#!/usr/bin/env python # LatticeSymmetry.py # Copyright (C) 2006 CCLRC, Graeme Winter # # This code is distributed under the BSD license, a copy of which is # included in the root directory of this package. # # A wrapper for the CCTBX jiffy program iotbx.lattice_symmetry which is # used like: # # iotbx.lattice_symmetry --unit-cell=a,b,c,alpha,beta,gamma --space-group=sg # # And gives a list of possible spacegroup / unit cell / reindex operators # for other likely lattices. Last is always P1 (P-1 strictly). # # 19 November 2007 # import os import sys if not os.path.join(os.environ['XIA2CORE_ROOT'], 'Python') in sys.path: sys.path.append(os.path.join(os.environ['XIA2CORE_ROOT'], 'Python')) if not os.environ['XIA2_ROOT'] in sys.path: sys.path.append(os.environ['XIA2_ROOT']) from Driver.DriverFactory import DriverFactory from lib.SymmetryLib import lauegroup_to_lattice from Handlers.Syminfo import Syminfo def LatticeSymmetry(DriverType = None): '''A factory for the LatticeSymmetry wrappers.''' DriverInstance = DriverFactory.Driver(DriverType) class LatticeSymmetryWrapper(DriverInstance.__class__): '''A wrapper class for iotbx.lattice_symmetry.''' def __init__(self): DriverInstance.__class__.__init__(self) self.set_executable('iotbx.lattice_symmetry') if 'phaser-1.3' in self.get_executable(): raise RuntimeError, \ 'unsupported version of lattice_symmetry' self._cell = None self._spacegroup = None # following on from the othercell wrapper... self._lattices = [] self._distortions = { } self._cells = { } self._reindex_ops = { } self._reindex_ops_basis = { } return def set_cell(self, cell): self._cell = cell return def set_spacegroup(self, spacegroup): self._spacegroup = spacegroup return def set_lattice(self, lattice): lattice_to_spacegroup = {'aP':1, 'mP':3, 'mC':5, 'oP':16, 'oC':20, 'oF':22, 'oI':23, 'tP':75, 'tI':79, 'hP':143, 'hR':146, 'cP':195, 'cF':196, 'cI':197} self._spacegroup = Syminfo.spacegroup_number_to_name( lattice_to_spacegroup[lattice]) # bug 22/JUL/08 latest lattice symmetry no longer recognises # the spacegroup H3... if self._spacegroup == 'H3': self._spacegroup = 'R3:H' return def generate(self): if not self._cell: raise RuntimeError, 'no unit cell specified' if not self._spacegroup: raise RuntimeError, 'no spacegroup specified' self.add_command_line('--unit_cell=%f,%f,%f,%f,%f,%f' % \ tuple(self._cell)) self.add_command_line('--space_group=%s' % self._spacegroup) self.start() self.close_wait() # now wade through all of the options and see which comes # out best for each lattice class... - as defined by the # minimum value of Maximal angular difference state = { } for o in self.get_all_output(): # print o[:-1] if ':' in o: count = o.find(':') left = o[:count] right = o[count + 1:] state[left.strip()] = right.strip() if 'Maximal angular difference' in o: # transform & digest results distortion = float(state[ 'Maximal angular difference'].split()[0]) # this appears to be getting the wrong cell - I want the # one which corresponds to the correct lattice, yes?! # cell = map(float, state[ # 'Symmetry-adapted cell'].replace( # '(', ' ').replace(')', ' ').replace(',', ' ').split()) cell = map(float, state[ 'Unit cell'].replace( '(', ' ').replace(')', ' ').replace(',', ' ').split()) lauegroup = '' # FIXME for more recent versions of cctbx the conventional # setting I 1 2/m 1 has appeared -> look at the # 'Symmetry in minimum-lengths cell' instead (equivalent # to changing lkey here to 'Conventional setting' # # No, can't do this because this now reports the Hall # symmetry not the Laue group. Will have to cope with # the I setting instead :o( lkey = 'Symmetry in minimum-lengths cell' for token in state[lkey].split('(')[0].split(): if token == '1': continue lauegroup += token # FIXME bug 3157 - there appears to be a bug in # recent versions of cctbx (cf. above) which means # a lauegroup of 'R-3m:R' is given -> correct this # in the string. Also :h as well :o( lauegroup = lauegroup.replace(':R', ':H') lauegroup = lauegroup.replace(':h', ':H') lattice = lauegroup_to_lattice(lauegroup) reindex_basis = state['Change of basis'] reindex = state['Inverse'] if not lattice in self._lattices: self._lattices.append(lattice) self._distortions[lattice] = distortion self._cells[lattice] = cell self._reindex_ops[lattice] = reindex self._reindex_ops_basis[lattice] = reindex_basis elif distortion < self._distortions[lattice]: self._distortions[lattice] = distortion self._cells[lattice] = cell self._reindex_ops[lattice] = reindex self._reindex_ops_basis[lattice] = reindex_basis state = { } return def get_lattices(self): return self._lattices def get_distortion(self, lattice): return self._distortions[lattice] def get_cell(self, lattice): return self._cells[lattice] def get_reindex_op(self, lattice): return self._reindex_ops[lattice] def get_reindex_op_basis(self, lattice): return self._reindex_ops_basis[lattice] def generate_primative_reindex(self): if not self._cell: raise RuntimeError, 'no unit cell specified' if not self._spacegroup: raise RuntimeError, 'no spacegroup specified' self.add_command_line('--unit_cell=%f,%f,%f,%f,%f,%f' % \ tuple(self._cell)) self.add_command_line('--space-group=%s' % self._spacegroup) self.start() self.close_wait() # triclinic solution will always come last so use this... cell = None reindex = None for line in self.get_all_output(): # print line[:-1] if 'Unit cell:' in line: cell_text = line.replace('Unit cell: (', '').replace( ')', '').strip().replace(',', ' ') cell = tuple(map(float, cell_text.split())) # if 'Change of basis:' in line: # reindex = line.replace('Change of basis:', '').strip() if 'Inverse:' in line: reindex = line.replace('Inverse:', '').strip() return cell, reindex.replace('*', '') return LatticeSymmetryWrapper() if __name__ == '__main__': ls = LatticeSymmetry() ls.set_lattice('cI') ls.set_cell((78.56, 78.56, 78.56, 90.00, 90.00, 90.00)) ls.generate() print ls.get_reindex_op('aP') cell = ls.get_cell('aP') print cell