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chemfp 3.5 documentation
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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W
Symbols
--arch=NAME
command line option
--with-avx2, --without-avx2
command line option
--with-openmp, --without-openmp
command line option
--with-ssse3, --without-ssse3
command line option
_
__call__() (chemfp.types.FingerprintFamily method)
__getitem__() (chemfp.arena.FingerprintArena method)
(chemfp.search.SearchResults method)
__init__() (chemfp.FingerprintIterator method)
(chemfp.Fingerprints method)
(chemfp.io.Location method)
__iter__() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintIterator method)
(chemfp.FingerprintReader method)
(chemfp.fps_io.FPSReader method)
(chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
__len__() (chemfp.arena.FingerprintArena method)
(chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
__repr__() (chemfp.base_toolkit.Format method)
(chemfp.Metadata method)
(chemfp.base_toolkit.FormatMetadata method)
(chemfp.io.Location method)
(chemfp.types.FingerprintFamily method)
__str__() (chemfp.Metadata method)
A
add_sdf_tag() (in module chemfp.text_toolkit)
add_tag() (chemfp._text_toolkit.TextRecord method)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
args (chemfp.base_toolkit.FormatMetadata attribute)
aromaticity (chemfp.Metadata attribute)
as_buffer() (chemfp.search.SearchResult method)
as_ctypes() (chemfp.search.SearchResult method)
as_numpy_array() (chemfp.search.SearchResult method)
B
base_name (chemfp.types.FingerprintFamily attribute)
(chemfp.types.FingerprintType attribute)
BaseMoleculeReader (class in chemfp.base_toolkit)
BaseMoleculeWriter (class in chemfp.base_toolkit)
byte_contains() (in module chemfp.bitops)
byte_contains_bit() (in module chemfp.bitops)
byte_difference() (in module chemfp.bitops)
byte_from_bitlist() (in module chemfp.bitops)
byte_hex_tanimoto() (in module chemfp.bitops)
byte_hex_tversky() (in module chemfp.bitops)
byte_intersect() (in module chemfp.bitops)
byte_intersect_popcount() (in module chemfp.bitops)
byte_popcount() (in module chemfp.bitops)
byte_tanimoto() (in module chemfp.bitops)
byte_to_bitlist() (in module chemfp.bitops)
byte_tversky() (in module chemfp.bitops)
byte_union() (in module chemfp.bitops)
C
CanRecord (class in chemfp._text_toolkit)
CanStringRecord (class in chemfp._text_toolkit)
category (chemfp.ChemFPProblem attribute)
CDKAtomPairs2DFingerprintType_v20 (class in chemfp.cdk_types)
CDKDaylightFingerprintType_v20 (class in chemfp.cdk_types)
CDKECFP0FingerprintType_v20 (class in chemfp.cdk_types)
CDKECFP2FingerprintType_v20 (class in chemfp.cdk_types)
CDKECFP4FingerprintType_v20 (class in chemfp.cdk_types)
CDKECFP6FingerprintType_v20 (class in chemfp.cdk_types)
CDKEStateFingerprintType_v20 (class in chemfp.cdk_types)
CDKExtendedFingerprintType_v20 (class in chemfp.cdk_types)
CDKFCFP0FingerprintType_v20 (class in chemfp.cdk_types)
CDKFCFP2FingerprintType_v20 (class in chemfp.cdk_types)
CDKFCFP4FingerprintType_v20 (class in chemfp.cdk_types)
CDKFCFP6FingerprintType_v20 (class in chemfp.cdk_types)
CDKGraphOnlyFingerprintType_v20 (class in chemfp.cdk_types)
CDKHybridizationFingerprintType_v20 (class in chemfp.cdk_types)
CDKKlekotaRothFingerprintType_v20 (class in chemfp.cdk_types)
CDKMACCSFingerprintType_v20 (class in chemfp.cdk_types)
CDKPubchemFingerprintType_v20 (class in chemfp.cdk_types)
CDKShortestPathFingerprintType_v20 (class in chemfp.cdk_types)
CDKSubstructureFingerprintType_v20 (class in chemfp.cdk_types)
check_fingerprint_problems() (in module chemfp)
check_metadata_problems() (in module chemfp)
chemfp (module)
chemfp._text_toolkit (module)
chemfp.arena (module)
chemfp.base_toolkit (module)
chemfp.bitops (module)
chemfp.cdk_patterns (module)
chemfp.cdk_toolkit (module)
chemfp.cdk_types (module)
chemfp.encodings (module)
chemfp.fpb_io (module)
