chemfp
chemfp-4.1
What’s new in chemfp 4.1
What’s new in chemfp 4.0
Installing chemfp
Working with the command-line tools
Help for the command-line tools
Getting started with the API
Fingerprint family and type examples
Toolkit API examples
Text toolkit examples
Examples
chemfp API
Licenses
chemfp
Docs
»
Index
Index
Symbols
|
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
Symbols
--with-openmp, --without-openmp
command line option
_
__call__() (chemfp.io.ProgressBar method)
(chemfp.types.FingerprintFamily method)
__enter__() (chemfp.io.ProgressBar method)
__exit__() (chemfp.io.ProgressBar method)
__getitem__() (chemfp.arena.FingerprintArena method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.fps_search.FPSSearchResults method)
(chemfp.search.SearchResults method)
__init__() (chemfp.FingerprintIterator method)
(chemfp.Fingerprints method)
(chemfp.io.Location method)
,
[1]
__iter__() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintIterator method)
(chemfp.FingerprintReader method)
(chemfp.fps_io.FPSReader method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.fps_search.FPSSearchResults method)
(chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
__len__() (chemfp.arena.FingerprintArena method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.fps_search.FPSSearchResults 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)
__version__ (in module chemfp)
__version_info__ (in module chemfp)
A
add_aliases() (chemfp.types.FingerprintTypeUnknownError method)
add_sdf_tag() (in module chemfp.text_toolkit)
,
[1]
add_tag() (chemfp._text_toolkit.TextRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
(in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
alignment (chemfp.arena.FingerprintArena attribute)
all_clusters (chemfp.highlevel.clustering.ButinaClusters attribute)
arena (chemfp.arena.FingerprintArena attribute)
arena_ids (chemfp.arena.FingerprintArena attribute)
args (chemfp.base_toolkit.FormatMetadata attribute)
,
[1]
aromaticity (chemfp.Metadata attribute)
,
[1]
as_buffer() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
as_ctypes() (chemfp.diversity.BasePicks method)
(chemfp.diversity.MaxMinCandidates method)
(chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.HeapSweepSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.diversity.MaxMinSearch method)
(chemfp.highlevel.diversity.SpherexSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
as_numpy() (chemfp.diversity.BasePicks method)
(chemfp.diversity.MaxMinCandidates method)
(chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.HeapSweepSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.diversity.MaxMinSearch method)
(chemfp.highlevel.diversity.SpherexSearch method)
as_numpy_array() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
assignments (chemfp.highlevel.clustering.ButinaClusters attribute)
atom_pair (in module chemfp.rdkit_toolkit)
atom_pairs2d (in module chemfp.cdk_toolkit)
avalon (in module chemfp.rdkit_toolkit)
B
base_name (chemfp.types.BaseFingerprintType attribute)
(chemfp.types.FingerprintFamily attribute)
,
[1]
(chemfp.types.FingerprintType attribute)
BaseFingerprintType (class in chemfp.types)
BaseHeapSweepSearch (class in chemfp.highlevel.diversity)
BaseMaxMinPicker (class in chemfp.diversity)
BaseMoleculeReader (class in chemfp.base_toolkit)
,
[1]
BaseMoleculeWriter (class in chemfp.base_toolkit)
,
[1]
BasePicks (class in chemfp.diversity)
BaseSimsearch (class in chemfp.highlevel.similarity)
BaseSmiRecord (class in chemfp.text_records)
BaseSpherexSearch (class in chemfp.highlevel.diversity)
butina() (in module chemfp)
ButinaClusters (class in chemfp.highlevel.clustering)
byte_contains() (in module chemfp.bitops)
,
[1]
byte_contains_bit() (in module chemfp.bitops)
,
[1]
byte_difference() (in module chemfp.bitops)
byte_from_bitlist() (in module chemfp.bitops)
,
[1]
byte_hex_tanimoto() (in module chemfp.bitops)
,
[1]
byte_hex_tversky() (in module chemfp.bitops)
,
[1]
byte_intersect() (in module chemfp.bitops)
,
[1]
byte_intersect_popcount() (in module chemfp.bitops)
,
[1]
byte_popcount() (in module chemfp.bitops)
,
[1]
byte_tanimoto() (in module chemfp.bitops)
,
[1]
byte_to_bitlist() (in module chemfp.bitops)
,
[1]
byte_tversky() (in module chemfp.bitops)
,
[1]
byte_union() (in module chemfp.bitops)
,
[1]
byte_union_popcount() (in module chemfp.bitops)
byte_xor() (in module chemfp.bitops)
byte_xor_popcount() (in module chemfp.bitops)
bytes_read (chemfp.io.Location attribute)
C
c (chemfp.diversity.Candidate attribute)
Candidate (class in chemfp.diversity)
candidate_arena (chemfp.diversity.BaseMaxMinPicker attribute)
candidate_idx (chemfp.diversity.Candidate attribute)
(chemfp.diversity.Pick attribute)
(chemfp.diversity.PickAndScore attribute)
candidates (chemfp.diversity.BaseMaxMinPicker attribute)
(chemfp.diversity.SphereExclusionPicker attribute)
CanRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
CanStringRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
category (chemfp.ChemFPProblem attribute)
,
[1]
cdk (in module chemfp)
cdk2fps() (in module chemfp)
CDKAtomPairs2DFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKBaseFingerprintType (class in chemfp.cdk_types)
CDKDaylightFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKECFP0FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKECFP2FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKECFP4FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKECFP6FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKEStateFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKExtendedFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKFCFP0FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKFCFP2FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKFCFP4FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKFCFP6FingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKGraphOnlyFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKHybridizationFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKKlekotaRothFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKMACCSFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKPubchemFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKShortestPathFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
CDKShortestPathFingerprintType_v27 (class in chemfp.cdk_types)
CDKSubstructureFingerprintType_v20 (class in chemfp.cdk_types)
,
[1]
check_fingerprint_problems() (in module chemfp)
,
[1]
check_metadata_problems() (in module chemfp)
,
[1]
chemfp (module)
,
[1]
chemfp._text_toolkit (module)
chemfp.arena (module)
,
[1]
chemfp.base_toolkit (module)
,
[1]
chemfp.bitops (module)
,
[1]
chemfp.cdk_patterns (module)
chemfp.cdk_toolkit (module)
,
[1]
chemfp.cdk_types (module)
,
[1]
chemfp.csv_readers (module)
chemfp.diversity (module)
chemfp.encodings (module)
,
[1]
chemfp.fpb_io (module)
,
[1]
chemfp.fps_io (module)
,
[1]
chemfp.fps_search (module)
chemfp.highlevel.clustering (module)
