#!/usr/bin/env python # Syminfo.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. # # 13th June 2006 # # A handler singleton for the information in the CCP4 symmetry library # syminfo.lib. # import sys import os import copy import re if not os.environ.has_key('XIA2_ROOT'): raise RuntimeError, 'XIA2_ROOT not defined' if not os.environ.has_key('XIA2CORE_ROOT'): raise RuntimeError, 'XIA2CORE_ROOT not defined' sys.path.append(os.path.join(os.environ['XIA2_ROOT'])) class _Syminfo(): '''An object to retain symmetry information.''' def __init__(self): '''Initialise everything.''' self._parse_symop() self._int_re = re.compile('^[0-9]*$') return def _generate_lattice(self, lattice_type, shortname): '''Generate a lattice name (e.g. tP) from TETRAGONAL and P422.''' hash = {'TRICLINIC':'a', 'MONOCLINIC':'m', 'ORTHORHOMBIC':'o', 'TETRAGONAL':'t', 'TRIGONAL':'h', 'HEXAGONAL':'h', 'CUBIC':'c'} lattice = '%s%s' % (hash[lattice_type.upper()], shortname[0].upper()) if lattice[1] != 'H': return lattice else: return '%sR' % lattice[0] def _parse_symop(self): '''Parse the CCP4 symop library.''' self._symop = { } self._spacegroup_name_to_lattice = { } self._spacegroup_short_to_long = { } self._spacegroup_long_to_short = { } self._spacegroup_name_to_number = { } self._spacegroup_name_to_pointgroup = { } current = 0 for line in open(os.path.join(os.environ['CLIBD'], 'symop.lib')).readlines(): if line[0] != ' ': list = line.split() index = int(list[0]) shortname = list[3] lattice_type = list[5].lower() longname = line.split('\'')[1] lattice = self._generate_lattice(lattice_type, shortname) pointgroup = '' for token in longname.split(): if len(longname.split()) <= 2: pointgroup += token[0] elif token[0] != '1': pointgroup += token[0] self._symop[index] = {'index':index, 'lattice_type':lattice_type, 'lattice':lattice, 'name':shortname, 'longname':longname, 'pointgroup':pointgroup, 'symops':0, 'operations':[]} if not self._spacegroup_name_to_lattice.has_key(shortname): self._spacegroup_name_to_lattice[shortname] = lattice if not self._spacegroup_name_to_number.has_key(shortname): self._spacegroup_name_to_number[shortname] = index if not self._spacegroup_long_to_short.has_key(longname): self._spacegroup_long_to_short[longname] = shortname if not self._spacegroup_short_to_long.has_key(shortname): self._spacegroup_short_to_long[shortname] = longname if not self._spacegroup_name_to_pointgroup.has_key(shortname): self._spacegroup_name_to_pointgroup[shortname] = pointgroup current = index else: self._symop[current]['symops'] += 1 self._symop[current]['operations'].append(line.strip()) return def get_syminfo(self, spacegroup_number): '''Return the syminfo for spacegroup number.''' return copy.deepcopy(self._symop[spacegroup_number]) def get_pointgroup(self, name): '''Get the pointgroup for this spacegroup, e.g. P422 for P43212.''' if self._spacegroup_long_to_short.has_key(name): name = self._spacegroup_long_to_short[name] return self._spacegroup_name_to_pointgroup[name.replace(' ', '')] def get_lattice(self, name): '''Get the lattice for a named spacegroup.''' # check that this isn't already a lattice name if name in ['aP', 'mP', 'mC', 'oP', 'oC', 'oI', 'oF', 'tP', 'tI', 'hR', 'hP', 'cP', 'cI', 'cF']: return name # introspect on the input to figure out what to return if type(name) == type(1): return self.get_syminfo(name)['lattice'] # check that this isn't a string of an integer - if it is # repeat above... if self._int_re.match(name): name = int(name) return self.get_syminfo(name)['lattice'] # ok this should be a "pure" spacegroup string if self._spacegroup_long_to_short.has_key(name): name = self._spacegroup_long_to_short[name] # The short name should not have a space in, sometimes this may # be foxed by someone passing in P 21 - this should fix it... return self._spacegroup_name_to_lattice[name.replace(' ', '')] def get_spacegroup_numbers(self): '''Get a list of all spacegroup numbers.''' numbers = self._symop.keys() numbers.sort() return numbers def spacegroup_number_to_name(self, spacegroup_number): '''Return the name of this spacegroup.''' return self._symop[spacegroup_number]['name'] def spacegroup_name_to_number(self, spacegroup): '''Return the number corresponding to this spacegroup.''' # check have not had number passed in try: number = int(spacegroup) return number except: pass spacegroup = spacegroup.strip() # check if this is a disputed spacegroup name if ':' in spacegroup and 'H' in spacegroup: spacegroup = spacegroup.split(':')[0].strip().replace('R', 'H') # next check to see if this is the long form if self._spacegroup_long_to_short.has_key(spacegroup): spacegroup = self._spacegroup_long_to_short[spacegroup] return self._spacegroup_name_to_number[spacegroup] def get_num_symops(self, spacegroup_number): '''Get the number of symmetry operations that spacegroup number has.''' return self._symop[spacegroup_number]['symops'] def get_symops(self, spacegroup): '''Get the operations for spacegroup number N.''' try: number = int(spacegroup) except ValueError, e: number = self.spacegroup_name_to_number(spacegroup) return self._symop[number]['operations'] def get_subgroups(self, spacegroup): '''Get the list of spacegroups which are included entirely in this spacegroup.''' try: number = int(spacegroup) except ValueError, e: number = self.spacegroup_name_to_number(spacegroup) symops = self._symop[number]['operations'] subgroups = [] for j in range(230): sub = True for s in self._symop[j + 1]['operations']: if not s in symops: sub = False if sub: subgroups.append(self.spacegroup_number_to_name(j + 1)) return subgroups Syminfo = _Syminfo() if __name__ == '__main__': for arg in sys.argv[1:]: for spacegroup in Syminfo.get_subgroups(arg): print spacegroup