Package org.biojava.nbio.structure.rcsb

Class RCSBLigandsFactory

java.lang.Object

org.biojava.nbio.structure.rcsb.RCSBLigandsFactory

public class RCSBLigandsFactory
extends Object

Fetches information from RCSB's RESTful Web Service Interface. A factory for RCSBLigands from ligandInfo 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:

 RCSBLigands ligands = RCSBLigandsFactory.getFromPdbIds("1w0p");
 List<RCSBLigand> list = ligands.getLigands();
 System.out.println(list.get(0).getFormula()); // prints "CA 2"
 System.out.println(list.get(1).getFormula()); // prints "C11 H19 N O9"
 

Since:

3.0.6

Author:

dmyerstu

See Also:

RCSB RESTful

Constructor Summary

Constructors

Constructor	Description
RCSBLigandsFactory()

Method Summary

Modifier and Type	Method	Description
static RCSBLigand	getFromHeteroAtomId(InputStream stream)
static RCSBLigand	getFromHeteroAtomId(String heteroAtomId)
static List<RCSBLigand>	getFromHeteroAtomIds(InputStream stream)
static List<RCSBLigand>	getFromHeteroAtomIds(String... heteroAtomIds)
static List<RCSBLigand>	getFromHeteroAtomIds(List<String> heteroAtomIds)
static RCSBLigands	getFromPdbId(InputStream stream)
static RCSBLigands	getFromPdbId(String pdbId)
static List<RCSBLigands>	getFromPdbIds(InputStream stream)
static RCSBLigands	getFromPdbIds(String pdbId)
static List<RCSBLigands>	getFromPdbIds(String... pdbIds)
static List<RCSBLigands>	getFromPdbIds(List<String> pdbIds)

Methods inherited from class java.lang.Object

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

Constructor Detail

RCSBLigandsFactory

public RCSBLigandsFactory()

Method Detail

getFromHeteroAtomId

public static RCSBLigand getFromHeteroAtomId(InputStream stream)

Returns:

A list of RCSBLigands from the XML file loaded as stream. Prefer calling getFromHeteroAtomId(String) if you want data directly from RCSB's RESTful service.

See Also:

RCSBDescriptionFactory.get(String)

getFromHeteroAtomId

public static RCSBLigand getFromHeteroAtomId(String heteroAtomId)

Returns:

An RCSBLigands from the XML file at "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required.

See Also:

RCSBDescriptionFactory.get(InputStream)

getFromHeteroAtomIds

public static List<RCSBLigand> getFromHeteroAtomIds(InputStream stream)

Returns:

A list of RCSBLigands from the XML file loaded as stream. Prefer calling getFromHeteroAtomId(String) if you want data directly from RCSB's RESTful service.

See Also:

RCSBDescriptionFactory.get(String)

getFromHeteroAtomIds

public static List<RCSBLigand> getFromHeteroAtomIds(List<String> heteroAtomIds)

Returns:

An RCSBLigands from the XML file at "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required.

See Also:

RCSBDescriptionFactory.get(InputStream)

getFromHeteroAtomIds

public static List<RCSBLigand> getFromHeteroAtomIds(String... heteroAtomIds)

Returns:

An RCSBLigands from the XML file at "http://www.pdb.org/pdb/rest/describeHet?chemicalID=hetid". This is the preferred factory method, unless a different URL or input source is required.

See Also:

RCSBDescriptionFactory.get(InputStream)

getFromPdbId

public static RCSBLigands getFromPdbId(InputStream stream)

Returns:

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

See Also:

RCSBDescriptionFactory.get(String)

getFromPdbId

public static RCSBLigands getFromPdbId(String pdbId)

Returns:

An RCSBLigands 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:

RCSBDescriptionFactory.get(InputStream)

getFromPdbIds

public static List<RCSBLigands> getFromPdbIds(InputStream stream)

Returns:

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

See Also:

RCSBDescriptionFactory.get(String)

getFromPdbIds

public static List<RCSBLigands> getFromPdbIds(List<String> pdbIds)

Returns:

An RCSBLigands 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:

RCSBDescriptionFactory.get(InputStream)

getFromPdbIds

public static RCSBLigands getFromPdbIds(String pdbId)

Returns:

An RCSBLigands 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:

RCSBDescriptionFactory.get(InputStream)

getFromPdbIds

public static List<RCSBLigands> getFromPdbIds(String... pdbIds)

Returns:

An RCSBLigands 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:

RCSBDescriptionFactory.get(InputStream)