chemfp.highlevel.conversion (module)
chemfp.highlevel.diversity (module)
chemfp.highlevel.similarity (module)
chemfp.io (module)
,
[1]
chemfp.openbabel_patterns (module)
chemfp.openbabel_toolkit (module)
,
[1]
chemfp.openbabel_types (module)
,
[1]
chemfp.openeye_patterns (module)
chemfp.openeye_toolkit (module)
,
[1]
chemfp.openeye_types (module)
,
[1]
chemfp.rdkit_patterns (module)
chemfp.rdkit_toolkit (module)
,
[1]
chemfp.rdkit_types (module)
,
[1]
chemfp.search (module)
,
[1]
chemfp.text_records (module)
chemfp.text_toolkit (module)
,
[1]
chemfp.toolkit (module)
chemfp.types (module)
,
[1]
ChemFPError
(class in chemfp)
ChemFPProblem
(class in chemfp)
circular (in module chemfp.openeye_toolkit)
clear() (chemfp.search.SearchResult method)
clear_all() (chemfp.search.SearchResults method)
clear_registry() (chemfp.io.Location method)
close() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintIterator method)
,
[1]
(chemfp.FingerprintWriter method)
,
[1]
(chemfp.base_toolkit.BaseMoleculeReader method)
,
[1]
(chemfp.base_toolkit.BaseMoleculeWriter method)
,
[1]
(chemfp.base_toolkit.MoleculeStringWriter method)
(chemfp.csv_readers.CSVIdAndMoleculeReader method)
(chemfp.csv_readers.CSVRowReader method)
(chemfp.fpb_io.InputOrderFPBWriter method)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(chemfp.fps_io.FPSWriter method)
,
[1]
(chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.similarity.BaseSimsearch method)
(chemfp.io.ProgressBar method)
closed (chemfp.base_toolkit.BaseMoleculeReader attribute)
,
[1]
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
,
[1]
(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)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter attribute)
,
[1]
(chemfp.fps_io.FPSReader attribute)
,
[1]
clusters (chemfp.highlevel.clustering.ButinaClusters attribute)
command line option
--with-openmp, --without-openmp
compression (chemfp.base_toolkit.Format attribute)
compute_fingerprint() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
compute_fingerprints() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
contains_arena() (in module chemfp.search)
,
[1]
contains_fp() (in module chemfp.search)
,
[1]
ConversionInfo (class in chemfp.highlevel.conversion)
convert2fps() (in module chemfp)
copy() (chemfp._text_toolkit.TextRecord method)
(chemfp.Metadata method)
,
[1]
(chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.io.Location method)
(chemfp.text_records.BaseSmiRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
(chemfp.types.FingerprintUnavailableError method)
copy_molecule() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
count() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
count_all() (chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
count_tanimoto_hits() (in module chemfp)
,
[1]
count_tanimoto_hits_arena() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
count_tanimoto_hits_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
count_tanimoto_hits_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
count_tversky_hits() (in module chemfp)
,
[1]
count_tversky_hits_arena() (in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
count_tversky_hits_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
count_tversky_hits_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
create_bytes() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
create_fasta() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_helm() (in module chemfp.rdkit_toolkit)
create_inchi() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_inchikey() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_inchikeystring() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_inchistring() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_molfile() (in module chemfp.cdk_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_oez() (in module chemfp.openeye_toolkit)
create_pdb() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_rdbinmol() (in module chemfp.rdkit_toolkit)
create_sdf() (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)
create_sdf3k() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_sequence() (in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
create_smi() (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)
create_smiles() (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)
create_smistring() (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)
create_string() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
CSVColumnDecodeError
CSVColumnError
CSVColumnIndexError
CSVColumnTitleError
CSVConfigurationError
CSVDialect (class in chemfp.csv_readers)
CSVDialectError
CSVFingerprintReader (class in chemfp.csv_readers)
CSVIdAndMoleculeReader (class in chemfp.csv_readers)
CSVRowReader (class in chemfp.csv_readers)
CSVUnicodeDecodeError
cumulative_score() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
cumulative_score_all() (chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
D
d (chemfp.diversity.Candidate attribute)
date (chemfp.Metadata attribute)
,
[1]
daylight (in module chemfp.cdk_toolkit)
depth (chemfp.diversity.Candidate attribute)
description (chemfp.ChemFPProblem attribute)
,
[1]
DISE_SMILES_LIST (chemfp.diversity.DISERanker attribute)
DISERanker (class in chemfp.diversity)
E
ecfp0 (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
ecfp10 (in module chemfp.openbabel_toolkit)
ecfp2 (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
ecfp4 (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
ecfp6 (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
ecfp8 (in module chemfp.openbabel_toolkit)
encoding (chemfp.text_records.BaseSmiRecord attribute)
(chemfp.text_records.SDFRecord attribute)
encoding_errors (chemfp.text_records.BaseSmiRecord attribute)
(chemfp.text_records.SDFRecord attribute)
EncodingError
end (chemfp.arena.FingerprintArena attribute)
end() (chemfp.io.Location method)
end_in_file (chemfp.csv_readers.CSVUnicodeDecodeError attribute)
end_padding (chemfp.arena.FingerprintArena attribute)
end_position (chemfp.io.Location attribute)
error_level (chemfp.ChemFPProblem attribute)
,
[1]
estate (in module chemfp.cdk_toolkit)
extended (in module chemfp.cdk_toolkit)
extensions (chemfp.base_toolkit.Format attribute)
F
fcfp0 (in module chemfp.cdk_toolkit)
fcfp2 (in module chemfp.cdk_toolkit)
fcfp4 (in module chemfp.cdk_toolkit)
fcfp6 (in module chemfp.cdk_toolkit)
filename (chemfp.base_toolkit.FormatMetadata attribute)
,
[1]
(chemfp.io.Location attribute)
,
[1]
fill_lower_triangle() (in module chemfp.search)
,
[1]
fingerprint_kwargs (chemfp.types.FingerprintType attribute)
FingerprintArena (class in chemfp.arena)
,
[1]
fingerprinter_can_fail (chemfp.cdk_types.CDKBaseFingerprintType attribute)
(chemfp.cdk_types.CDKShortestPathFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKShortestPathFingerprintType_v27 attribute)
(chemfp.types.BaseFingerprintType attribute)
FingerprintFamily (class in chemfp.types)
