def tst_pgtools():
unit_cell = uctbx.unit_cell('40, 40, 60, 90.0, 90.0, 90.0')
mi = flex.miller_index(((2,4,6), (2,4,8)))
xs = crystal.symmetry(unit_cell, "P 1 2 1")
ms = miller.set(xs, mi)
# Go to the minimum cell, for safety
cob_min_cell = ms.change_of_basis_op_to_minimum_cell()
ms_new = ms.change_basis( cob_min_cell )
lattice_group = sgtbx.lattice_symmetry.group(
ms_new.unit_cell(),
max_delta=5.0)
point_group_low = ms_new.space_group().build_derived_point_group()
point_group_high = lattice_group.build_derived_point_group()
pgtree = pt.point_group_graph(point_group_low,point_group_high)
# find the possible routes from 'P 2' to 'P 4 2 2'
atlas = pgtree.graph.find_all_paths( 'P 1 2 1', 'P 4 2 2')
route_1 = ['P 1 2 1', 'P 4 2 2']
route_2 = ['P 1 2 1', 'P 2 2 2', 'P 4 2 2']
assert route_1 in atlas
assert route_2 in atlas
assert len(atlas)==2
# Now lets 'disqualify' point group 'P 2 2 2'
pgtree.remove_point_group_and_its_super_groups_from_graph(
str(sgtbx.space_group_info(16)))
assert len(pgtree.graph.node_objects)==1
assert pgtree.graph.node_objects.has_key ( 'P 1 2 1' )
def tst_pgtools():
unit_cell = uctbx.unit_cell('40, 40, 60, 90.0, 90.0, 90.0')
mi = flex.miller_index(((2, 4, 6), (2, 4, 8)))
xs = crystal.symmetry(unit_cell, "P 1 2 1")
ms = miller.set(xs, mi)
# Go to the minimum cell, for safety
cob_min_cell = ms.change_of_basis_op_to_minimum_cell()
ms_new = ms.change_basis(cob_min_cell)
lattice_group = sgtbx.lattice_symmetry.group(ms_new.unit_cell(),
max_delta=5.0)
point_group_low = ms_new.space_group().build_derived_point_group()
point_group_high = lattice_group.build_derived_point_group()
pgtree = pt.point_group_graph(point_group_low, point_group_high)
# find the possible routes from 'P 2' to 'P 4 2 2'
atlas = pgtree.graph.find_all_paths('P 1 2 1', 'P 4 2 2')
route_1 = ['P 1 2 1', 'P 4 2 2']
route_2 = ['P 1 2 1', 'P 2 2 2', 'P 4 2 2']
assert route_1 in atlas
assert route_2 in atlas
assert len(atlas) == 2
# Now lets 'disqualify' point group 'P 2 2 2'
pgtree.remove_point_group_and_its_super_groups_from_graph(
str(sgtbx.space_group_info(16)))
assert len(pgtree.graph.node_objects) == 1
assert pgtree.graph.node_objects.has_key('P 1 2 1')
def run(sg1):
sg_high = sgtbx.space_group_info( sg1 ).group()
sg_low = sgtbx.space_group_info( "p1" ).group()
graph_object = pointgroup_tools.point_group_graph( sg_low, sg_high, False,True)
graph_object.graph.show()
out = """ """
out += "digraph f { "
out += "rankdir=LR"
for pg in graph_object.graph.node_objects:
for next_pg in graph_object.graph.edge_objects[ pg ]:
pg = pg.replace( "\"","''" )
next_pg = next_pg.replace( "\"","''" )
out += "\""+pg+"\" -> \""+next_pg+"\" ;"
out += "}"
cmnd = """dot -Tpng > sg_graph.png << EOF
%s
EOF
"""%(out)
print
print "Command for dot (graphviz package) to show relations between groups: "
print cmnd
def create_all_subgroups( sg1,show_all=True, reverse=False ):
sg_high = sgtbx.space_group_info( sg1 ).group()
sg_low = sgtbx.space_group_info( "p1" ).group()
graph_object = pointgroup_tools.point_group_graph( sg_low, sg_high, False,True)
highest_sg = str( sgtbx.space_group_info( sg1 ) )
rev_dict = reverse_dict( graph_object.graph.o )
maximal_subgroups = get_maximal_subgroup( highest_sg, rev_dict )
if show_all:
print "Subgroups of input space groups which can be constructed by introducing one single operator (and group completion) in the subgroup:"
for sg in rev_dict[ highest_sg ]:
line = " "
line += sg+(30-len(sg))*" "+str(graph_object.graph.edge_objects[ sg ][highest_sg])+(90-len( str(graph_object.graph.edge_objects[ sg ][highest_sg]) ))*" "
print line
print
print "Maximal subgroup detected in the full sub-group-graph: "
for sg in maximal_subgroups:
line = " "
line += sg
print line
print
print
print
print " Cosets for each maximal sub-group and the input space group are listed:"
for sg in maximal_subgroups:
print "-----------------------------------------------------------------"
show_cosets.run( sg,highest_sg )
print "-----------------------------------------------------------------"
print
print
print
print
else:
print "Maximal subgroups of %s: "%(sg1)
for sg in maximal_subgroups:
line = " "
line += sg
print line
print
print
print
if reverse:
print "Minimal supergroups generated by the sub-groups of the input space group:"
tmp_sg = sgtbx.space_group_info( sg1 )
for sg in maximal_subgroups:
tmp_sgsg = sgtbx.space_group_info( sg )
cb_op = tmp_sgsg.change_of_basis_op_to_reference_setting()
okai=False
try:
new_sg = tmp_sg.change_basis( cb_op )
okai=True
print new_sg ," is a minimal supergroup of ", tmp_sgsg.change_basis(cb_op)
except Exception: pass
if not okai:
print "%s (%s) is a minimal supergroup of %s [*]"%(tmp_sg,cb_op, tmp_sgsg.change_basis(cb_op))
print
print
print