Index

_

__call__() (chemfp.io.ProgressBar method) __enter__() (chemfp.io.ProgressBar method) __exit__() (chemfp.io.ProgressBar method) __getitem__() (chemfp.fps_search.FPSSearchResult method) (chemfp.fps_search.FPSSearchResults method) __init__() (chemfp.io.Location method)

__iter__() (chemfp.fps_search.FPSSearchResult method) (chemfp.fps_search.FPSSearchResults method) __len__() (chemfp.fps_search.FPSSearchResult method) (chemfp.fps_search.FPSSearchResults 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) add_tag() (chemfp.text_records.SDFRecord method) (chemfp.text_records.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) alignment (chemfp.arena.FingerprintArena attribute) all_clusters (chemfp.highlevel.clustering.ButinaClusters property) alpha (chemfp.search.SearchResults attribute) arena (chemfp.arena.FingerprintArena attribute) (chemfp.highlevel.clustering.ButinaClusters attribute) argname (chemfp.csv_readers.CSVColumnError attribute) args (chemfp.base_toolkit.FormatMetadata attribute) aromaticity (chemfp.Metadata attribute) as_buffer() (chemfp.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) as_ctypes() (chemfp.clustering.ButinaAssignments method) (chemfp.clustering.ButinaCluster method) (chemfp.clustering.ButinaRankings method) (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)

as_numpy() (chemfp.clustering.ButinaAssignments method) (chemfp.clustering.ButinaCluster method) (chemfp.clustering.ButinaRankings method) (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) assignment_type (chemfp.clustering.ButinaAssignment attribute) assignments (chemfp.clustering.ButinaClusterer attribute) (chemfp.highlevel.clustering.ButinaClusters property) atom_pair (in module chemfp.rdkit_toolkit) atom_pair_v2 (in module chemfp.rdkit_toolkit) atom_pair_v3 (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 property) (chemfp.types.FingerprintUnavailableError attribute) BaseFingerprintType (class in chemfp.types) BaseHeapSweepSearch (class in chemfp.highlevel.diversity) BaseMaxMinPicker (class in chemfp.diversity) BaseMoleculeReader (class in chemfp.base_toolkit) BaseMoleculeWriter (class in chemfp.base_toolkit) BasePicks (class in chemfp.diversity) BaseSimsearch (class in chemfp.highlevel.similarity) BaseSmiRecord (class in chemfp.text_records) BaseSpherexSearch (class in chemfp.highlevel.diversity) beta (chemfp.search.SearchResults attribute) butina() (in module chemfp) butina_threshold (chemfp.highlevel.clustering.ButinaClusters attribute) ButinaAssignment (class in chemfp.clustering) ButinaAssignments (class in chemfp.clustering) ButinaAssignmentType (class in chemfp.clustering) ButinaCluster (class in chemfp.clustering) ButinaClusterer (class in chemfp.clustering)

ButinaClusters (class in chemfp.highlevel.clustering) ButinaRanking (class in chemfp.clustering) ButinaRankings (class in chemfp.clustering) byte_contains() (in module chemfp.bitops) byte_contains_bit() (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) byte_union_popcount() (in module chemfp.bitops) byte_xor() (in module chemfp.bitops) byte_xor_popcount() (in module chemfp.bitops) bytes_read (chemfp.csv_readers.CSVUnicodeDecodeError attribute) (chemfp.io.Location property)