chemfp.fps_io (module)
chemfp.io (module)
chemfp.openbabel_patterns (module)
chemfp.openbabel_toolkit (module)
chemfp.openbabel_types (module)
chemfp.openeye_patterns (module)
chemfp.openeye_toolkit (module)
chemfp.openeye_types (module)
chemfp.rdkit_patterns (module)
chemfp.rdkit_toolkit (module)
chemfp.rdkit_types (module)
chemfp.search (module)
chemfp.text_toolkit (module)
chemfp.toolkit (module)
chemfp.types (module)
ChemFPError (class in chemfp)
ChemFPProblem (class in chemfp)
clear() (chemfp.search.SearchResult method)
clear_all() (chemfp.search.SearchResults method)
close() (chemfp.base_toolkit.BaseMoleculeReader method)
(chemfp.FingerprintIterator method)
(chemfp.FingerprintWriter method)
(chemfp.base_toolkit.BaseMoleculeWriter method)
(chemfp.fpb_io.InputOrderFPBWriter method)
(chemfp.fpb_io.OrderedFPBWriter method)
(chemfp.fps_io.FPSReader method)
(chemfp.fps_io.FPSWriter method)
closed (chemfp.base_toolkit.BaseMoleculeReader attribute)
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
(chemfp.base_toolkit.IdAndMoleculeReader attribute)
(chemfp.base_toolkit.IdAndRecordReader attribute)
(chemfp.base_toolkit.MoleculeReader attribute)
(chemfp.base_toolkit.MoleculeStringWriter attribute)
(chemfp.base_toolkit.MoleculeWriter attribute)
(chemfp.base_toolkit.RecordReader attribute)
(chemfp.fpb_io.InputOrderFPBWriter attribute)
(chemfp.fpb_io.OrderedFPBWriter attribute)
(chemfp.fps_io.FPSReader attribute)
command line option
--arch=NAME
--with-avx2, --without-avx2
--with-openmp, --without-openmp
--with-ssse3, --without-ssse3
compute_fingerprint() (chemfp.types.FingerprintType method)
compute_fingerprints() (chemfp.types.FingerprintType method)
contains_arena() (in module chemfp.search)
contains_fp() (in module chemfp.search)
copy() (chemfp._text_toolkit.TextRecord method)
(chemfp.Metadata method)
(chemfp.arena.FingerprintArena method)
copy_molecule() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
count() (chemfp.search.SearchResult method)
count_all() (chemfp.search.SearchResults method)
count_tanimoto_hits() (in module chemfp)
count_tanimoto_hits_arena() (chemfp.fps_io.FPSReader method)
(in module chemfp.search)
count_tanimoto_hits_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
count_tanimoto_hits_symmetric() (in module chemfp)
(in module chemfp.search)
count_tversky_hits() (in module chemfp)
count_tversky_hits_arena() (in module chemfp.search)
count_tversky_hits_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
count_tversky_hits_symmetric() (in module chemfp)
(in module chemfp.search)
create_bytes() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
create_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
cumulative_score() (chemfp.search.SearchResult method)
cumulative_score_all() (chemfp.search.SearchResults method)
D
date (chemfp.Metadata attribute)
description (chemfp.ChemFPProblem attribute)
E
error_level (chemfp.ChemFPProblem attribute)
F
filename (chemfp.base_toolkit.FormatMetadata attribute)
(chemfp.io.Location attribute)
fill_lower_triangle() (in module chemfp.search)
fingerprint_kwargs (chemfp.types.FingerprintType attribute)
FingerprintArena (class in chemfp.arena)
FingerprintFamily (class in chemfp.types)
FingerprintIterator (class in chemfp)
FingerprintList (class in chemfp.arena)
FingerprintReader (class in chemfp)
fingerprints (chemfp.arena.FingerprintArena attribute)
Fingerprints (class in chemfp)
FingerprintType (class in chemfp.types)
FingerprintWriter (class in chemfp)
first_line (chemfp.io.Location attribute)
format (chemfp.fpb_io.InputOrderFPBWriter attribute)
(chemfp.fpb_io.OrderedFPBWriter attribute)
Format (class in chemfp.base_toolkit)
format_ids_and_scores_as_bytes() (chemfp.search.SearchResult method)
FormatMetadata (class in chemfp.base_toolkit)
FPSReader (class in chemfp.fps_io)
FPSWriter (class in chemfp.fps_io)
from_base64() (in module chemfp.encodings)
