org.rcsb.mmtf.decoder

Class ReaderUtils

java.lang.Object

org.rcsb.mmtf.decoder.ReaderUtils

public class ReaderUtils
extends java.lang.Object

This class provides methods to retrieve and decode MMTF data from the MMTF server and MMTF files.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
ReaderUtils()

Method Summary

Modifier and Type	Method and Description
static byte[]	deflateGzip(byte[] inputBytes) Deflate a gzip byte array.
static byte[]	getByteArrayFromUrl(java.lang.String pdbId) Gets the GZIP compressed and messagepack serialized data from the MMTF servers
static byte[]	getByteArrayFromUrl(java.lang.String pdbId, boolean https, boolean reduced) Gets the GZIP compressed and messagepack serialized data from the MMTF servers.
static MmtfStructure	getDataFromFile(java.nio.file.Path filePath) Reads and deserializes an uncompressed MMTF file.
static MmtfStructure	getDataFromInputStream(java.io.InputStream inStream) Read an input stream to an MmtfStructure object.
static MmtfStructure	getDataFromUrl(java.lang.String pdbId) Returns a full (atom atom) MmmtfStructure given a PDB Id from the MMTF web server using HTTP.
static MmtfStructure	getDataFromUrl(java.lang.String pdbId, boolean https, boolean reduced) Returns an MmmtfStructure given a PDB Id from the MMTF web server.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReaderUtils

public ReaderUtils()

Method Detail

getDataFromUrl

public static MmtfStructure getDataFromUrl(java.lang.String pdbId)
                                    throws java.io.IOException

Returns a full (atom atom) MmmtfStructure given a PDB Id from the MMTF web server using HTTP.

Parameters:

pdbId - the pdb code for the desired structure.

Returns:

MmtfStructure containing the decoded structure

Throws:

java.io.IOException - if the data cannot be read from the URL

getDataFromUrl

public static MmtfStructure getDataFromUrl(java.lang.String pdbId,
                                           boolean https,
                                           boolean reduced)
                                    throws java.io.IOException

Returns an MmmtfStructure given a PDB Id from the MMTF web server. It requests, gets, decompresses, deserializes and decodes the message pack byte array from the MMTF web server. This methods support http and https protocols and two MMTF representations: full and reduced. reduced: C-alpha atoms for polypeptides, P for polynucleotides, and all atom for all other groups (residues) at 0.1 A coordinate precision; full: all atoms at 0.001 A coordinate precision

Parameters:

pdbId - the pdb code for the desired structure.

Returns:

decoded MmmtfStructure

Throws:

java.io.IOException - if the data cannot be read from the URL

getByteArrayFromUrl

public static byte[] getByteArrayFromUrl(java.lang.String pdbId)
                                  throws java.io.IOException

Gets the GZIP compressed and messagepack serialized data from the MMTF servers

Parameters:

pdbId - the PDB code for the data required

Returns:

the byte array (GZIP compressed) of the data from the URL

Throws:

java.io.IOException - an error reading the URL

getByteArrayFromUrl

public static byte[] getByteArrayFromUrl(java.lang.String pdbId,
                                         boolean https,
                                         boolean reduced)
                                  throws java.io.IOException

Gets the GZIP compressed and messagepack serialized data from the MMTF servers. This methods support http and https protocols and two MMTF representations: full and reduced. reduced: C-alpha atoms for polypeptides, P for polynucleotides, and all atom for all other groups (residues) at 0.1 A coordinate precision; full: all atoms at 0.001 A coordinate precision

Parameters:

pdbId - the PDB Id to retrieve

Returns:

the byte array (GZIP compressed) of the data from the URL

Throws:

java.io.IOException - an error reading the URL

deflateGzip

public static byte[] deflateGzip(byte[] inputBytes)
                          throws java.io.IOException

Deflate a gzip byte array.

Parameters:

inputBytes - a gzip compressed byte array

Returns:

a deflated byte array

Throws:

java.io.IOException - error in gzip input stream

getDataFromFile

public static MmtfStructure getDataFromFile(java.nio.file.Path filePath)
                                     throws java.io.IOException

Reads and deserializes an uncompressed MMTF file.

Parameters:

filePath - the full path of the file to be read

Returns:

the deserialized MmtfStructure

Throws:

java.io.IOException - an error reading the file

getDataFromInputStream

public static MmtfStructure getDataFromInputStream(java.io.InputStream inStream)
                                            throws java.io.IOException

Read an input stream to an MmtfStructure object.

Parameters:

inStream - the InputStream to read.

Returns:

the MmtfStructure to be returned

Throws:

java.io.IOException - if the inStream cannot be read