def test_partial_threshold_search(self):
threshold = 0.1
N = len(fps)
result = search.SearchResults(N, fps.arena_ids)
expected = [[] for i in range(N)]
for i in range(0, N, 13):
for j in range(i, N, 8):
search.partial_threshold_tanimoto_search_symmetric(
result, fps, threshold, i, i + 13, j, j + 8)
slow_threshold_search(expected, fps, threshold, i, i + 13, j,
j + 8)
_compare_search_results(self, result, expected)
counts_before = map(len, result)
search.fill_lower_triangle(result)
counts_after = map(len, result)
self.assertNotEqual(counts_before, counts_after)
self.assertSequenceEqual(
counts_after, search.count_tanimoto_hits_symmetric(fps, threshold))
normal = search.threshold_tanimoto_search_symmetric(fps, threshold)
_compare_search_results(self, result,
list(normal.iter_indices_and_scores()))
def test_symmetric(self):
# query[i] always matches target[i] so x[i] will be at least one
x = search.count_tanimoto_hits_arena(fps, fps, 0.6)
# This only processes the upper-triangle, and not the diagonal
y = search.count_tanimoto_hits_symmetric(fps, 0.6)
self.assertEquals(len(x), len(y))
for i in range(len(x)):
self.assertEquals(x[i]-1, y[i])
def test_symmetric(self):
# query[i] always matches target[i] so x[i] will be at least one
x = search.count_tanimoto_hits_arena(fps, fps, 0.6)
# This only processes the upper-triangle, and not the diagonal
y = search.count_tanimoto_hits_symmetric(fps, 0.6)
self.assertEquals(len(x), len(y))
for i in range(len(x)):
self.assertEquals(x[i] - 1, y[i])
def test_partial_counts(self):
threshold = 0.2
N = len(fps)
counts = array.array("i", [0]*N)
expected = [0] * N
for i in range(0, N, 10):
for j in range(i, N, 8):
slow_counts(expected, fps, threshold, i, i+10, j, j+8)
search.partial_count_tanimoto_hits_symmetric(counts, fps, threshold,
i, i+10, j, j+8)
self.assertSequenceEqual(counts, expected)
normal = search.count_tanimoto_hits_symmetric(fps, threshold)
self.assertSequenceEqual(normal, expected)
def test_partial_counts(self):
threshold = 0.2
N = len(fps)
counts = array.array("i", [0] * N)
expected = [0] * N
for i in range(0, N, 10):
for j in range(i, N, 8):
slow_counts(expected, fps, threshold, i, i + 10, j, j + 8)
search.partial_count_tanimoto_hits_symmetric(
counts, fps, threshold, i, i + 10, j, j + 8)
self.assertSequenceEqual(counts, expected)
normal = search.count_tanimoto_hits_symmetric(fps, threshold)
self.assertSequenceEqual(normal, expected)
def test_partial_threshold_search(self):
threshold = 0.1
N = len(fps)
result = search.SearchResults(N, fps.arena_ids)
expected = [[] for i in range(N)]
for i in range(0, N, 13):
for j in range(i, N, 8):
search.partial_threshold_tanimoto_search_symmetric(result, fps, threshold,
i, i+13, j, j+8)
slow_threshold_search(expected, fps, threshold, i, i+13, j, j+8)
_compare_search_results(self, result, expected)
counts_before = map(len, result)
search.fill_lower_triangle(result)
counts_after = map(len, result)
self.assertNotEqual(counts_before, counts_after)
self.assertSequenceEqual(counts_after,
search.count_tanimoto_hits_symmetric(fps, threshold))
normal = search.threshold_tanimoto_search_symmetric(fps, threshold)
_compare_search_results(self, result, list(normal.iter_indices_and_scores()))
def do_NxN_searches(args, k, threshold, target_filename):
t1 = time.time()
