def get_top_solutions(self, ai, input_directions, size, cutoff_divisor):
# size was 30 in the Rossmann DPS paper
kval_cutoff = ai.getXyzSize() / cutoff_divisor
hemisphere_solutions = flex.Direction()
hemisphere_solutions.reserve(size)
for i in range(len(input_directions)):
sampled_direction = ai.fft_result(input_directions[i])
if sampled_direction.kval > kval_cutoff:
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size() < 3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval
for x in range(len(hemisphere_solutions))
])
perm = flex.sort_permutation(kvals, True)
# conventional algorithm; just take the top scoring hits.
# use this for quick_grid, when it is known ahead of time
# that many (hundreds) of directions will be retained
hemisphere_solutions_sort = flex.Direction(
[hemisphere_solutions[p] for p in perm[0:min(size, len(perm))]])
return hemisphere_solutions_sort
def find_basis_vectors(self, reciprocal_lattice_vectors):
"""Find a list of likely basis vectors.
Args:
reciprocal_lattice_vectors (scitbx.array_family.flex.vec3_double):
The list of reciprocal lattice vectors to search for periodicity.
"""
used_in_indexing = flex.bool(reciprocal_lattice_vectors.size(), True)
logger.info("Indexing from %i reflections" % used_in_indexing.count(True))
vectors, weights = self.score_vectors(reciprocal_lattice_vectors)
perm = flex.sort_permutation(weights, reverse=True)
vectors = vectors.select(perm)
weights = weights.select(perm)
groups = group_vectors(vectors, weights, max_groups=self._params.max_vectors)
unique_vectors = []
unique_weights = []
for g in groups:
idx = flex.max_index(flex.double(g.weights))
unique_vectors.append(g.vectors[idx])
unique_weights.append(g.weights[idx])
logger.info("Number of unique vectors: %i" % len(unique_vectors))
for v, w in zip(unique_vectors, unique_weights):
logger.debug("%s %s %s" % (w, v.length(), str(v.elems)))
return unique_vectors, used_in_indexing
def get_top_solutions(self,ai,input_directions,size,cutoff_divisor):
# size was 30 in the Rossmann DPS paper
kval_cutoff = ai.getXyzSize()/cutoff_divisor;
hemisphere_solutions = flex.Direction();
hemisphere_solutions.reserve(size);
for i in xrange(len(input_directions)):
sampled_direction = ai.fft_result(input_directions[i])
if sampled_direction.kval > kval_cutoff:
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size()<3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval for x in xrange(len(hemisphere_solutions))])
perm = flex.sort_permutation(kvals,True)
# conventional algorithm; just take the top scoring hits.
# use this for quick_grid, when it is known ahead of time
# that many (hundreds) of directions will be retained
hemisphere_solutions_sort = flex.Direction(
[hemisphere_solutions[p] for p in perm[0:min(size,len(perm))]])
return hemisphere_solutions_sort;
def get_top_solutions(self, ai, input_directions, size, cutoff_divisor,
grid):
kval_cutoff = ai.getXyzSize() / cutoff_divisor
hemisphere_solutions = flex.Direction()
hemisphere_solutions.reserve(size)
#print "# of input directions", len(input_directions)
for i in range(len(input_directions)):
D = sampled_direction = ai.fft_result(input_directions[i])
#hardcoded parameter in for silicon example. Not sure at this point how
#robust the algorithm is when this value is relaxed.
if D.real < self.max_cell and sampled_direction.kval > kval_cutoff:
if diagnostic: directional_show(D, "%5d" % i)
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size() < 3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval
for x in range(len(hemisphere_solutions))
])
perm = flex.sort_permutation(kvals, True)
# need to be more clever than just taking the top 30.
# one huge cluster around a strong basis direction could dominate the
# whole hemisphere map, preventing the discovery of three basis vectors
perm_idx = 0
unique_clusters = 0
hemisphere_solutions_sort = flex.Direction()
while perm_idx < len(perm) and \
unique_clusters < size:
test_item = hemisphere_solutions[perm[perm_idx]]
direction_ok = True
for list_item in hemisphere_solutions_sort:
distance = math.sqrt(
math.pow(list_item.dvec[0] - test_item.dvec[0], 2) +
math.pow(list_item.dvec[1] - test_item.dvec[1], 2) +
math.pow(list_item.dvec[2] - test_item.dvec[2], 2))
if distance < 0.087: #i.e., 5 degrees radius for clustering analysis
direction_ok = False
break
if direction_ok:
unique_clusters += 1
hemisphere_solutions_sort.append(test_item)
perm_idx += 1
return hemisphere_solutions_sort
def get_top_solutions(self, ai, input_directions, size, cutoff_divisor,
grid):
# size was 30 in the Rossmann DPS paper
kval_cutoff = ai.getXyzSize() / cutoff_divisor
hemisphere_solutions = flex.Direction()
hemisphere_solutions.reserve(size)
for i in range(len(input_directions)):
D = sampled_direction = ai.fft_result(input_directions[i])
if D.real < self.max_cell_input and sampled_direction.kval > kval_cutoff:
#directional_show(D, "ddd %5d"%i)
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size() < 3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval
for x in range(len(hemisphere_solutions))
])
perm = flex.sort_permutation(kvals, True)
# need to be more clever than just taking the top 30.
# one huge cluster around a strong basis direction could dominate the
# whole hemisphere map, preventing the discovery of three basis vectors
perm_idx = 0
unique_clusters = 0
hemisphere_solutions_sort = flex.Direction()
while perm_idx < len(perm) and \
unique_clusters < size:
test_item = hemisphere_solutions[perm[perm_idx]]
direction_ok = True
for list_item in hemisphere_solutions_sort:
distance = math.sqrt(
math.pow(list_item.dvec[0] - test_item.dvec[0], 2) +
math.pow(list_item.dvec[1] - test_item.dvec[1], 2) +
math.pow(list_item.dvec[2] - test_item.dvec[2], 2))
if distance < 0.087: #i.e., 5 degrees
direction_ok = False
break
if direction_ok:
unique_clusters += 1
hemisphere_solutions_sort.append(test_item)
perm_idx += 1
return hemisphere_solutions_sort
def get_top_solutions(self,ai,input_directions,size,cutoff_divisor,grid):
kval_cutoff = ai.getXyzSize()/cutoff_divisor;
hemisphere_solutions = flex.Direction();
hemisphere_solutions.reserve(size);
#print "# of input directions", len(input_directions)
for i in xrange(len(input_directions)):
D = sampled_direction = ai.fft_result(input_directions[i])
#hardcoded parameter in for silicon example. Not sure at this point how
#robust the algorithm is when this value is relaxed.
if D.real < self.max_cell and sampled_direction.kval > kval_cutoff:
if diagnostic: directional_show(D, "%5d"%i)
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size()<3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval for x in xrange(len(hemisphere_solutions))])
perm = flex.sort_permutation(kvals,True)
# need to be more clever than just taking the top 30.
# one huge cluster around a strong basis direction could dominate the
# whole hemisphere map, preventing the discovery of three basis vectors
perm_idx = 0
unique_clusters = 0
hemisphere_solutions_sort = flex.Direction()
while perm_idx < len(perm) and \
unique_clusters < size:
test_item = hemisphere_solutions[perm[perm_idx]]
direction_ok = True
for list_item in hemisphere_solutions_sort:
distance = math.sqrt(math.pow(list_item.dvec[0]-test_item.dvec[0],2) +
math.pow(list_item.dvec[1]-test_item.dvec[1],2) +
math.pow(list_item.dvec[2]-test_item.dvec[2],2)
)
if distance < 0.087: #i.e., 5 degrees radius for clustering analysis
direction_ok=False
break
if direction_ok:
unique_clusters+=1
hemisphere_solutions_sort.append(test_item)
perm_idx+=1
return hemisphere_solutions_sort;
def get_top_solutions(self,ai,input_directions,size,cutoff_divisor,grid):
# size was 30 in the Rossmann DPS paper
kval_cutoff = ai.getXyzSize()/cutoff_divisor;
hemisphere_solutions = flex.Direction();
hemisphere_solutions.reserve(size);
for i in xrange(len(input_directions)):
D = sampled_direction = ai.fft_result(input_directions[i])
if D.real < self.max_cell_input and sampled_direction.kval > kval_cutoff:
#directional_show(D, "ddd %5d"%i)
hemisphere_solutions.append(sampled_direction)
if (hemisphere_solutions.size()<3):
return hemisphere_solutions
kvals = flex.double([
hemisphere_solutions[x].kval for x in xrange(len(hemisphere_solutions))])
perm = flex.sort_permutation(kvals,True)
# need to be more clever than just taking the top 30.
# one huge cluster around a strong basis direction could dominate the
# whole hemisphere map, preventing the discovery of three basis vectors
perm_idx = 0
unique_clusters = 0
hemisphere_solutions_sort = flex.Direction()
while perm_idx < len(perm) and \
unique_clusters < size:
test_item = hemisphere_solutions[perm[perm_idx]]
direction_ok = True
for list_item in hemisphere_solutions_sort:
distance = math.sqrt(math.pow(list_item.dvec[0]-test_item.dvec[0],2) +
math.pow(list_item.dvec[1]-test_item.dvec[1],2) +
math.pow(list_item.dvec[2]-test_item.dvec[2],2)
)
if distance < 0.087: #i.e., 5 degrees
direction_ok=False
break
if direction_ok:
unique_clusters+=1
hemisphere_solutions_sort.append(test_item)
perm_idx+=1
return hemisphere_solutions_sort;