org.biojava.bio.structure.io
Class MMCIFFileReader

java.lang.Object
  org.biojava.bio.structure.io.MMCIFFileReader

All Implemented Interfaces:

StructureIO, StructureIOFile

public class MMCIFFileReader
extends Object
implements StructureIOFile

How to parse an mmCif file:

  public static void main(String[] args){
        String filename =  "/path/to/something.cif.gz" ;

        StructureIOFile reader = new MMCIFFileReader();

        try{
            Structure struc = reader.getStructure(filename);
            System.out.println(struc);
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    

Since:

1.7

Author:

Andreas Prlic

Constructor Summary

MMCIFFileReader()

Method Summary

void	addExtension(String ext) add a known File extension.
void	clearExtensions() clear all file extensions
String	getPath() get the directory path to the files
Structure	getStructure(File filename) Opens filename, parses it and returns a Structure object.
Structure	getStructure(String filename) Opens filename, parses it and returns a Structure object .
Structure	getStructureById(String pdbId) Get a structure by PDB code.
boolean	isAutoFetch() Fetch files automatically from FTP server.
static void	main(String[] args)
void	setAutoFetch(boolean autoFetch) Tell the parser to fetch missing PDB files from the FTP server automatically.
void	setPath(String path) Set path to file / connection string to db.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MMCIFFileReader

public MMCIFFileReader()

Method Detail

main

public static void main(String[] args)

addExtension

public void addExtension(String ext)

Description copied from interface: StructureIOFile

add a known File extension.

Specified by:

addExtension in interface StructureIOFile

Parameters:

ext - a String ...

clearExtensions

public void clearExtensions()

Description copied from interface: StructureIOFile

clear all file extensions

Specified by:

clearExtensions in interface StructureIOFile

getStructure

public Structure getStructure(String filename)
                       throws IOException

Opens filename, parses it and returns a Structure object .

Specified by:

getStructure in interface StructureIOFile

Parameters:

filename - a String

Returns:

the Structure object

Throws:

IOException - ...

getStructure

public Structure getStructure(File filename)
                       throws IOException

Opens filename, parses it and returns a Structure object.

Specified by:

getStructure in interface StructureIOFile

Parameters:

filename - a File object

Returns:

the Structure object

Throws:

IOException - ...

setPath

public void setPath(String path)

Description copied from interface: StructureIOFile

Set path to file / connection string to db. This is for installations of PDB/mmCif where all files are located in one directory.

Specified by:

setPath in interface StructureIOFile

Parameters:

path - a String specifying the path value

getPath

public String getPath()

Description copied from interface: StructureIOFile

get the directory path to the files

Specified by:

getPath in interface StructureIOFile

Returns:

path

getStructureById

public Structure getStructureById(String pdbId)
                           throws IOException

Get a structure by PDB code. This works if a PATH has been set via setPath, or if setAutoFetch has been set to true.

Specified by:

getStructureById in interface StructureIO

Parameters:

pdbId - a 4 letter PDB code.

Returns:

a Structure object

Throws:

IOException - ...

isAutoFetch

public boolean isAutoFetch()

Description copied from interface: StructureIOFile

Fetch files automatically from FTP server. Default: false

Specified by:

isAutoFetch in interface StructureIOFile

Returns:

flag is true or false.

setAutoFetch

public void setAutoFetch(boolean autoFetch)

Description copied from interface: StructureIOFile

Tell the parser to fetch missing PDB files from the FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.

Specified by:

setAutoFetch in interface StructureIOFile

Parameters:

autoFetch - flag.