from_binary_lsb() (in module chemfp.encodings)
from_binary_msb() (in module chemfp.encodings)
from_cactvs() (in module chemfp.encodings)
from_daylight() (in module chemfp.encodings)
from_destination() (chemfp.io.Location method)
from_hex() (in module chemfp.encodings)
from_hex_lsb() (in module chemfp.encodings)
from_hex_msb() (in module chemfp.encodings)
from_kwargs() (chemfp.types.FingerprintFamily method)
from_on_bit_positions() (in module chemfp.encodings)
from_source() (chemfp.io.Location method)
from_text_settings() (chemfp.types.FingerprintFamily method)
G
get_by_id() (chemfp.arena.FingerprintArena method)
get_default_reader_args() (chemfp.base_toolkit.Format method)
get_default_writer_args() (chemfp.base_toolkit.Format method)
get_defaults() (chemfp.types.FingerprintFamily method)
get_fingerprint() (chemfp.arena.FingerprintArena method)
get_fingerprint_by_id() (chemfp.arena.FingerprintArena method)
get_fingerprint_families() (in module chemfp)
get_fingerprint_family() (chemfp.types.FingerprintType method)
(in module chemfp)
get_fingerprint_family_names() (in module chemfp)
get_fingerprint_type() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintReader method)
(chemfp.fps_io.FPSReader method)
(in module chemfp)
get_fingerprint_type_from_text_settings() (in module chemfp)
get_format() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_formats() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_id() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_ids() (chemfp.search.SearchResult method)
get_ids_and_scores() (chemfp.search.SearchResult method)
get_index_by_id() (chemfp.arena.FingerprintArena method)
get_indices() (chemfp.search.SearchResult method)
get_indices_and_scores() (chemfp.search.SearchResult method)
get_indices_as_numpy_array() (chemfp.search.SearchResult method)
get_input_format() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_input_format_from_source() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_input_formats() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_kwargs_from_text_settings() (chemfp.types.FingerprintFamily method)
get_license_date() (in module chemfp)
get_max_threads() (in module chemfp)
get_metadata() (chemfp.types.FingerprintType method)
get_num_threads() (in module chemfp)
get_output_format() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_output_format_from_destination() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_output_formats() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_reader_args_from_text_settings() (chemfp.base_toolkit.Format method)
get_scores() (chemfp.search.SearchResult method)
get_scores_as_numpy_array() (chemfp.search.SearchResult method)
get_sdf_id() (in module chemfp.text_toolkit)
get_sdf_tag() (in module chemfp.text_toolkit)
get_sdf_tag_pairs() (in module chemfp.text_toolkit)
get_tag() (chemfp._text_toolkit.TextRecord method)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_tag_as_bytes() (chemfp._text_toolkit.TextRecord method)
get_tag_pairs() (chemfp._text_toolkit.TextRecord method)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
get_tag_pairs_as_bytes() (chemfp._text_toolkit.TextRecord method)
get_toolkit() (in module chemfp)
get_toolkit_names() (in module chemfp)
get_type() (chemfp.types.FingerprintType method)
get_unqualified_reader_args() (chemfp.base_toolkit.Format method)
get_unqualified_writer_args() (chemfp.base_toolkit.Format method)
get_writer_args_from_text_settings() (chemfp.base_toolkit.Format method)
getvalue() (chemfp.base_toolkit.MoleculeStringWriter method)
H
has_fingerprint_family() (in module chemfp)
has_toolkit() (in module chemfp)
hex_contains() (in module chemfp.bitops)
hex_contains_bit() (in module chemfp.bitops)
hex_decode() (in module chemfp.bitops)
hex_difference() (in module chemfp.bitops)
hex_encode() (in module chemfp.bitops)
hex_encode_as_bytes() (in module chemfp.bitops)
hex_from_bitlist() (in module chemfp.bitops)
