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 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, javax.xml.bind.JAXBException
      Load all SpaceGroup information from the file spacegroups.xml
      Returns:
      a map providing information for all spacegroups
      Throws:
      IOException
      javax.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: