org.biojava.nbio.structure.rcsb

Class RCSBDescriptionFactory

java.lang.Object

org.biojava.nbio.structure.rcsb.RCSBDescriptionFactory

public class RCSBDescriptionFactory
extends Object

Fetches information from RCSB's RESTful Web Service Interface. A factory for RCSBDescriptions from describeMol XML files. The factory methods will return null if the data was not found (rather than throwing an exception); client code should test for this. This is for consistency: if the factory could not read some part (corresponding to a field in a class in rcsb.descriptions) of the XML file, either because it was blank or contained an error that could not be safely ignored, that field will simply be null. This holds even for numerical values. On some parse errors, the error will additionally be printed to standard error. Example usage:

 RCSBDescription description = RCSBDescriptionFactory.get("1w0p");
 RCSBLigand firstLigand = ligands.getLigands().get(0);
 System.out.println(description.getPdbId()); // prints "1w0p"
 

Since:

3.0.6

Author:

dmyerstu

See Also:

RCSB RESTful TODO: Handle queries with more than 1 PDB Id.

Constructor Summary

Constructors

Constructor and Description
RCSBDescriptionFactory()

Method Summary

Methods

Modifier and Type	Method and Description
static RCSBDescription	get(InputStream stream)
static RCSBDescription	get(String pdbId)

Methods inherited from class java.lang.Object

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

Constructor Detail

RCSBDescriptionFactory

public RCSBDescriptionFactory()

Method Detail

get

public static RCSBDescription get(InputStream stream)

Returns:

An RCSBDescription from the XML file loaded as stream. Prefer calling get(String) if you want data directly from RCSB's RESTful service.

See Also:

get(String)

get

public static RCSBDescription get(String pdbId)

Returns:

An RCSBDescription from the XML file at "http://www.pdb.org/pdb/rest/describeMol?structureId=pdbId". This is the preferred factory method, unless a different URL or input source is required.

See Also:

get(InputStream)