hex_intersect() (in module chemfp.bitops)
hex_intersect_popcount() (in module chemfp.bitops)
hex_isvalid() (in module chemfp.bitops)
hex_popcount() (in module chemfp.bitops)
hex_tanimoto() (in module chemfp.bitops)
hex_to_bitlist() (in module chemfp.bitops)
hex_tversky() (in module chemfp.bitops)
hex_union() (in module chemfp.bitops)
I
id_bytes (chemfp._text_toolkit.TextRecord attribute)
IdAndMoleculeReader (class in chemfp.base_toolkit)
IdAndRecordReader (class in chemfp.base_toolkit)
ids (chemfp.arena.FingerprintArena attribute)
InputOrderFPBWriter (class in chemfp.fpb_io)
is_available (chemfp.base_toolkit.Format attribute)
is_input_format (chemfp.base_toolkit.Format attribute)
is_licensed() (in module chemfp)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
is_output_format (chemfp.base_toolkit.Format attribute)
iter_arenas() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintReader method)
(chemfp.fps_io.FPSReader method)
iter_ids() (chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
iter_ids_and_scores() (chemfp.search.SearchResults method)
iter_indices() (chemfp.search.SearchResults method)
iter_indices_and_scores() (chemfp.search.SearchResults method)
iter_scores() (chemfp.search.SearchResults method)
K
knearest_tanimoto_search() (in module chemfp)
knearest_tanimoto_search_arena() (chemfp.fps_io.FPSReader method)
(in module chemfp.search)
knearest_tanimoto_search_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
knearest_tanimoto_search_symmetric() (in module chemfp)
(in module chemfp.search)
knearest_tversky_search() (in module chemfp)
knearest_tversky_search_arena() (in module chemfp.search)
knearest_tversky_search_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
knearest_tversky_search_symmetric() (in module chemfp)
(in module chemfp.search)
L
load_fingerprints() (in module chemfp)
location (chemfp.base_toolkit.BaseMoleculeReader attribute)
(chemfp.ParseError attribute)
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
(chemfp.base_toolkit.IdAndMoleculeReader attribute)
(chemfp.base_toolkit.IdAndRecordReader attribute)
(chemfp.base_toolkit.MoleculeReader attribute)
(chemfp.base_toolkit.MoleculeStringWriter attribute)
(chemfp.base_toolkit.MoleculeWriter attribute)
(chemfp.base_toolkit.RecordReader attribute)
(chemfp.fps_io.FPSReader attribute)
Location (class in chemfp.io)
M
make_fingerprinter() (chemfp.types.FingerprintType method)
make_id_and_molecule_fingerprint_parser() (chemfp.types.FingerprintType method)
make_id_and_molecule_parser() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
metadata (chemfp.arena.FingerprintArena attribute)
(chemfp.base_toolkit.BaseMoleculeReader attribute)
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
(chemfp.base_toolkit.IdAndMoleculeReader attribute)
(chemfp.base_toolkit.IdAndRecordReader attribute)
(chemfp.base_toolkit.MoleculeReader attribute)
(chemfp.base_toolkit.MoleculeStringWriter attribute)
(chemfp.base_toolkit.MoleculeWriter attribute)
(chemfp.base_toolkit.RecordReader attribute)
(chemfp.fpb_io.InputOrderFPBWriter attribute)
(chemfp.fpb_io.OrderedFPBWriter attribute)
(chemfp.fps_io.FPSReader attribute)
Metadata (class in chemfp)
mol (chemfp.io.Location attribute)
MoleculeReader (class in chemfp.base_toolkit)
MoleculeStringWriter (class in chemfp.base_toolkit)
MoleculeWriter (class in chemfp.base_toolkit)
msg (chemfp.ParseError attribute)
N
name (chemfp.types.FingerprintFamily attribute)
(chemfp.types.FingerprintType attribute)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
num_bits (chemfp.Metadata attribute)
(chemfp.types.FingerprintType attribute)
num_bytes (chemfp.Metadata attribute)
O
offsets (chemfp.io.Location attribute)
open() (in module chemfp)
open_fingerprint_writer() (in module chemfp)
open_molecule_writer() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
open_molecule_writer_to_bytes() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