# load_fingerprints sorts the fingerprints based on popcount
# I want the output to be in the same order as the input.
# This means I need to do some reordering. Consider:
# 0003 ID_A
# 010a ID_B
# 1000 ID_C
# I use this to generate:
# original_ids = ["ID_A", "ID_B", "ID_C"]
# targets.ids = [2, 0, 1]
# original_index_to_current_index = {2:0, 0:1, 1:2}
# current_index_to_original_index = {0:2, 1:0, 2:1}
original_ids = []
fps = chemfp.open(target_filename)
def get_index_to_id(fps):
for i, (id, fp) in enumerate(fps):
original_ids.append(id)
yield i, fp
targets = chemfp.load_fingerprints(get_index_to_id(fps), fps.metadata)
original_index_to_current_index = dict(zip(targets.ids, xrange(len(targets))))
current_index_to_original_id = dict((i, original_ids[original_index])
for i, original_index in enumerate(targets.ids))
t2 = time.time()
outfile = io.open_output(args.output)
with io.ignore_pipe_errors:
type = "Tanimoto k=%(k)s threshold=%(threshold)s NxN=full" % dict(
k=k, threshold=threshold, max_score=1.0)
if args.count:
type = "Count threshold=%(threshold)s NxN=full" % dict(
threshold=threshold)
write_count_magic(outfile)
else:
write_simsearch_magic(outfile)
write_simsearch_header(outfile, {
"num_bits": targets.metadata.num_bits,
"software": SOFTWARE,
"type": type,
"targets": target_filename,
"target_sources": targets.metadata.sources})
if args.count:
counts = search.count_tanimoto_hits_symmetric(targets, threshold,
batch_size=args.batch_size)
for original_index, original_id in enumerate(original_ids):
current_index = original_index_to_current_index[original_index]
count = counts[current_index]
outfile.write("%d\t%s\n" % (count, original_id))
else:
hit_formatter = "\t%s\t" + get_float_formatter(targets.metadata.num_bytes)
if k == "all":
results = search.threshold_tanimoto_search_symmetric(targets, threshold,
batch_size=args.batch_size)
else:
results = search.knearest_tanimoto_search_symmetric(targets, k, threshold,
batch_size=args.batch_size)
for original_index, original_id in enumerate(original_ids):
current_index = original_index_to_current_index[original_index]
new_indices_and_scores = results[current_index].get_ids_and_scores()
outfile.write("%d\t%s" % (len(new_indices_and_scores), original_id))
for (new_index, score) in new_indices_and_scores:
original_id = original_ids[new_index]
outfile.write(hit_formatter % (original_id, score))
outfile.write("\n") # XXX flush?
t3 = time.time()
if args.times:
sys.stderr.write("open %.2f search %.2f total %.2f\n" % (t2-t1, t3-t2, t3-t1))
def do_NxN_searches(args, k, threshold, target_filename):
t1 = time.time()
# load_fingerprints sorts the fingerprints based on popcount
# I want the output to be in the same order as the input.
# This means I need to do some reordering. Consider:
# 0003 ID_A
# 010a ID_B
# 1000 ID_C
# I use this to generate:
# original_ids = ["ID_A", "ID_B", "ID_C"]
# targets.ids = [2, 0, 1]
# original_index_to_current_index = {2:0, 0:1, 1:2}
# current_index_to_original_index = {0:2, 1:0, 2:1}
original_ids = []
fps = chemfp.open(target_filename)
def get_index_to_id(fps):
for i, (id, fp) in enumerate(fps):
original_ids.append(id)
yield i, fp
targets = chemfp.load_fingerprints(get_index_to_id(fps), fps.metadata)
original_index_to_current_index = dict(
zip(targets.ids, xrange(len(targets))))
current_index_to_original_id = dict(
(i, original_ids[original_index])
for i, original_index in enumerate(targets.ids))
t2 = time.time()
outfile = io.open_output(args.output)
with io.ignore_pipe_errors:
type = "Tanimoto k=%(k)s threshold=%(threshold)s NxN=full" % dict(
k=k, threshold=threshold, max_score=1.0)
if args.count:
type = "Count threshold=%(threshold)s NxN=full" % dict(
threshold=threshold)
write_count_magic(outfile)
else:
write_simsearch_magic(outfile)
write_simsearch_header(
outfile, {
"num_bits": targets.metadata.num_bits,
"software": SOFTWARE,
"type": type,
"targets": target_filename,
"target_sources": targets.metadata.sources
})
if args.count:
counts = search.count_tanimoto_hits_symmetric(
targets, threshold, batch_size=args.batch_size)
for original_index, original_id in enumerate(original_ids):
current_index = original_index_to_current_index[original_index]
count = counts[current_index]
outfile.write("%d\t%s\n" % (count, original_id))
else:
hit_formatter = "\t%s\t" + get_float_formatter(
targets.metadata.num_bytes)
if k == "all":
results = search.threshold_tanimoto_search_symmetric(
targets, threshold, batch_size=args.batch_size)
else:
results = search.knearest_tanimoto_search_symmetric(
targets, k, threshold, batch_size=args.batch_size)
for original_index, original_id in enumerate(original_ids):
current_index = original_index_to_current_index[original_index]
new_indices_and_scores = results[
current_index].get_ids_and_scores()
outfile.write("%d\t%s" %
(len(new_indices_and_scores), original_id))
for (new_index, score) in new_indices_and_scores:
original_id = original_ids[new_index]
outfile.write(hit_formatter % (original_id, score))
outfile.write("\n") # XXX flush?
t3 = time.time()
if args.times:
sys.stderr.write("open %.2f search %.2f total %.2f\n" %
(t2 - t1, t3 - t2, t3 - t1))
def test_zeros(self):
y = search.count_tanimoto_hits_symmetric(zeros, 0.9)
self.assertSequenceEqual(y, [0, 0, 0, 0, 1, 1])
y = search.count_tanimoto_hits_symmetric(zeros, 0.001)
self.assertSequenceEqual(y, [0, 0, 1, 2, 2, 3])
def test_zeros(self):
y = search.count_tanimoto_hits_symmetric(zeros, 0.9)
self.assertSequenceEqual(y, [0, 0, 0, 0, 1, 1])
y = search.count_tanimoto_hits_symmetric(zeros, 0.001)
self.assertSequenceEqual(y, [0, 0, 1, 2, 2, 3])