org.biojava.bio.structure.io

Class PDBMSDReader

java.lang.Object

org.biojava.bio.structure.io.PDBMSDReader

All Implemented Interfaces:

StructureIO

public class PDBMSDReader
extends java.lang.Object
implements StructureIO

retreive a structure from an installation of the MSD - search database ( http://www.ebi.ac.uk/msd/index.html , http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )

Field Summary

Fields

Modifier and Type	Field and Description
protected javax.sql.DataSource	dataSource

Constructor Summary

Constructors

Constructor and Description
PDBMSDReader()

Method Summary

Methods

Modifier and Type	Method and Description
Structure	getStructureById(java.lang.String pdbId) Get a structure by providing a PDB code.
void	setDBConnection(java.lang.String dbDriver, java.lang.String dbUrl, java.lang.String dbUsername, java.lang.String dbPassword) open a database conenction to the MSD search database

Methods inherited from class java.lang.Object

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

Field Detail

dataSource

protected javax.sql.DataSource dataSource

Constructor Detail

PDBMSDReader

public PDBMSDReader()

Method Detail

setDBConnection

public void setDBConnection(java.lang.String dbDriver,
                   java.lang.String dbUrl,
                   java.lang.String dbUsername,
                   java.lang.String dbPassword)
                     throws java.sql.SQLException

open a database conenction to the MSD search database

Parameters:

dbDriver - specified which JDBC driver to use e.g.

dbUrl - connection string

dbUsername - the username in the db

dbPassword - password to use

Throws:

java.sql.SQLException

getStructureById

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

Get a structure by providing a PDB code. expects connections parameters to be set a system properties.

Specified by:

getStructureById in interface StructureIO

Parameters:

pdbId - a String specifying the id value (PDB code)

Returns:

a Structure object, or null if no structure with matching PDB code has been found

Throws:

java.io.IOException - ...