,
[1]
FingerprintIterator (class in chemfp)
,
[1]
FingerprintList (class in chemfp.arena)
,
[1]
FingerprintReader (class in chemfp)
,
[1]
fingerprints (chemfp.arena.FingerprintArena attribute)
,
[1]
Fingerprints (class in chemfp)
,
[1]
FingerprintType (class in chemfp.types)
,
[1]
FingerprintTypeError
FingerprintTypeParameterError
FingerprintTypeUnknownError
FingerprintUnavailableError
FingerprintValueError
FingerprintWriter (class in chemfp)
,
[1]
first_line (chemfp.io.Location attribute)
,
[1]
first_line_bytes (chemfp.io.Location attribute)
FixedSizeFingerprint (class in chemfp.rdkit_types)
format (chemfp.FingerprintWriter attribute)
(chemfp.fpb_io.InputOrderFPBWriter attribute)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter attribute)
,
[1]
(chemfp.fps_io.FPSWriter attribute)
Format (class in chemfp.base_toolkit)
,
[1]
format_ids_and_scores_as_bytes() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
FormatMetadata (class in chemfp.base_toolkit)
,
[1]
fp2 (in module chemfp.openbabel_toolkit)
fp3 (in module chemfp.openbabel_toolkit)
fp4 (in module chemfp.openbabel_toolkit)
fp_title (chemfp.csv_readers.CSVFingerprintReader attribute)
FPBError
FPSReader (class in chemfp.fps_io)
,
[1]
FPSSearchResult (class in chemfp.fps_search)
FPSSearchResults (class in chemfp.fps_search)
FPSWriter (class in chemfp.fps_io)
,
[1]
from_base64() (in module chemfp.encodings)
,
[1]
from_binary_lsb() (in module chemfp.encodings)
,
[1]
from_binary_msb() (in module chemfp.encodings)
,
[1]
from_cactvs() (in module chemfp.encodings)
,
[1]
from_candidates() (chemfp.diversity.HeapSweepPicker static method)
(chemfp.diversity.MaxMinPicker static method)
(chemfp.diversity.SphereExclusionPicker static method)
from_candidates_and_initial_pick() (chemfp.diversity.MaxMinPicker static method)
(chemfp.diversity.SphereExclusionPicker static method)
from_candidates_and_initial_picks() (chemfp.diversity.SphereExclusionPicker static method)
from_candidates_and_references() (chemfp.diversity.MaxMinPicker static method)
(chemfp.diversity.SphereExclusionPicker static method)
from_csr() (in module chemfp.search)
from_daylight() (in module chemfp.encodings)
,
[1]
from_destination() (chemfp.io.Location class method)
(chemfp.io.Location method)
from_dialect() (chemfp.csv_readers.CSVDialect class method)
from_dise_paper (chemfp.diversity.DISERanker attribute)
from_fingerprints (chemfp.diversity.DISERanker attribute)
from_hex() (in module chemfp.encodings)
,
[1]
from_hex_lsb() (in module chemfp.encodings)
,
[1]
from_hex_msb() (in module chemfp.encodings)
,
[1]
from_inchi() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_inchistring() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_kwargs() (chemfp.types.FingerprintFamily method)
,
[1]
from_mol() (chemfp.types.FingerprintType method)
from_molfile() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_mols() (chemfp.types.FingerprintType method)
from_npz_name() (chemfp.search.MatrixType method)
from_on_bit_positions() (in module chemfp.encodings)
,
[1]
from_sdf() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_smi() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_smiles() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_smiles_list (chemfp.diversity.DISERanker attribute)
from_smistring() (chemfp.cdk_types.CDKBaseFingerprintType method)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType method)
(chemfp.rdkit_types.RDKitBaseFingerprintType method)
from_source() (chemfp.io.Location class method)
(chemfp.io.Location method)
from_text_settings() (chemfp.types.FingerprintFamily method)
,
[1]
G
get_all_names() (chemfp.types.FingerprintTypeUnknownError method)
get_all_neighbors() (chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_bit_counts() (chemfp.arena.FingerprintArena method)
get_bit_counts_as_numpy() (chemfp.arena.FingerprintArena method)
get_by_id() (chemfp.arena.FingerprintArena method)
,
[1]
get_counts() (chemfp.diversity.PicksAndCounts method)
(chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_decoder() (in module chemfp.encodings)
get_decoder_names() (in module chemfp.encodings)
get_default_progressbar() (in module chemfp)
get_default_reader_args() (chemfp.base_toolkit.Format method)
,
[1]
get_default_writer_args() (chemfp.base_toolkit.Format method)
,
[1]
get_defaults() (chemfp.types.FingerprintFamily method)
,
[1]
get_description() (chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.conversion.ConversionInfo method)
(chemfp.highlevel.diversity.BaseHeapSweepSearch method)
(chemfp.highlevel.diversity.BaseSpherexSearch method)
(chemfp.highlevel.similarity.BaseSimsearch method)
get_dialect() (in module chemfp.csv_readers)
get_dialect_name() (chemfp.csv_readers.CSVDialect method)
(in module chemfp.csv_readers)
get_dise_ranker() (in module chemfp.diversity)
get_dise_ranks() (in module chemfp.diversity)
get_fingerprint() (chemfp.arena.FingerprintArena method)
,
[1]
get_fingerprint_by_id() (chemfp.arena.FingerprintArena method)
,
[1]
get_fingerprint_families() (in module chemfp)
,
[1]
get_fingerprint_family() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
(chemfp.types.FingerprintTypeParameterError method)
(in module chemfp)
,
[1]
get_fingerprint_family_names() (in module chemfp)
,
[1]
get_fingerprint_type() (chemfp.arena.FingerprintArena method)
(chemfp.FingerprintReader method)
,
[1]
(chemfp.fps_io.FPSReader method)
(in module chemfp)
,
[1]
get_fingerprint_type_from_text_settings() (in module chemfp)
,
[1]
get_format() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_formats() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_heapsweep_picker() (in module chemfp.diversity)
get_help() (chemfp.types.FingerprintTypeUnknownError method)
get_id() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_ids() (chemfp.diversity.BasePicks method)
(chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndCounts method)
(chemfp.diversity.PicksAndScores method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.HeapSweepSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.diversity.MaxMinSearch method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_ids_and_counts() (chemfp.diversity.PicksAndCounts method)
(chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_ids_and_neighbors() (chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_ids_and_scores() (chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_index_by_id() (chemfp.arena.FingerprintArena method)
,
[1]
get_indices() (chemfp.diversity.BasePicks method)
(chemfp.diversity.MaxMinCandidates method)
(chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.diversity.SphereExclusionCandidates method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.HeapSweepSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.diversity.MaxMinSearch method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_indices_and_counts() (chemfp.diversity.PicksAndCounts method)
(chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_indices_and_neighbors() (chemfp.diversity.PicksAndNeighbors method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
get_indices_and_scores() (chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_indices_as_numpy_array() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_input_format() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_input_format_from_source() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_input_formats() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_kwargs_from_text_settings() (chemfp.types.FingerprintFamily method)
,
[1]
get_license_date() (in module chemfp)
get_max_threads() (in module chemfp)
,
[1]
get_maxmin_picker() (in module chemfp.diversity)
get_metadata() (chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.types.FingerprintType method)
,
[1]
get_npz_name() (chemfp.search.MatrixType method)
get_npz_names() (chemfp.search.MatrixType method)
get_num_threads() (in module chemfp)
,
[1]
get_output_format() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_output_format_from_destination() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_output_formats() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_ranks() (chemfp.diversity.SphereExclusionCandidates method)
get_reader_args_from_text_settings() (chemfp.base_toolkit.Format method)
,
[1]
get_registry() (chemfp.io.Location method)
get_scores() (chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_scores_as_numpy_array() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
get_sdf_id() (in module chemfp.text_toolkit)
,
[1]
get_sdf_tag() (in module chemfp.text_toolkit)
,
[1]
get_sdf_tag_pairs() (in module chemfp.text_toolkit)
,
[1]
get_search_results() (in module chemfp.search)
get_sphere_exclusion_picker() (in module chemfp.diversity)
get_suggestions() (chemfp.types.FingerprintTypeUnknownError method)
get_tag() (chemfp._text_toolkit.TextRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
(in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_tag_as_bytes() (chemfp._text_toolkit.TextRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
get_tag_pairs() (chemfp._text_toolkit.TextRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
(in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
get_tag_pairs_as_bytes() (chemfp._text_toolkit.TextRecord method)
(chemfp.text_records.SDFRecord method)
(chemfp.text_records.TextRecord method)
get_tanimoto_precision() (in module chemfp.bitops)
get_times_description() (chemfp.highlevel.clustering.ButinaClusters method)
get_toolkit() (in module chemfp)
,
[1]
get_toolkit_names() (in module chemfp)
,
[1]
get_type() (chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
get_unqualified_reader_args() (chemfp.base_toolkit.Format method)
,
[1]
get_unqualified_writer_args() (chemfp.base_toolkit.Format method)
,
[1]
get_writer_args_from_text_settings() (chemfp.base_toolkit.Format method)
,
[1]
getvalue() (chemfp.base_toolkit.MoleculeStringWriter method)
,
[1]
graph_only (in module chemfp.cdk_toolkit)
H
has_fingerprint_family() (in module chemfp)
,
[1]
has_toolkit() (in module chemfp)
,
[1]
heapsweep() (in module chemfp)
HeapSweepPicker (class in chemfp.diversity)
HeapSweepScoreSearch (class in chemfp.highlevel.diversity)
HeapSweepSearch (class in chemfp.highlevel.diversity)
hex_contains() (in module chemfp.bitops)
,
[1]
hex_contains_bit() (in module chemfp.bitops)
,
[1]
hex_decode() (in module chemfp.bitops)
,
[1]
hex_difference() (in module chemfp.bitops)
hex_encode() (in module chemfp.bitops)
,
[1]
hex_encode_as_bytes() (in module chemfp.bitops)
,
[1]
hex_from_bitlist() (in module chemfp.bitops)
,
[1]
hex_intersect() (in module chemfp.bitops)
,
[1]
hex_intersect_popcount() (in module chemfp.bitops)
,
[1]
hex_isvalid() (in module chemfp.bitops)
,
[1]
hex_popcount() (in module chemfp.bitops)
,
[1]
hex_tanimoto() (in module chemfp.bitops)
,
[1]
hex_to_bitlist() (in module chemfp.bitops)
,
[1]
hex_tversky() (in module chemfp.bitops)
,
[1]
hex_union() (in module chemfp.bitops)
,
[1]
hex_xor() (in module chemfp.bitops)
hybridization (in module chemfp.cdk_toolkit)
I
id (chemfp.text_records.BaseSmiRecord attribute)
(chemfp.text_records.SDFRecord attribute)
id_bytes (chemfp._text_toolkit.TextRecord attribute)
(chemfp.text_records.SDFRecord attribute)
(chemfp.text_records.TextRecord attribute)
id_title (chemfp.csv_readers.CSVFingerprintReader attribute)
(chemfp.csv_readers.CSVIdAndMoleculeReader attribute)
IdAndMoleculeReader (class in chemfp.base_toolkit)
,
[1]
IdAndRecordReader (class in chemfp.base_toolkit)
,
[1]
ids (chemfp.arena.FingerprintArena attribute)
,
[1]
import_decoder() (in module chemfp.encodings)
include_help() (chemfp.types.FingerprintTypeUnknownError method)
InputOrderFPBWriter (class in chemfp.fpb_io)
,
[1]
is_available (chemfp.base_toolkit.Format attribute)
,
[1]
(chemfp.openbabel_types.OpenBabelECFP0FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP10FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP8FingerprintType_v1 attribute)
is_input_format (chemfp.base_toolkit.Format attribute)
,
[1]
is_licensed() (in module chemfp)
(in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
is_output_format (chemfp.base_toolkit.Format attribute)
,
[1]
is_valid_aromaticity() (in module chemfp.openeye_toolkit)
iter_arenas() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.FingerprintReader method)
,
[1]
(chemfp.fps_io.FPSReader method)
iter_blocks() (chemfp.fps_io.FPSReader method)
iter_ids() (chemfp.diversity.BaseMaxMinPicker method)
(chemfp.diversity.SphereExclusionPicker method)
(chemfp.fps_search.FPSSearchResults method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
(chemfp.search.SearchResults method)
,
[1]
iter_ids_and_counts() (chemfp.diversity.SphereExclusionPicker method)
iter_ids_and_neighbors() (chemfp.diversity.SphereExclusionPicker method)
iter_ids_and_scores() (chemfp.diversity.BaseMaxMinPicker method)
(chemfp.fps_search.FPSSearchResults method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
iter_indices() (chemfp.diversity.BaseMaxMinPicker method)
(chemfp.diversity.SphereExclusionPicker method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
iter_indices_and_counts() (chemfp.diversity.SphereExclusionPicker method)
iter_indices_and_neighbors() (chemfp.diversity.SphereExclusionPicker method)
iter_indices_and_scores() (chemfp.diversity.BaseMaxMinPicker method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
iter_rows() (chemfp.fps_io.FPSReader method)
iter_scores() (chemfp.fps_search.FPSSearchResults method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
K
klekota_roth (in module chemfp.cdk_toolkit)
knearest_tanimoto_search() (in module chemfp)
,
[1]
knearest_tanimoto_search_arena() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
knearest_tanimoto_search_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
knearest_tanimoto_search_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
knearest_tversky_search() (in module chemfp)
,
[1]
knearest_tversky_search_arena() (in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
knearest_tversky_search_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
knearest_tversky_search_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
L
lineno (chemfp.io.Location attribute)
load() (chemfp.FingerprintReader method)
load_fingerprints() (in module chemfp)
,
[1]
load_fingerprints_from_string() (in module chemfp)
load_output() (chemfp.highlevel.conversion.ConversionInfo method)
location (chemfp.base_toolkit.BaseMoleculeReader attribute)
,
[1]
(chemfp.ParseError attribute)
,
[1]
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
,
[1]
(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)
,
[1]
Location (class in chemfp.io)
,
[1]
M
maccs (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
maccs166 (in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
make_fingerprinter() (chemfp.openbabel_types.OpenBabelBaseMACCSFingerprintType method)
(chemfp.openbabel_types.OpenBabelFP2FingerprintType_v1 method)
(chemfp.openbabel_types.OpenBabelFP3FingerprintType_v1 method)
(chemfp.openbabel_types.OpenBabelFP4FingerprintType_v1 method)
(chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
(chemfp.types.ThreadsafeFingerprinterMixin method)
make_id_and_molecule_fingerprint_parser() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
make_id_and_molecule_parser() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
matrix_type (chemfp.highlevel.similarity.BaseSimsearch attribute)
(chemfp.search.SearchResults attribute)
matrix_type_name (chemfp.highlevel.similarity.BaseSimsearch attribute)
(chemfp.search.SearchResults attribute)
MatrixType (class in chemfp.search)
max() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
maxmin() (in module chemfp)
MaxMinCandidates (class in chemfp.diversity)
MaxMinPicker (class in chemfp.diversity)
MaxMinScoreSearch (class in chemfp.highlevel.diversity)
MaxMinSearch (class in chemfp.highlevel.diversity)
mdl_screen (in module chemfp.openeye_toolkit)
metadata (chemfp.arena.FingerprintArena attribute)
,
[1]
(chemfp.base_toolkit.BaseMoleculeReader attribute)
,
[1]
(chemfp.base_toolkit.BaseMoleculeWriter attribute)
,
[1]
(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)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter attribute)
,
[1]
(chemfp.fps_io.FPSReader attribute)
,
[1]
Metadata (class in chemfp)
,
[1]
min() (chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
module (chemfp.cdk_types.CDKBaseFingerprintType attribute)
(chemfp.openbabel_types.OpenBabelBaseFingerprintType attribute)
(chemfp.rdkit_types.RDKitBaseFingerprintType attribute)
mol (chemfp.io.Location attribute)
,
[1]
mol_title (chemfp.csv_readers.CSVIdAndMoleculeReader attribute)
molecule_screen (in module chemfp.openeye_toolkit)
MoleculeReader (class in chemfp.base_toolkit)
,
[1]
MoleculeStringWriter (class in chemfp.base_toolkit)
,
[1]
MoleculeWriter (class in chemfp.base_toolkit)
,
[1]
morgan (in module chemfp.rdkit_toolkit)
morgan1 (in module chemfp.rdkit_toolkit)
morgan2 (in module chemfp.rdkit_toolkit)
morgan3 (in module chemfp.rdkit_toolkit)
morgan4 (in module chemfp.rdkit_toolkit)
move_pick_index_to_first() (chemfp.diversity.PicksAndScores method)
msg (chemfp.ParseError attribute)
,
[1]
MultiQuerySimsearch (class in chemfp.highlevel.similarity)
N
name (chemfp.base_toolkit.Format attribute)
(chemfp.cdk_types.CDKAtomPairs2DFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKDaylightFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKECFP0FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKECFP2FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKECFP4FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKECFP6FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKEStateFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKExtendedFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKFCFP0FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKFCFP2FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKFCFP4FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKFCFP6FingerprintType_v20 attribute)
(chemfp.cdk_types.CDKGraphOnlyFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKHybridizationFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKKlekotaRothFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKMACCSFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKPubchemFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKShortestPathFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKShortestPathFingerprintType_v27 attribute)
(chemfp.cdk_types.CDKSubstructureFingerprintType_v20 attribute)
(chemfp.openbabel_types.OpenBabelECFP0FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP10FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP2FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP4FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP6FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelECFP8FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelFP2FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelFP3FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelFP4FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelMACCSFingerprintType_v2 attribute)
(chemfp.openeye_types.OpenEyeCircularFingerprintType_v2 attribute)
(chemfp.openeye_types.OpenEyeMACCSFingerprintType_v2 attribute)
(chemfp.openeye_types.OpenEyeMACCSFingerprintType_v3 attribute)
(chemfp.openeye_types.OpenEyeMDLScreenFingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyeMoleculeScreenFingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyePathFingerprintType_v2 attribute)
(chemfp.openeye_types.OpenEyeSMARTSScreenFingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyeTreeFingerprintType_v2 attribute)
(chemfp.rdkit_types.RDKitAtomPairFingerprint_v1 attribute)
(chemfp.rdkit_types.RDKitAtomPairFingerprint_v2 attribute)
(chemfp.rdkit_types.RDKitAvalonFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitFingerprintType_v2 attribute)
(chemfp.rdkit_types.RDKitMACCSFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitMACCSFingerprintType_v2 attribute)
(chemfp.rdkit_types.RDKitMorganFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitPatternFingerprint_v1 attribute)
(chemfp.rdkit_types.RDKitPatternFingerprint_v2 attribute)
(chemfp.rdkit_types.RDKitPatternFingerprint_v3 attribute)
(chemfp.rdkit_types.RDKitPatternFingerprint_v4 attribute)
(chemfp.rdkit_types.RDKitSECFPFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitTorsionFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitTorsionFingerprintType_v2 attribute)
(chemfp.rdkit_types.RDKitTorsionFingerprintType_v3 attribute)
(chemfp.types.BaseFingerprintType attribute)
(chemfp.types.FingerprintFamily attribute)
,
[1]
(chemfp.types.FingerprintType attribute)
(in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
Neighbors (class in chemfp.diversity)
next() (chemfp.fps_io.FPSReader method)