open_molecule_writer_to_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
OpenBabelECFP0FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelECFP10FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelECFP2FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelECFP4FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelECFP6FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelECFP8FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelFP2FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelFP3FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelFP4FingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelMACCSFingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelMACCSFingerprintType_v2 (class in chemfp.openbabel_types)
OpenEyeCircularFingerprintType_v2 (class in chemfp.openeye_types)
OpenEyeMACCSFingerprintType_v2 (class in chemfp.openeye_types)
OpenEyeMACCSFingerprintType_v3 (class in chemfp.openeye_types)
OpenEyeMDLScreenFingerprintType_v1 (class in chemfp.openeye_types)
OpenEyeMoleculeScreenFingerprintType_v1 (class in chemfp.openeye_types)
OpenEyePathFingerprintType_v2 (class in chemfp.openeye_types)
OpenEyeSMARTSScreenFingerprintType_v1 (class in chemfp.openeye_types)
OpenEyeTreeFingerprintType_v2 (class in chemfp.openeye_types)
OrderedFPBWriter (class in chemfp.fpb_io)
output_recno (chemfp.io.Location attribute)
P
parse_id_and_molecule() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
parse_id_and_molecule_fingerprint() (chemfp.types.FingerprintType method)
parse_molecule() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
parse_molecule_fingerprint() (chemfp.types.FingerprintType method)
ParseError (class in chemfp)
partial_count_tanimoto_hits_symmetric() (in module chemfp.search)
partial_count_tversky_hits_symmetric() (in module chemfp.search)
partial_threshold_tanimoto_search_symmetric() (in module chemfp.search)
partial_threshold_tversky_search_symmetric() (in module chemfp.search)
prefix (chemfp.base_toolkit.Format attribute)
Python Enhancement Proposals
PEP 343
R
random_choice() (chemfp.arena.FingerprintArena method)
(chemfp.arena.FingerprintList method)
RDKitAtomPairFingerprint_v1 (class in chemfp.rdkit_types)
RDKitAtomPairFingerprint_v2 (class in chemfp.rdkit_types)
RDKitAvalonFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitFingerprintType_v2 (class in chemfp.rdkit_types)
RDKitMACCSFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitMACCSFingerprintType_v2 (class in chemfp.rdkit_types)
RDKitMorganFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitPatternFingerprint_v1 (class in chemfp.rdkit_types)
RDKitPatternFingerprint_v2 (class in chemfp.rdkit_types)
RDKitPatternFingerprint_v3 (class in chemfp.rdkit_types)
RDKitSECFPFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitTorsionFingerprintType_v1 (class in chemfp.rdkit_types)
RDKitTorsionFingerprintType_v2 (class in chemfp.rdkit_types)
RDMACCSCDKFingerprinter_v1 (class in chemfp.cdk_patterns)
RDMACCSCDKFingerprinter_v2 (class in chemfp.cdk_patterns)
RDMACCSOpenBabelFingerprinter_v1 (class in chemfp.openbabel_patterns)
RDMACCSOpenBabelFingerprinter_v2 (class in chemfp.openbabel_patterns)
RDMACCSOpenEyeFingerprinter_v1 (class in chemfp.openeye_patterns)
RDMACCSOpenEyeFingerprinter_v2 (class in chemfp.openeye_patterns)
RDMACCSRDKitFingerprinter_v1 (class in chemfp.rdkit_patterns)
RDMACCSRDKitFingerprinter_v2 (class in chemfp.rdkit_patterns)
read_ids_and_molecules() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
read_ids_and_molecules_from_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
read_molecule_fingerprints() (chemfp.types.FingerprintType method)
(in module chemfp)
read_molecule_fingerprints_from_string() (chemfp.types.FingerprintType method)
(in module chemfp)
read_molecules() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
read_molecules_from_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
