MMCIFFileReader

java.lang.Object
- org.biojava.nbio.structure.io.LocalPDBDirectory
- - org.biojava.nbio.structure.io.MMCIFFileReader

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

Nested Class Summary
- Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
  LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String[] MMCIF_OBSOLETE_DIR

static java.lang.String[] MMCIF_SPLIT_DIR
- Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
  DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, PDB_FILE_SERVER_PROPERTY

Fields
Modifier and Type	Field and Description
`static java.lang.String[]`	`MMCIF_OBSOLETE_DIR`
`static java.lang.String[]`	`MMCIF_SPLIT_DIR`

Constructor Summary

Constructors
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.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
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)`

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, isAutoFetch, prefetchStructure, setAutoFetch, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MMCIF_SPLIT_DIR
```
public static final java.lang.String[] MMCIF_SPLIT_DIR
```
  - MMCIF_OBSOLETE_DIR
```
public static final java.lang.String[] MMCIF_OBSOLETE_DIR
```
- Constructor Detail
  - MMCIFFileReader
```
public MMCIFFileReader()
```
    Constructs a new MMCIFFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false
  - 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.
- Method Detail
  - main
```
public static void main(java.lang.String[] args)
                 throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - 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 class LocalPDBDirectory
    
    Returns:
    
    Throws:
    
    java.io.IOException
  - getMMcifConsumer
```
public SimpleMMcifConsumer getMMcifConsumer()
```
  - 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 class LocalPDBDirectory
    
    Returns:
    
    The filename, e.g. "4hhb.pdb.gz"
  - 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 class LocalPDBDirectory
    
    Returns:
    
    A list of directories, relative to the /pub/pdb directory on the server
  - 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 class LocalPDBDirectory
    
    Returns:
    
    A list of directories, relative to the /pub/pdb directory on the server

Class MMCIFFileReader

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

Field Summary

Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

Constructor Summary

Method Summary

Methods inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

Methods inherited from class java.lang.Object

Field Detail

MMCIF_SPLIT_DIR

MMCIF_OBSOLETE_DIR

Constructor Detail

MMCIFFileReader

MMCIFFileReader

Method Detail

main

getStructure

getMMcifConsumer

getFilename

getSplitDirPath

getObsoleteDirPath