NO_DIAGONAL (chemfp.search.MatrixType attribute)
NoFingerprintParametersMixin (class in chemfp.types)
num_bits (chemfp.arena.FingerprintArena attribute)
(chemfp.Metadata attribute)
,
[1]
(chemfp.cdk_types.CDKAtomPairs2DFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKEStateFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKKlekotaRothFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKMACCSFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKPubchemFingerprintType_v20 attribute)
(chemfp.cdk_types.CDKSubstructureFingerprintType_v20 attribute)
(chemfp.openbabel_types.OpenBabelBaseMACCSFingerprintType attribute)
(chemfp.openbabel_types.OpenBabelFP2FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelFP3FingerprintType_v1 attribute)
(chemfp.openbabel_types.OpenBabelFP4FingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyeMACCSFingerprintType_v2 attribute)
(chemfp.openeye_types.OpenEyeMACCSFingerprintType_v3 attribute)
(chemfp.openeye_types.OpenEyeMDLScreenFingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyeMoleculeScreenFingerprintType_v1 attribute)
(chemfp.openeye_types.OpenEyeSMARTSScreenFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitMACCSFingerprintType_v1 attribute)
(chemfp.rdkit_types.RDKitMACCSFingerprintType_v2 attribute)
(chemfp.types.FingerprintType attribute)
num_bytes (chemfp.arena.FingerprintArena attribute)
(chemfp.Metadata attribute)
,
[1]
num_input_records (chemfp.highlevel.conversion.ConversionInfo attribute)
num_output_records (chemfp.highlevel.conversion.ConversionInfo attribute)
NxM (chemfp.search.MatrixType attribute)
NxN (chemfp.search.MatrixType attribute)
NxNSimsearch (class in chemfp.highlevel.similarity)
O
ob2fps() (in module chemfp)
oe2fps() (in module chemfp)
offsets (chemfp.io.Location attribute)
,
[1]
open() (in module chemfp)
,
[1]
open_fasta_writer() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_fasta_writer_to_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_fingerprint_writer() (in module chemfp)
,
[1]
open_from_string() (in module chemfp)
open_inchi_writer() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_inchi_writer_to_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_inchikey_writer() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_inchikey_writer_to_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_molecule_writer() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
open_molecule_writer_to_bytes() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
open_molecule_writer_to_string() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
open_oez_writer() (in module chemfp.openeye_toolkit)
open_oez_writer_to_string() (in module chemfp.openeye_toolkit)
open_output() (chemfp.highlevel.conversion.ConversionInfo method)
open_pdb_writer() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_pdb_writer_to_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_sdf3k_writer() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_sdf3k_writer_to_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
open_sdf_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)
open_sdf_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)
open_smi_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)
open_smi_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)
openbabel (in module chemfp)
OpenBabelBaseFingerprintType (class in chemfp.openbabel_types)
OpenBabelBaseMACCSFingerprintType (class in chemfp.openbabel_types)
OpenBabelECFP0FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFP10FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFP2FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFP4FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFP6FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFP8FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelECFPBaseFingerprintType (class in chemfp.openbabel_types)
OpenBabelFP2FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelFP3FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelFP4FingerprintType_v1 (class in chemfp.openbabel_types)
,
[1]
OpenBabelMACCSFingerprintType_v1 (class in chemfp.openbabel_types)
OpenBabelMACCSFingerprintType_v2 (class in chemfp.openbabel_types)
,
[1]
openeye (in module chemfp)
OpenEyeCircularFingerprintType_v2 (class in chemfp.openeye_types)
,
[1]
OpenEyeMACCSFingerprintType_v2 (class in chemfp.openeye_types)
,
[1]
OpenEyeMACCSFingerprintType_v3 (class in chemfp.openeye_types)
,
[1]
OpenEyeMDLScreenFingerprintType_v1 (class in chemfp.openeye_types)
,
[1]
OpenEyeMoleculeScreenFingerprintType_v1 (class in chemfp.openeye_types)
,
[1]
OpenEyePathFingerprintType_v2 (class in chemfp.openeye_types)
,
[1]
OpenEyeSMARTSScreenFingerprintType_v1 (class in chemfp.openeye_types)
,
[1]
OpenEyeTreeFingerprintType_v2 (class in chemfp.openeye_types)
,
[1]
OrderedFPBWriter (class in chemfp.fpb_io)
,
[1]
output_recno (chemfp.io.Location attribute)
,
[1]
P
parse_fasta() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_helm() (in module chemfp.rdkit_toolkit)
parse_id_and_molecule() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
parse_id_and_molecule_fingerprint() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
parse_inchi() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_inchistring() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_molecule() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
parse_molecule_fingerprint() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
parse_molfile() (in module chemfp.cdk_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_oez() (in module chemfp.openeye_toolkit)
parse_pdb() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_rdbinmol() (in module chemfp.rdkit_toolkit)
parse_sdf() (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)
parse_sequence() (in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
parse_smi() (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)
parse_smiles() (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)
parse_smistring() (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)
ParseError
(class in chemfp)
partial_count_tanimoto_hits_symmetric() (in module chemfp.search)
,
[1]
partial_count_tversky_hits_symmetric() (in module chemfp.search)
,
[1]
partial_threshold_tanimoto_search_symmetric() (in module chemfp.search)
,
[1]
partial_threshold_tversky_search_symmetric() (in module chemfp.search)
,
[1]
path (in module chemfp.openeye_toolkit)
pattern (in module chemfp.rdkit_toolkit)
Pick (class in chemfp.diversity)
pick_n() (chemfp.diversity.HeapSweepPicker method)
(chemfp.diversity.MaxMinPicker method)
(chemfp.diversity.SphereExclusionPicker method)
pick_n_with_counts() (chemfp.diversity.SphereExclusionPicker method)
pick_n_with_neighbors() (chemfp.diversity.SphereExclusionPicker method)
pick_n_with_scores() (chemfp.diversity.HeapSweepPicker method)
(chemfp.diversity.MaxMinPicker method)
PickAndScore (class in chemfp.diversity)
picks (chemfp.diversity.BaseMaxMinPicker attribute)