read_sdf_ids_and_records() (in module chemfp.text_toolkit)
read_sdf_ids_and_records_from_string() (in module chemfp.text_toolkit)
read_sdf_ids_and_values() (in module chemfp.text_toolkit)
read_sdf_ids_and_values_from_string() (in module chemfp.text_toolkit)
read_sdf_records() (in module chemfp.text_toolkit)
read_sdf_records_from_string() (in module chemfp.text_toolkit)
recno (chemfp.io.Location attribute)
record (chemfp._text_toolkit.TextRecord attribute)
(chemfp.io.Location attribute)
record_format (chemfp._text_toolkit.TextRecord attribute)
(chemfp.base_toolkit.FormatMetadata attribute)
(chemfp.io.Location attribute)
RecordReader (class in chemfp.base_toolkit)
reorder() (chemfp.search.SearchResult method)
reorder_all() (chemfp.search.SearchResults method)
S
sample() (chemfp.arena.FingerprintArena method)
save() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintReader method)
(chemfp.fps_io.FPSReader method)
SDFRecord (class in chemfp._text_toolkit)
SearchResult (class in chemfp.search)
SearchResults (class in chemfp.search)
set_id() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
set_num_threads() (in module chemfp)
set_sdf_id() (in module chemfp.text_toolkit)
severity (chemfp.ChemFPProblem attribute)
shape (chemfp.search.SearchResults attribute)
smiles (chemfp._text_toolkit.TextRecord attribute)
SmiRecord (class in chemfp._text_toolkit)
SmiStringRecord (class in chemfp._text_toolkit)
software (chemfp.Metadata attribute)
(chemfp.types.FingerprintType attribute)
(in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
sources (chemfp.Metadata attribute)
SubstructCDKFingerprinter_v1 (class in chemfp.cdk_patterns)
SubstructOpenBabelFingerprinter_v1 (class in chemfp.openbabel_patterns)
SubstructOpenEyeFingerprinter_v1 (class in chemfp.openeye_patterns)
SubstructRDKitFingerprintType_v1 (class in chemfp.rdkit_patterns)
supports_io (chemfp.base_toolkit.Format attribute)
T
TextRecord (class in chemfp._text_toolkit)
threshold_tanimoto_search() (in module chemfp)
threshold_tanimoto_search_arena() (chemfp.fps_io.FPSReader method)
(in module chemfp.search)
threshold_tanimoto_search_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
threshold_tanimoto_search_symmetric() (in module chemfp)
(in module chemfp.search)
threshold_tversky_search() (in module chemfp)
threshold_tversky_search_arena() (in module chemfp.search)
threshold_tversky_search_fp() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
(in module chemfp.search)
threshold_tversky_search_symmetric() (in module chemfp)
(in module chemfp.search)
to_csr() (chemfp.search.SearchResults method)
to_numpy_array() (chemfp.arena.FingerprintArena method)
to_numpy_bitarray() (chemfp.arena.FingerprintArena method)
toolkit (chemfp.types.FingerprintFamily attribute)
(chemfp.types.FingerprintType attribute)
train_test_split() (chemfp.arena.FingerprintArena method)
type (chemfp.Metadata attribute)
U
UsmRecord (class in chemfp._text_toolkit)
UsmStringRecord (class in chemfp._text_toolkit)
V
version (chemfp.types.FingerprintFamily attribute)
(chemfp.types.FingerprintType attribute)
W
where() (chemfp.io.Location method)
write_fingerprint() (chemfp.FingerprintWriter method)
(chemfp.fpb_io.InputOrderFPBWriter method)
(chemfp.fpb_io.OrderedFPBWriter method)
(chemfp.fps_io.FPSWriter method)
write_fingerprints() (chemfp.FingerprintWriter method)
(chemfp.fpb_io.InputOrderFPBWriter method)
(chemfp.fpb_io.OrderedFPBWriter method)
(chemfp.fps_io.FPSWriter method)
write_id_and_molecule() (chemfp.base_toolkit.BaseMoleculeWriter method)
write_ids_and_molecules() (chemfp.base_toolkit.BaseMoleculeWriter method)
write_molecule() (chemfp.base_toolkit.BaseMoleculeWriter method)
write_molecules() (chemfp.base_toolkit.BaseMoleculeWriter method)
Links
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chemfp at Read The Docs
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