def count_tanimoto_hits_arena(query_arena, target_arena, threshold=0.7):
"""For each fingerprint in `query_arena`, count the number of hits in `target_arena` at least `threshold` similar to it
Example::
queries = chemfp.load_fingerprints("queries.fps")
targets = chemfp.load_fingerprints("targets.fps")
counts = chemfp.search.count_tanimoto_hits_arena(queries, targets, threshold=0.1)
print counts[:10]
The result is implementation specific. You'll always be able to
get its length and do an index lookup to get an integer
count. Currently it's a ctype array of longs, but it could be an
array.array or Python list in the future.
:param query_arena: The query fingerprints.
:type query_arena: a FingerprintArena
:param target_arena: The target fingerprints.
:param threshold: The minimum score threshold.
:type threshold: float between 0.0 and 1.0, inclusive
:returns: an array of counts
"""
_require_matching_sizes(query_arena, target_arena)
counts = (ctypes.c_int * len(query_arena))()
_chemfp.count_tanimoto_arena(
threshold, target_arena.num_bits, query_arena.start_padding,
query_arena.end_padding, query_arena.storage_size, query_arena.arena,
query_arena.start, query_arena.end, target_arena.start_padding,
target_arena.end_padding, target_arena.storage_size,
target_arena.arena, target_arena.start, target_arena.end,
target_arena.popcount_indices, counts)
return counts
def count_tanimoto_hits_fp(query_fp, target_arena, threshold=0.7):
"""Count the number of hits in `target_arena` at least `threshold` similar to the `query_fp`
Example::
query_id, query_fp = chemfp.load_fingerprints("queries.fps")[0]
targets = chemfp.load_fingerprints("targets.fps")
print chemfp.search.count_tanimoto_hits_fp(query_fp, targets, threshold=0.1)
:param query_fp: the query fingerprint
:type query_fp: a byte string
:param target_arena: the target arena
:type target_fp: a FingerprintArena
:param threshold: The minimum score threshold.
:type threshold: float between 0.0 and 1.0, inclusive
:returns: an integer count
"""
_require_matching_fp_size(query_fp, target_arena)
# Improve the alignment so the faster algorithms can be used
query_start_padding, query_end_padding, query_fp = _chemfp.align_fingerprint(
query_fp, target_arena.alignment, target_arena.storage_size)
counts = array.array("i", (0 for i in xrange(len(query_fp))))
_chemfp.count_tanimoto_arena(
threshold, target_arena.num_bits, query_start_padding,
query_end_padding, target_arena.storage_size, query_fp, 0, 1,
target_arena.start_padding, target_arena.end_padding,
target_arena.storage_size, target_arena.arena, target_arena.start,
target_arena.end, target_arena.popcount_indices, counts)
return counts[0]
def count_tanimoto_hits_arena(query_arena, target_arena, threshold=0.7):
"""For each fingerprint in `query_arena`, count the number of hits in `target_arena` at least `threshold` similar to it
Example::
queries = chemfp.load_fingerprints("queries.fps")
targets = chemfp.load_fingerprints("targets.fps")
counts = chemfp.search.count_tanimoto_hits_arena(queries, targets, threshold=0.1)
print counts[:10]
The result is implementation specific. You'll always be able to
get its length and do an index lookup to get an integer
count. Currently it's a ctype array of longs, but it could be an
array.array or Python list in the future.
:param query_arena: The query fingerprints.
:type query_arena: a FingerprintArena
:param target_arena: The target fingerprints.
:param threshold: The minimum score threshold.
:type threshold: float between 0.0 and 1.0, inclusive
:returns: an array of counts
"""
_require_matching_sizes(query_arena, target_arena)
counts = (ctypes.c_int*len(query_arena))()
_chemfp.count_tanimoto_arena(threshold, target_arena.num_bits,
query_arena.start_padding, query_arena.end_padding,
query_arena.storage_size,
query_arena.arena, query_arena.start, query_arena.end,
target_arena.start_padding, target_arena.end_padding,
target_arena.storage_size,
target_arena.arena, target_arena.start, target_arena.end,
target_arena.popcount_indices,
counts)
return counts
def count_tanimoto_hits_fp(query_fp, target_arena, threshold=0.7):
"""Count the number of hits in `target_arena` at least `threshold` similar to the `query_fp`
Example::
query_id, query_fp = chemfp.load_fingerprints("queries.fps")[0]
targets = chemfp.load_fingerprints("targets.fps")
print chemfp.search.count_tanimoto_hits_fp(query_fp, targets, threshold=0.1)
:param query_fp: the query fingerprint
:type query_fp: a byte string
:param target_arena: the target arena
:type target_fp: a FingerprintArena
:param threshold: The minimum score threshold.
:type threshold: float between 0.0 and 1.0, inclusive
:returns: an integer count
"""
_require_matching_fp_size(query_fp, target_arena)
# Improve the alignment so the faster algorithms can be used
query_start_padding, query_end_padding, query_fp = _chemfp.align_fingerprint(
query_fp, target_arena.alignment, target_arena.storage_size)
counts = array.array("i", (0 for i in xrange(len(query_fp))))
_chemfp.count_tanimoto_arena(threshold, target_arena.num_bits,
query_start_padding, query_end_padding,
target_arena.storage_size, query_fp, 0, 1,
target_arena.start_padding, target_arena.end_padding,
target_arena.storage_size, target_arena.arena,
target_arena.start, target_arena.end,
target_arena.popcount_indices,
counts)
return counts[0]
def count_tanimoto_hits(query_arena, target_arena, threshold):
require_matching_sizes(query_arena, target_arena)
counts = (ctypes.c_int * len(query_arena))()
_chemfp.count_tanimoto_arena(
threshold, target_arena.num_bits, query_arena.start_padding,
query_arena.end_padding, query_arena.storage_size, query_arena.arena,
query_arena.start, query_arena.end, target_arena.start_padding,
target_arena.end_padding, target_arena.storage_size,
target_arena.arena, target_arena.start, target_arena.end,
target_arena.popcount_indices, counts)
return counts
def count_tanimoto_hits_fp(query_fp, target_arena, threshold):
require_matching_fp_size(query_fp, target_arena)
# Improve the alignment so the faster algorithms can be used
query_start_padding, query_end_padding, query_fp = _chemfp.align_fingerprint(
query_fp, target_arena.alignment, target_arena.storage_size)
counts = array.array("i", (0 for i in xrange(len(query_fp))))
_chemfp.count_tanimoto_arena(
threshold, target_arena.num_bits, query_start_padding,
query_end_padding, target_arena.storage_size, query_fp, 0, 1,
target_arena.start_padding, target_arena.end_padding,
target_arena.storage_size, target_arena.arena, target_arena.start,
target_arena.end, target_arena.popcount_indices, counts)
return counts[0]
