Class SymoplibParser


  • 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
    • Constructor Summary

      Constructors 
      Constructor Description
      SymoplibParser()  
    • 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.xml
      static java.util.TreeMap<java.lang.Integer,​SpaceGroup> parseSymopLib​(java.io.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 Detail

      • SymoplibParser

        public SymoplibParser()
    • Method Detail

      • 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 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
      • 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
      • getAllSpaceGroups

        public static java.util.TreeMap<java.lang.Integer,​SpaceGroup> getAllSpaceGroups()
      • 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: