Source Code for Module EDUtilsSymmetry

  1  # 
  2  #    Project: The EDNA Kernel 
  3  #             http://www.edna-site.org 
  4  # 
  5  #    File: "$Id$" 
  6  # 
  7  #    Copyright (C) 2008-2009 European Synchrotron Radiation Facility 
  8  #                            Grenoble, France 
  9  # 
 10  #    Principal authors: Marie-Francoise Incardona (incardon@esrf.fr) 
 11  #                       Olof Svensson (svensson@esrf.fr)  
 12  # 
 13  #    This program is free software: you can redistribute it and/or modify 
 14  #    it under the terms of the GNU Lesser General Public License as published 
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 21  #    GNU Lesser General Public License for more details. 
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 23  #    You should have received a copy of the GNU General Public License 
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 27   
 28  __authors__ = [ "Marie-Francoise Incardona", "Olof Svensson" ] 
 29  __contact__ = "svensson@esrf.fr" 
 30  __license__ = "LGPLv3+" 
 31  __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" 
 32   
 33   
 34 -class EDUtilsSymmetry: 
 35      """ 
 36      This utility class contains methods useful for handling symmetries. 
 37      """ 
 38   
 39      @staticmethod 
 40 -    def getMinimumSymmetrySpaceGroupFromBravaisLattice(_strBravaisLattice): 
 41          """ 
 42          This static method returns a string containing the name of the space 
 43          group with minimum symmetry that corresponds to a given two-letter Bravais 
 44          Lattice. 
 45           
 46          Note that the "hR" Bravais Lattice is translated into the "H3" and not the 
 47          "R3" space group since the "H3" space group is the one used in MX in general 
 48          and in particular for structures deposited in the PDB. 
 49           
 50          If the Bravais Lattice is not recognised a "None" object is returned. 
 51          """ 
 52          strSpaceGroup = None 
 53          strBravaisLattice = _strBravaisLattice 
 54          if strBravaisLattice == "aP": 
 55              strSpaceGroup = "P1" 
 56   
 57          elif strBravaisLattice == "mP": 
 58              strSpaceGroup = "P2" 
 59   
 60          elif strBravaisLattice == "mC" or \ 
 61                 strBravaisLattice == "mI": 
 62              strSpaceGroup = "C2" 
 63   
 64          elif strBravaisLattice == "oP": 
 65              strSpaceGroup = "P222" 
 66   
 67          elif strBravaisLattice == "oA" or \ 
 68                 strBravaisLattice == "oB" or \ 
 69                 strBravaisLattice == "oC" or \ 
 70                 strBravaisLattice == "oS": 
 71              strSpaceGroup = "C222" 
 72   
 73          elif strBravaisLattice == "oF": 
 74              strSpaceGroup = "F222" 
 75   
 76          elif strBravaisLattice == "oI": 
 77              strSpaceGroup = "I222" 
 78   
 79          elif strBravaisLattice == "tP" or \ 
 80                 strBravaisLattice == "tC": 
 81              strSpaceGroup = "P4" 
 82   
 83          elif strBravaisLattice == "tI" or \ 
 84                 strBravaisLattice == "tF": 
 85              strSpaceGroup = "I4" 
 86   
 87          elif strBravaisLattice == "hP": 
 88              strSpaceGroup = "P3" 
 89   
 90          elif strBravaisLattice == "hR": 
 91              strSpaceGroup = "H3" 
 92   
 93          elif strBravaisLattice == "cP": 
 94              strSpaceGroup = "P23" 
 95   
 96          elif strBravaisLattice == "cF": 
 97              strSpaceGroup = "F23" 
 98   
 99          elif strBravaisLattice == "cI": 
100              strSpaceGroup = "I23" 
101   
102          return strSpaceGroup 
103   
104   
105   
106      @staticmethod 
107 -    def getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(_strSpaceGroupId, _strSymmetryTableFileName): 
108          """ 
109          """ 
110          return EDUtilsSymmetry.getNumberOfSymmetryOperators(_strSpaceGroupId, 0, _strSymmetryTableFileName) 
111   
112   
113      @staticmethod 
114 -    def getNumberOfSymmetryOperatorsFromSpaceGroupName(_strSpaceGroupName, _strSymmetryTableFileName): 
115          """ 
116          """ 
117          return EDUtilsSymmetry.getNumberOfSymmetryOperators(_strSpaceGroupName, 3, _strSymmetryTableFileName) 
118   
119   
120   
121      @staticmethod 
122 -    def getNumberOfSymmetryOperators(_strSpaceGroupIdOrName, _iIndex, _strSymmetryTableFileName): 
123          """ 
124          """ 
125          strNumOperators = None 
126          symmetryTableFile = open(_strSymmetryTableFileName) 
127          for strLine in symmetryTableFile.xreadlines(): 
128              listItems = strLine.split(" ") 
129              if (len(listItems) > 3 and listItems[_iIndex] == _strSpaceGroupIdOrName): 
130                  strNumOperators = listItems[1] 
131          return strNumOperators 
132   
133      @staticmethod 
134 -    def getITNumberFromSpaceGroupName(_strSpaceGroupName, _strSymmetryTableFileName): 
135          """ 
136          """ 
137          iITNumber = None 
138          symmetryTableFile = open(_strSymmetryTableFileName) 
139          for strLine in symmetryTableFile.xreadlines(): 
140              listItems = strLine.split(" ") 
141              if len(listItems) > 3: 
142                  if _strSpaceGroupName == listItems[3]: 
143                      iITNumber = int(listItems[0]) 
144          return iITNumber 
145