(chemfp.diversity.SphereExclusionPicker attribute)
(chemfp.highlevel.diversity.BaseHeapSweepSearch attribute)
Picks (class in chemfp.diversity)
PicksAndCounts (class in chemfp.diversity)
PicksAndNeighbors (class in chemfp.diversity)
PicksAndScores (class in chemfp.diversity)
popcount (chemfp.diversity.Candidate attribute)
(chemfp.diversity.Pick attribute)
popcount_indices (chemfp.arena.FingerprintArena attribute)
position (chemfp.io.Location attribute)
position_units (chemfp.io.Location attribute)
prefix (chemfp.base_toolkit.Format attribute)
,
[1]
print_report() (in module chemfp.bitops)
progress_bar() (chemfp.io.Location method)
ProgressBar (class in chemfp.io)
pubchem (in module chemfp.cdk_toolkit)
Python Enhancement Proposals
PEP 343
Q
query_id (chemfp.fps_search.FPSSearchResult attribute)
(chemfp.highlevel.similarity.SingleQuerySimsearch attribute)
(chemfp.search.SearchResult attribute)
query_ids (chemfp.fps_search.FPSSearchResults attribute)
(chemfp.highlevel.similarity.MultiQuerySimsearch attribute)
(chemfp.highlevel.similarity.NxNSimsearch attribute)
(chemfp.search.SearchResults attribute)
R
random_choice() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.arena.FingerprintList method)
,
[1]
rank_arena (chemfp.diversity.DISERanker attribute)
rdk (in module chemfp.rdkit_toolkit)
rdkit (in module chemfp)
rdkit2fps() (in module chemfp)
RDKitAtomPairFingerprint_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitAtomPairFingerprint_v2 (class in chemfp.rdkit_types)
,
[1]
RDKitAvalonFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitBaseAtomPairFingerprintType (class in chemfp.rdkit_types)
RDKitBaseFingerprintType (class in chemfp.rdkit_types)
RDKitBasePatternFingerprint (class in chemfp.rdkit_types)
RDKitBaseTorsionFingerprintType (class in chemfp.rdkit_types)
RDKitFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitFingerprintType_v2 (class in chemfp.rdkit_types)
,
[1]
RDKitMACCSFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitMACCSFingerprintType_v2 (class in chemfp.rdkit_types)
,
[1]
RDKitMorganFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitPatternFingerprint_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitPatternFingerprint_v2 (class in chemfp.rdkit_types)
,
[1]
RDKitPatternFingerprint_v3 (class in chemfp.rdkit_types)
,
[1]
RDKitPatternFingerprint_v4 (class in chemfp.rdkit_types)
RDKitSECFPFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitTorsionFingerprintType_v1 (class in chemfp.rdkit_types)
,
[1]
RDKitTorsionFingerprintType_v2 (class in chemfp.rdkit_types)
,
[1]
RDKitTorsionFingerprintType_v3 (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_csv_ids_and_fingerprints() (in module chemfp.csv_readers)
read_csv_ids_and_molecules() (in module chemfp.cdk_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
(in module chemfp.text_toolkit)
read_csv_ids_and_molecules_with_parser() (in module chemfp.csv_readers)
read_csv_rows() (in module chemfp.csv_readers)
read_fasta_ids_and_molecules() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_fasta_ids_and_molecules_from_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_fasta_molecules() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_fasta_molecules_from_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_ids_and_molecules() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
read_ids_and_molecules_from_string() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
read_inchi_ids_and_molecules() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_inchi_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)
read_inchi_molecules() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_inchi_molecules_from_string() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_molecule_fingerprints() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
(in module chemfp)
,
[1]
read_molecule_fingerprints_from_string() (chemfp.types.BaseFingerprintType method)
(chemfp.types.FingerprintType method)
,
[1]
(in module chemfp)
,
[1]
read_molecules() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
read_molecules_from_string() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
read_oez_ids_and_molecules() (in module chemfp.openeye_toolkit)
read_oez_ids_and_molecules_from_string() (in module chemfp.openeye_toolkit)
read_oez_molecules() (in module chemfp.openeye_toolkit)
read_oez_molecules_from_string() (in module chemfp.openeye_toolkit)
read_pdb_ids_and_molecules() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_pdb_ids_and_molecules_from_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_pdb_molecules() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_pdb_molecules_from_string() (in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
read_sdf_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)
read_sdf_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)
read_sdf_ids_and_records() (in module chemfp.text_toolkit)
,
[1]
read_sdf_ids_and_records_from_string() (in module chemfp.text_toolkit)
,
[1]
read_sdf_ids_and_values() (in module chemfp.text_toolkit)
,
[1]
read_sdf_ids_and_values_from_string() (in module chemfp.text_toolkit)
,
[1]
read_sdf_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)
read_sdf_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)
read_sdf_records() (in module chemfp.text_toolkit)
,
[1]
read_sdf_records_from_string() (in module chemfp.text_toolkit)
,
[1]
read_smi_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)
read_smi_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)
read_smi_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)
read_smi_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)
recno (chemfp.io.Location attribute)
,
[1]
record (chemfp._text_toolkit.TextRecord attribute)
(chemfp.io.Location attribute)
,
[1]
(chemfp.text_records.BaseSmiRecord attribute)
(chemfp.text_records.SDFRecord attribute)
(chemfp.text_records.TextRecord attribute)
record_format (chemfp._text_toolkit.TextRecord attribute)
(chemfp.base_toolkit.FormatMetadata attribute)
,
[1]
(chemfp.io.Location attribute)
,
[1]
(chemfp.text_records.CanRecord attribute)
(chemfp.text_records.CanStringRecord attribute)
(chemfp.text_records.SDFRecord attribute)
(chemfp.text_records.SmiRecord attribute)
(chemfp.text_records.SmiStringRecord attribute)
(chemfp.text_records.TextRecord attribute)
(chemfp.text_records.UsmRecord attribute)
(chemfp.text_records.UsmStringRecord attribute)
RecordReader (class in chemfp.base_toolkit)
,
[1]
reference_popcount (chemfp.diversity.Candidate attribute)
register() (chemfp.io.Location method)
reorder() (chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
,
[1]
reorder_all() (chemfp.fps_search.FPSSearchResults method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
row (chemfp.io.Location attribute)
S
sample() (chemfp.arena.FingerprintArena method)
,
[1]
save() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.FingerprintReader method)
,
[1]
