Package org.biojava.nbio.structure.xtal
Class SymoplibParser
- java.lang.Object
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- org.biojava.nbio.structure.xtal.SymoplibParser
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public class SymoplibParser extends java.lang.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
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Constructor Summary
Constructors Constructor Description SymoplibParser()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.util.TreeMap<java.lang.Integer,SpaceGroup>
getAllSpaceGroups()
static SpaceGroup
getSpaceGroup(int id)
Gets the space group for the given standard identifier.static SpaceGroup
getSpaceGroup(java.lang.String shortName)
Get the space group for the given international short name, using the PDB format, e.g.static java.util.TreeMap<java.lang.Integer,SpaceGroup>
parseSpaceGroupsXML(java.io.InputStream spaceGroupIS)
Load all SpaceGroup information from the file spacegroups.xmlstatic java.util.TreeMap<java.lang.Integer,SpaceGroup>
parseSymopLib(java.io.InputStream symoplibIS)
A parser for the symop.lib file provided by CCP4.
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Method Detail
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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:
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parseSpaceGroupsXML
public static java.util.TreeMap<java.lang.Integer,SpaceGroup> parseSpaceGroupsXML(java.io.InputStream spaceGroupIS) throws java.io.IOException, javax.xml.bind.JAXBException
Load all SpaceGroup information from the file spacegroups.xml- Returns:
- a map providing information for all spacegroups
- Throws:
java.io.IOException
javax.xml.bind.JAXBException
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getSpaceGroup
public static SpaceGroup getSpaceGroup(java.lang.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
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getAllSpaceGroups
public static java.util.TreeMap<java.lang.Integer,SpaceGroup> getAllSpaceGroups()
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parseSymopLib
public static java.util.TreeMap<java.lang.Integer,SpaceGroup> parseSymopLib(java.io.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:
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