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 java.lang.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

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	lineSplit

Constructor Summary

Constructors

Constructor and Description
MMCIFFileReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	addExtension(java.lang.String ext) add a known File extension.
void	clearExtensions() clear all file extensions
java.io.File	downloadPDB(java.lang.String pdbId)
FileParsingParameters	getFileParsingParameters() Get the parameters that should be used for file parsing
SimpleMMcifConsumer	getMMcifConsumer()
java.lang.String	getPath() get the directory path to the files
Structure	getStructure(java.io.File filename) Opens filename, parses it and returns a Structure object.
Structure	getStructure(java.lang.String filename) Opens filename, parses it and returns a Structure object .
Structure	getStructureById(java.lang.String pdbId) Get a structure by PDB code.
boolean	isAutoFetch() Fetch files automatically from FTP server.
boolean	isPdbDirectorySplit() Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
static void	main(java.lang.String[] args)
Structure	parseFromInputStream(java.io.InputStream inStream)
void	setAutoFetch(boolean autoFetch) Tell the parser to fetch missing PDB files from the FTP server automatically.
void	setFileParsingParameters(FileParsingParameters params) Set the parameters that should be used for file parsing
void	setMMCifConsumer(SimpleMMcifConsumer consumer)
void	setPath(java.lang.String path) Set path to file / connection string to db.
void	setPdbDirectorySplit(boolean pdbDirectorySplit) Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

Methods inherited from class java.lang.Object

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

Field Detail

lineSplit

public static final java.lang.String lineSplit

Constructor Detail

MMCIFFileReader

public MMCIFFileReader()

Method Detail

main

public static void main(java.lang.String[] args)

addExtension

public void addExtension(java.lang.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(java.lang.String filename)
                       throws java.io.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:

java.io.IOException - ...

getStructure

public Structure getStructure(java.io.File filename)
                       throws java.io.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:

java.io.IOException - ...

parseFromInputStream

public Structure parseFromInputStream(java.io.InputStream inStream)
                               throws java.io.IOException

Throws:

java.io.IOException

setPath

public void setPath(java.lang.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 java.lang.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(java.lang.String pdbId)
                           throws java.io.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

Specified by:

getStructureById in interface StructureIOFile

Parameters:

pdbId - a 4 letter PDB code.

Returns:

a Structure object

Throws:

java.io.IOException - ...

downloadPDB

public java.io.File downloadPDB(java.lang.String pdbId)

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.

isPdbDirectorySplit

public boolean isPdbDirectorySplit()

Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

Specified by:

isPdbDirectorySplit in interface StructureIOFile

Returns:

boolean. default is false (all files in one directory)

setPdbDirectorySplit

public void setPdbDirectorySplit(boolean pdbDirectorySplit)

Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

Specified by:

setPdbDirectorySplit in interface StructureIOFile

Parameters:

pdbDirectorySplit - boolean. If set to false all files are in one directory.

getFileParsingParameters

public FileParsingParameters getFileParsingParameters()

Description copied from interface: StructureIOFile

Get the parameters that should be used for file parsing

Specified by:

getFileParsingParameters in interface StructureIOFile

Returns:

the FileParsingParameters that are configuring the behavior of the parser

setFileParsingParameters

public void setFileParsingParameters(FileParsingParameters params)

Description copied from interface: StructureIOFile

Set the parameters that should be used for file parsing

Specified by:

setFileParsingParameters in interface StructureIOFile

Parameters:

params - FileParsingParameters

getMMcifConsumer

public SimpleMMcifConsumer getMMcifConsumer()

setMMCifConsumer

public void setMMCifConsumer(SimpleMMcifConsumer consumer)