(chemfp.fps_io.FPSReader method)
(chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.io.Location method)
(chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
score (chemfp.diversity.PickAndScore attribute)
scores (chemfp.fps_search.FPSSearchResult attribute)
sdf2fps() (in module chemfp)
SDFRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
SearchResult (class in chemfp.search)
,
[1]
SearchResults (class in chemfp.search)
,
[1]
secfp (in module chemfp.rdkit_toolkit)
set_default_progressbar() (in module chemfp)
set_id() (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
,
[1]
(in module chemfp.toolkit)
set_num_threads() (in module chemfp)
,
[1]
set_sdf_id() (in module chemfp.text_toolkit)
,
[1]
set_toolkit_name() (chemfp.types.FingerprintTypeUnknownError method)
severity (chemfp.ChemFPProblem attribute)
,
[1]
shape (chemfp.highlevel.similarity.MultiQuerySimsearch attribute)
(chemfp.highlevel.similarity.NxNSimsearch attribute)
(chemfp.search.SearchResults attribute)
,
[1]
shortest_path (in module chemfp.cdk_toolkit)
simsearch() (in module chemfp)
SingleQuerySimsearch (class in chemfp.highlevel.similarity)
smarts_screen (in module chemfp.openeye_toolkit)
smiles (chemfp._text_toolkit.TextRecord attribute)
(chemfp.text_records.BaseSmiRecord attribute)
(chemfp.text_records.TextRecord attribute)
SmiRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
SmiStringRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
software (chemfp.cdk_types.CDKBaseFingerprintType attribute)
(chemfp.Metadata attribute)
,
[1]
(chemfp.openbabel_types.OpenBabelBaseFingerprintType attribute)
(chemfp.rdkit_types.RDKitBaseFingerprintType attribute)
(chemfp.types.BaseFingerprintType attribute)
(chemfp.types.FingerprintType attribute)
,
[1]
SOFTWARE (in module chemfp)
software (in module chemfp.cdk_toolkit)
,
[1]
(in module chemfp.openbabel_toolkit)
,
[1]
(in module chemfp.openeye_toolkit)
,
[1]
(in module chemfp.rdkit_toolkit)
,
[1]
(in module chemfp.text_toolkit)
(in module chemfp.toolkit)
sources (chemfp.Metadata attribute)
,
[1]
SphereExclusionCandidates (class in chemfp.diversity)
SphereExclusionPicker (class in chemfp.diversity)
spherex() (in module chemfp)
SpherexCountSearch (class in chemfp.highlevel.diversity)
SpherexNeighborSearch (class in chemfp.highlevel.diversity)
SpherexSearch (class in chemfp.highlevel.diversity)
start_in_file (chemfp.csv_readers.CSVUnicodeDecodeError attribute)
start_padding (chemfp.arena.FingerprintArena attribute)
start_position (chemfp.io.Location attribute)
storage_size (chemfp.arena.FingerprintArena attribute)
STRICTLY_UPPER_TRIANGULAR (chemfp.search.MatrixType 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)
substructure (in module chemfp.cdk_toolkit)
supports_io (chemfp.base_toolkit.Format attribute)
,
[1]
T
target_ids (chemfp.highlevel.similarity.BaseSimsearch attribute)
(chemfp.search.SearchResult attribute)
(chemfp.search.SearchResults attribute)
target_start (chemfp.search.SearchResult attribute)
TextRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
ThreadsafeFingerprinterMixin (class in chemfp.types)
threshold (chemfp.diversity.SphereExclusionPicker attribute)
threshold_tanimoto_search() (in module chemfp)
,
[1]
threshold_tanimoto_search_arena() (chemfp.arena.FingerprintArena method)
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
threshold_tanimoto_search_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
threshold_tanimoto_search_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
threshold_tversky_search() (in module chemfp)
,
[1]
threshold_tversky_search_arena() (in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
threshold_tversky_search_fp() (chemfp.arena.FingerprintArena method)
,
[1]
(chemfp.fps_io.FPSReader method)
,
[1]
(in module chemfp.fps_search)
(in module chemfp.search)
,
[1]
threshold_tversky_search_symmetric() (in module chemfp)
,
[1]
(in module chemfp.search)
,
[1]
to_csr() (chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.search.SearchResults method)
,
[1]
to_numpy_array() (chemfp.arena.FingerprintArena method)
,
[1]
to_numpy_bitarray() (chemfp.arena.FingerprintArena method)
,
[1]
to_pandas() (chemfp.diversity.BasePicks method)
(chemfp.diversity.Neighbors method)
(chemfp.diversity.PicksAndCounts method)
(chemfp.diversity.PicksAndNeighbors method)
(chemfp.diversity.PicksAndScores method)
(chemfp.fps_search.FPSSearchResult method)
(chemfp.fps_search.FPSSearchResults method)
(chemfp.highlevel.clustering.ButinaClusters method)
(chemfp.highlevel.diversity.HeapSweepScoreSearch method)
(chemfp.highlevel.diversity.HeapSweepSearch method)
(chemfp.highlevel.diversity.MaxMinScoreSearch method)
(chemfp.highlevel.diversity.MaxMinSearch method)
(chemfp.highlevel.diversity.SpherexCountSearch method)
(chemfp.highlevel.diversity.SpherexNeighborSearch method)
(chemfp.highlevel.diversity.SpherexSearch method)
(chemfp.highlevel.similarity.MultiQuerySimsearch method)
(chemfp.highlevel.similarity.NxNSimsearch method)
(chemfp.highlevel.similarity.SingleQuerySimsearch method)
(chemfp.search.SearchResult method)
(chemfp.search.SearchResults method)
toolkit (chemfp.types.BaseFingerprintType attribute)
(chemfp.types.FingerprintFamily attribute)
,
[1]
(chemfp.types.FingerprintType attribute)
,
[1]
toolkit_name (chemfp.base_toolkit.Format attribute)
torsion (in module chemfp.rdkit_toolkit)
train_test_split() (chemfp.arena.FingerprintArena method)
,
[1]
translate_record() (in module chemfp.cdk_toolkit)
(in module chemfp.openbabel_toolkit)
(in module chemfp.openeye_toolkit)
(in module chemfp.rdkit_toolkit)
tree (in module chemfp.openeye_toolkit)
type (chemfp.Metadata attribute)
,
[1]
U
update() (chemfp.io.ProgressBar method)
UPPER_TRIANGULAR (chemfp.search.MatrixType attribute)
use_environment_variables() (in module chemfp.bitops)
UsmRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
UsmStringRecord (class in chemfp._text_toolkit)
(class in chemfp.text_records)
V
VariableSizeFingerprint (class in chemfp.rdkit_types)
version (chemfp.types.BaseFingerprintType attribute)
(chemfp.types.FingerprintFamily attribute)
,
[1]
(chemfp.types.FingerprintType attribute)
W
where() (chemfp.io.Location method)
,
[1]
write_fingerprint() (chemfp.FingerprintWriter method)
,
[1]
(chemfp.fpb_io.InputOrderFPBWriter method)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter method)
,
[1]
(chemfp.fps_io.FPSWriter method)
,
[1]
write_fingerprints() (chemfp.FingerprintWriter method)
,
[1]
(chemfp.fpb_io.InputOrderFPBWriter method)
,
[1]
(chemfp.fpb_io.OrderedFPBWriter method)
,
[1]
(chemfp.fps_io.FPSWriter method)
,
[1]
write_id_and_molecule() (chemfp.base_toolkit.BaseMoleculeWriter method)
,
[1]
write_ids_and_molecules() (chemfp.base_toolkit.BaseMoleculeWriter method)
,
[1]
write_molecule() (chemfp.base_toolkit.BaseMoleculeWriter method)
,
[1]
write_molecules() (chemfp.base_toolkit.BaseMoleculeWriter method)
,
[1]
Read the Docs
v: chemfp-4.1
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