def get_symops_from_supergroup_that_are_not_in_subgroup(self, sg_high):
coset = cosets.left_decomposition(g=sg_high, h=self.sg_low)
for set in coset.partitions[1:]:
if self.enforce_point_groups:
if set[0].r().determinant() > 0:
self.symops.append(set[0])
else:
self.symops.append(set[0])
def get_symops_from_supergroup_that_are_not_in_subgroup(self, sg_high):
coset = cosets.left_decomposition(g=sg_high,
h=self.sg_low)
for set in coset.partitions[1:]:
if self.enforce_point_groups:
if set[0].r().determinant()>0:
self.symops.append(set[0])
else:
self.symops.append(set[0])
def coset_lookup(pg_low, pg_high):
coset = cosets.left_decomposition(g=pg_high, h=pg_low)
full_cosets = []
for set in coset.partitions:
if (set[0].r().determinant() > 0):
tmp = []
for symop in set:
tmp.append(symop.r().as_hkl())
full_cosets.append(tmp)
return full_cosets
def coset_lookup(pg_low,
pg_high):
coset = cosets.left_decomposition(g=pg_high,
h=pg_low)
full_cosets = []
for set in coset.partitions:
if (set[0].r().determinant()>0):
tmp = []
for symop in set:
tmp.append(symop.r().as_hkl())
full_cosets.append(tmp)
return full_cosets
def run(g,h,out=None):
if out is None:
out = sys.stdout
g = sgtbx.space_group_info( g ).group()
h = sgtbx.space_group_info( h ).group()
success = False
try:
cc = cosets.left_decomposition( h,g)
cc.show(out=out)
success = True
except Exception: pass
if not success:
print >> out, "Coset decomposition not successfull."
print >> out, "Group %s might not be a subgroup of %s"%(sgtbx.space_group_info( group=g ), sgtbx.space_group_info( group=h ) )
print >> out, "Sorry....."
def run(g, h, out=None):
if out is None:
out = sys.stdout
g = sgtbx.space_group_info(g).group()
h = sgtbx.space_group_info(h).group()
success = False
try:
cc = cosets.left_decomposition(h, g)
cc.show(out=out)
success = True
except Exception:
pass
if not success:
print >> out, "Coset decomposition not successfull."
print >> out, "Group %s might not be a subgroup of %s" % (
sgtbx.space_group_info(group=g), sgtbx.space_group_info(group=h))
print >> out, "Sorry....."
def cluster_analysis(self):
from cctbx.sgtbx import cosets
if self.params.cluster.method == 'dbscan':
self.dbscan_clustering()
elif self.params.cluster.method == 'bisect':
self.bisect_clustering()
elif self.params.cluster.method == 'minimize_divide':
self.minimize_divide_clustering()
elif self.params.cluster.method == 'agglomerative':
self.agglomerative_clustering()
elif self.params.cluster.method == 'seed':
self.seed_clustering()
# Number of clusters in labels, ignoring noise if present.
n_clusters = len(set(
self.cluster_labels)) - (1 if -1 in self.cluster_labels else 0)
cluster_miller_arrays = []
space_groups = []
sym_ops = [
sgtbx.rt_mx(s).new_denominators(1, 12)
for s in self.target.get_sym_ops()
]
self.space_groups = space_groups
reindexing_ops = {}
space_groups = {}
for dataset_id in range(len(self.datasets)):
sg = copy.deepcopy(self.input_space_group)
ref_sym_op_id = None
ref_cluster_id = None
for sym_op_id in range(len(sym_ops)):
i_cluster = self.cluster_labels[len(self.datasets) * sym_op_id
+ dataset_id]
if i_cluster < 0:
continue
if ref_sym_op_id is None:
ref_sym_op_id = sym_op_id
ref_cluster_id = i_cluster
continue
op = sym_ops[ref_sym_op_id].inverse().multiply(
sym_ops[sym_op_id])
if i_cluster == ref_cluster_id:
sg.expand_smx(op.new_denominators(1, 12))
sg.make_tidy()
space_groups[dataset_id] = sg
coset = cosets.left_decomposition(
self.target._lattice_group,
sg.info().primitive_setting().group())
reindexing_ops[dataset_id] = {}
for i_cluster in range(n_clusters):
isel = (self.cluster_labels == i_cluster).iselection()
dataset_ids = isel % len(self.datasets)
idx = flex.first_index(dataset_ids, dataset_id)
sel = (dataset_ids == dataset_id).iselection()
if idx >= 0:
sym_op_id = isel[idx] // len(self.datasets)
for s in sel:
sym_op_id = isel[s] // len(self.datasets)
for partition in coset.partitions:
if sym_ops[sym_op_id] in partition:
if i_cluster not in reindexing_ops[dataset_id]:
reindexing_ops[dataset_id][
i_cluster] = partition[0].as_xyz()
#else:
#assert reindexing_ops[dataset_id][i_cluster] == partition[0].as_xyz()
self.space_groups = space_groups
self.reindexing_ops = reindexing_ops
