Package org.biojava.nbio.structure.xtal

Class SymoplibParser

java.lang.Object

org.biojava.nbio.structure.xtal.SymoplibParser

public class SymoplibParser
extends Object

A class containing static methods to parse the symop.lib file from the CCP4 package. The file contains the transformations belonging to all protein crystallography space groups. See http://structure.usc.edu/ccp4/symlib.html for documentation

Author:

duarte_j

Constructor Summary

Constructors

Constructor	Description
SymoplibParser()

Method Summary

Modifier and Type	Method	Description
static TreeMap<Integer,SpaceGroup>	getAllSpaceGroups()
static SpaceGroup	getSpaceGroup(int id)	Gets the space group for the given standard identifier.
static SpaceGroup	getSpaceGroup(String shortName)	Get the space group for the given international short name, using the PDB format, e.g.
static TreeMap<Integer,SpaceGroup>	parseSpaceGroupsXML(InputStream spaceGroupIS)	Load all SpaceGroup information from the file spacegroups.xml
static TreeMap<Integer,SpaceGroup>	parseSymopLib(InputStream symoplibIS)	A parser for the symop.lib file provided by CCP4.

Methods inherited from class java.lang.Object

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

Constructor Details

SymoplibParser

public SymoplibParser()

Method Details

getSpaceGroup

public static SpaceGroup getSpaceGroup(int id)

Gets the space group for the given standard identifier. See for example http://en.wikipedia.org/wiki/Space_group

Parameters:

id -

Returns:

parseSpaceGroupsXML

public static TreeMap<Integer,SpaceGroup> parseSpaceGroupsXML(InputStream spaceGroupIS)
                                                       throws IOException,
jakarta.xml.bind.JAXBException

Load all SpaceGroup information from the file spacegroups.xml

Returns:

a map providing information for all spacegroups

Throws:

IOException

jakarta.xml.bind.JAXBException

getSpaceGroup

public static SpaceGroup getSpaceGroup(String shortName)

Get the space group for the given international short name, using the PDB format, e.g. 'P 21 21 21' or 'C 1 c 1'

Parameters:

shortName -

Returns:

the SpaceGroup or null if the shortName is not valid

getAllSpaceGroups

public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups()

parseSymopLib

public static TreeMap<Integer,SpaceGroup> parseSymopLib(InputStream symoplibIS)

A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava. It can be downloaded from: http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup

Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml

Parameters:

symoplibIS -

Returns: