org.biojava.nbio.structure.io.mmtf

Class MmtfActions

java.lang.Object

org.biojava.nbio.structure.io.mmtf.MmtfActions

public class MmtfActions
extends java.lang.Object

A class of functions for reading and writing Biojava structures using MMTF

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
MmtfActions()

Method Summary

Modifier and Type	Method and Description
static Structure	readFromFile(java.nio.file.Path filePath) Get a Structure object from a mmtf file.
static Structure	readFromInputStream(java.io.InputStream inStream) Read a Biojava structure from an InputStream
static Structure	readFromWeb(java.lang.String pdbId) Get a Biojava structure from the mmtf REST service.
static void	writeToFile(Structure structure, java.nio.file.Path path) Write a Structure object to a file.
static void	writeToOutputStream(Structure structure, java.io.OutputStream outputStream) Write a Structure object to an OutputStream

Methods inherited from class java.lang.Object

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

Constructor Detail

MmtfActions

public MmtfActions()

Method Detail

readFromFile

public static Structure readFromFile(java.nio.file.Path filePath)
                              throws java.io.IOException

Get a Structure object from a mmtf file.

Parameters:

filePath - the mmtf file

Returns:

a Structure object relating to the input byte array.

Throws:

java.io.IOException

writeToFile

public static void writeToFile(Structure structure,
                               java.nio.file.Path path)
                        throws java.io.IOException

Write a Structure object to a file.

Parameters:

structure - the Structure to write

path - the file to write

Throws:

java.io.IOException

writeToOutputStream

public static void writeToOutputStream(Structure structure,
                                       java.io.OutputStream outputStream)
                                throws java.io.IOException

Write a Structure object to an OutputStream

Parameters:

structure - the Structure to write

outputStream - the OutputStream to write to

Throws:

java.io.IOException - an error transferring the byte[]

readFromWeb

public static Structure readFromWeb(java.lang.String pdbId)
                             throws java.io.IOException

Get a Biojava structure from the mmtf REST service.

Parameters:

pdbId - the PDB code of the required structure

Returns:

a Structure object relating to the input byte array

Throws:

java.io.IOException

readFromInputStream

public static Structure readFromInputStream(java.io.InputStream inStream)
                                     throws java.io.IOException

Read a Biojava structure from an InputStream

Parameters:

inStream - the InputStream to read from

Returns:

the parsed Structure

Throws:

java.io.IOException