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) (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) CanRecord (class in chemfp.text_records) CanStringRecord (class in chemfp.text_records) category (chemfp.ChemFPProblem attribute) cdk (in module chemfp) cdk2fps() (in module chemfp) CDKAtomPairs2DFingerprintType_v20 (class in chemfp.cdk_types) CDKBaseFingerprintType (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) CDKPubchemFingerprintType_v29 (class in chemfp.cdk_types) CDKShortestPathFingerprintType_v20 (class in chemfp.cdk_types) CDKShortestPathFingerprintType_v27 (class in chemfp.cdk_types) CDKSubstructureFingerprintType_v20 (class in chemfp.cdk_types) CENTER (chemfp.clustering.ButinaAssignmentType attribute) check_fingerprint_problems() (in module chemfp) check_metadata_problems() (in module chemfp) chemfp module chemfp.arena module chemfp.base_toolkit module chemfp.bitops module chemfp.cdk_toolkit module chemfp.cdk_types module chemfp.clustering module chemfp.csv_readers module chemfp.diversity module chemfp.encodings module chemfp.fpb_io module chemfp.fps_io module chemfp.fps_search module chemfp.highlevel.clustering module chemfp.highlevel.conversion module chemfp.highlevel.diversity module chemfp.highlevel.simarray module chemfp.highlevel.similarity module chemfp.io module chemfp.jcmapper_types module chemfp.openbabel_toolkit module chemfp.openbabel_types module chemfp.openeye_toolkit module chemfp.openeye_types module chemfp.rdkit_toolkit module chemfp.rdkit_types module chemfp.search module chemfp.simarray_io module chemfp.text_records module chemfp.text_toolkit module chemfp.toolkit module chemfp.types module ChemFPError ChemFPProblem circular (in module chemfp.openeye_toolkit) close() (chemfp.arena.FingerprintArena method) (chemfp.base_toolkit.BaseMoleculeReader method) (chemfp.base_toolkit.BaseMoleculeWriter method) (chemfp.base_toolkit.MoleculeStringWriter method) (chemfp.csv_readers.CSVIdAndMoleculeReader method) (chemfp.csv_readers.CSVRowReader method) (chemfp.FingerprintIterator method) (chemfp.FingerprintWriter method) (chemfp.fpb_io.FPBFingerprintArena method) (chemfp.fpb_io.InputOrderFPBWriter method) (chemfp.fpb_io.OrderedFPBWriter method) (chemfp.fps_io.FPSReader method) (chemfp.fps_io.FPSWriter method) (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.highlevel.simarray.SimarrayResult method) (chemfp.highlevel.similarity.BaseSimsearch method) (chemfp.io.ProgressBar method) (chemfp.simarray_io.SimarrayFileContent method) closed (chemfp.base_toolkit.BaseMoleculeReader attribute) (chemfp.base_toolkit.BaseMoleculeWriter attribute) (chemfp.csv_readers.CSVRowReader attribute) (chemfp.FingerprintWriter attribute) (chemfp.fpb_io.InputOrderFPBWriter attribute) (chemfp.fpb_io.OrderedFPBWriter attribute) (chemfp.fps_io.FPSReader attribute) (chemfp.fps_io.FPSWriter attribute) (chemfp.highlevel.simarray.SimarrayResult attribute) cluster_idx (chemfp.clustering.ButinaAssignment attribute) (chemfp.clustering.ButinaCluster attribute) clusterer (chemfp.highlevel.clustering.ButinaClusters attribute) clusters (chemfp.clustering.ButinaClusterer attribute) (chemfp.highlevel.clustering.ButinaClusters property) column (chemfp.csv_readers.CSVColumnError attribute) compression (chemfp.base_toolkit.Format attribute) compute_fingerprint() (chemfp.types.BaseFingerprintType method) (chemfp.types.FingerprintType method)

compute_fingerprints() (chemfp.types.BaseFingerprintType method) (chemfp.types.FingerprintType method) contains_arena() (in module chemfp.search) contains_fp() (in module chemfp.search) ConversionInfo (class in chemfp.highlevel.conversion) convert2fps() (in module chemfp) copy() (chemfp.arena.FingerprintArena method) (chemfp.Metadata method) (chemfp.text_records.CanRecord method) (chemfp.text_records.CanStringRecord method) (chemfp.text_records.SDFRecord method) (chemfp.text_records.SmiRecord method) (chemfp.text_records.SmiStringRecord method) (chemfp.text_records.TextRecord method) (chemfp.text_records.UsmRecord method) (chemfp.text_records.UsmStringRecord method) (chemfp.types.FingerprintUnavailableError 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.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) count_all() (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method) count_tanimoto_hits() (in module chemfp) count_tanimoto_hits_arena() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (in module chemfp.search) count_tanimoto_hits_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (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.fps_search) (in module chemfp.search) count_tversky_hits_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (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_fasta() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.toolkit) create_inchikey() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) create_inchikeystring() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) create_inchistring() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) create_molfile() (in module chemfp.cdk_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (in module chemfp.toolkit) create_sdf3k() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) create_sequence() (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (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) 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) cumulative_score_all() (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method) current_position (chemfp.io.ProgressBar attribute)

