public class MMCIFFileReader extends LocalPDBDirectory
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); }
LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior
Modifier and Type | Field and Description |
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static java.lang.String[] |
MMCIF_OBSOLETE_DIR |
static java.lang.String[] |
MMCIF_SPLIT_DIR |
DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, PDB_FILE_SERVER_PROPERTY
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
getFilename(java.lang.String pdbId)
Converts a PDB ID into a filename with the proper extension
|
SimpleMMcifConsumer |
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) |
addExtension, checkFileExists, clearExtensions, deleteStructure, downloadStructure, getDir, getExtensions, getFetchBehavior, getFileParsingParameters, getInputStream, getLocalFile, getObsoleteBehavior, getPath, getServerName, getStructure, getStructure, getStructure, getStructureById, initPaths, isAutoFetch, prefetchStructure, setAutoFetch, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath
public static final java.lang.String[] MMCIF_SPLIT_DIR
public static final java.lang.String[] MMCIF_OBSOLETE_DIR
public MMCIFFileReader()
UserConfiguration
,
i.e. to system property/environment variable UserConfiguration.PDB_DIR
.
Both autoFetch and splitDir are initialized to falsepublic MMCIFFileReader(java.lang.String path)
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
public Structure getStructure(java.io.InputStream inStream) throws java.io.IOException
LocalPDBDirectory
getStructure
in class LocalPDBDirectory
java.io.IOException
public SimpleMMcifConsumer getMMcifConsumer()
protected java.lang.String getFilename(java.lang.String pdbId)
LocalPDBDirectory
getFilename
in class LocalPDBDirectory
protected java.lang.String[] getSplitDirPath()
LocalPDBDirectory
getSplitDirPath
in class LocalPDBDirectory
protected java.lang.String[] getObsoleteDirPath()
LocalPDBDirectory
getObsoleteDirPath
in class LocalPDBDirectory