleteDirPath()
Location of obsolete files within the directory, as an array of paths.protected java.lang.String[]
getSplitDirPath()
Location of split files within the directory, as an array of paths.Structure
getStructure(java.io.InputStream inStream)
Handles the actual parsing of the file into a Structure object.static void
main(java.lang.String[] args)
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Methods inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
addExtension, checkFileExists, clearExtensions, deleteStructure, downloadStructure, getDir, getExtensions, getFetchBehavior, getFileParsingParameters, getInputStream, getLocalFile, getObsoleteBehavior, getPath, getServerName, getStructure, getStructure, getStructure, getStructureById, initPaths, prefetchStructure, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath
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Constructor Detail
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MMCIFFileReader
public MMCIFFileReader()
Constructs a new MMCIFFileReader, initializing the extensions member variable. The path is initialized in the same way asUserConfiguration
, i.e. to system property/environment variableUserConfiguration.PDB_DIR
. Both autoFetch and splitDir are initialized to false
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MMCIFFileReader
public MMCIFFileReader(java.lang.String path)
Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.
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Method Detail
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main
public static void main(java.lang.String[] args) throws java.lang.Exception
- Throws:
java.lang.Exception
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getStructure
public Structure getStructure(java.io.InputStream inStream) throws java.io.IOException
Description copied from class:LocalPDBDirectory
Handles the actual parsing of the file into a Structure object.- Specified by:
getStructure
in classLocalPDBDirectory
- Returns:
- Throws:
java.io.IOException
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getMMcifConsumer
public SimpleMMcifConsumer getMMcifConsumer()
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getFilename
protected java.lang.String getFilename(java.lang.String pdbId)
Description copied from class:LocalPDBDirectory
Converts a PDB ID into a filename with the proper extension- Specified by:
getFilename
in classLocalPDBDirectory
- Returns:
- The filename, e.g. "4hhb.pdb.gz"
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getSplitDirPath
protected java.lang.String[] getSplitDirPath()
Description copied from class:LocalPDBDirectory
Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.- Specified by:
getSplitDirPath
in classLocalPDBDirectory
- Returns:
- A list of directories, relative to the /pub/pdb directory on the server
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getObsoleteDirPath
protected java.lang.String[] getObsoleteDirPath()
Description copied from class:LocalPDBDirectory
Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.- Specified by:
getObsoleteDirPath
in classLocalPDBDirectory
- Returns:
- A list of directories, relative to the /pub/pdb directory on the server
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