D

d (chemfp.diversity.Candidate attribute) date (chemfp.Metadata attribute) daylight (in module chemfp.cdk_toolkit) decode_err (chemfp.csv_readers.CSVColumnDecodeError attribute) decoder_name (chemfp.csv_readers.CSVColumnDecodeError attribute) default_dtype (chemfp.search.SimarrayMetric property) depth (chemfp.diversity.Candidate attribute) description (chemfp.ChemFPProblem attribute) (chemfp.highlevel.conversion.ConversionInfo attribute) destination_location (chemfp.highlevel.conversion.ConversionInfo attribute) dialect (chemfp.csv_readers.CSVFingerprintReader attribute) (chemfp.csv_readers.CSVIdAndMoleculeReader attribute) (chemfp.csv_readers.CSVRowReader attribute)

direction_msg (chemfp.highlevel.diversity.BaseSpherexSearch attribute) dise_arena (chemfp.diversity.DISERanker attribute) DISE_SMILES_LIST (chemfp.diversity.DISERanker attribute) DISERanker (class in chemfp.diversity) dtype_str (chemfp.highlevel.simarray.SimarrayResult attribute) (chemfp.search.SimarrayContent attribute) (chemfp.search.SimarrayProcessor property) (chemfp.simarray_io.SimarrayFileContent property) DTypeValueError

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.csv_readers.CSVUnicodeDecodeError attribute) (chemfp.text_records.BaseSmiRecord attribute) (chemfp.text_records.CanRecord attribute) (chemfp.text_records.SDFRecord attribute) (chemfp.text_records.SmiRecord attribute) (chemfp.text_records.UsmRecord attribute)

encoding_errors (chemfp.text_records.BaseSmiRecord attribute) (chemfp.text_records.CanRecord attribute) (chemfp.text_records.SDFRecord attribute) (chemfp.text_records.SmiRecord attribute) (chemfp.text_records.UsmRecord attribute) EncodingError end (chemfp.arena.FingerprintArena attribute) (chemfp.csv_readers.CSVUnicodeDecodeError attribute) end_in_file (chemfp.csv_readers.CSVUnicodeDecodeError property) end_padding (chemfp.arena.FingerprintArena attribute) end_position (chemfp.io.Location property) entry_index (chemfp.clustering.ButinaRanking attribute) error_level (chemfp.ChemFPProblem attribute) ErrorHandler (class in chemfp.io) estate (in module chemfp.cdk_toolkit) extended (in module chemfp.cdk_toolkit) extensions (chemfp.base_toolkit.Format property)

F

FALSE_SINGLETON (chemfp.clustering.ButinaAssignmentType attribute) false_singletons (chemfp.highlevel.clustering.ButinaClusters attribute) family_name (chemfp.types.FingerprintTypeUnknownError attribute) 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) (chemfp.io.Location attribute) fill_lower_triangle() (in module chemfp.search) fingerprint_kwargs (chemfp.types.BaseFingerprintType attribute) FingerprintArena (class in chemfp.arena) 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) FingerprintIterator (class in chemfp) FingerprintList (class in chemfp.arena) FingerprintReader (class in chemfp) fingerprints (chemfp.arena.FingerprintArena attribute) Fingerprints (class in chemfp) fingerprints_filename (chemfp.highlevel.clustering.ButinaClusters attribute) FingerprintType (class in chemfp.types) FingerprintTypeError FingerprintTypeParameterError FingerprintTypeUnknownError FingerprintUnavailableError FingerprintValueError FingerprintWriter (class in chemfp) first_line (chemfp.io.Location property) first_line_bytes (chemfp.io.Location property) FixedSizeFingerprint (class in chemfp.rdkit_types) format (chemfp.FingerprintWriter attribute) (chemfp.fps_io.FPSWriter attribute) Format (class in chemfp.base_toolkit) format_ids_and_scores_as_bytes() (chemfp.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) FormatMetadata (class in chemfp.base_toolkit) fp2 (in module chemfp.openbabel_toolkit) fp3 (in module chemfp.openbabel_toolkit) fp4 (in module chemfp.openbabel_toolkit) fp_column (chemfp.csv_readers.CSVFingerprintReader attribute) fp_title (chemfp.csv_readers.CSVFingerprintReader property) FPBError FPBFingerprintArena (class in chemfp.fpb_io) FPSReader (class in chemfp.fps_io) FPSSearchResult (class in chemfp.fps_search) FPSSearchResults (class in chemfp.fps_search) 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_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) from_destination() (chemfp.io.Location class method) from_dialect() (chemfp.csv_readers.CSVDialect class method) from_dise_paper() (chemfp.diversity.DISERanker static method) from_fingerprints() (chemfp.diversity.DISERanker static method) from_hex() (in module chemfp.encodings) from_hex_lsb() (in module chemfp.encodings) from_hex_msb() (in module chemfp.encodings) 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) 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 static method) from_NxM() (chemfp.search.SimarrayProcessor class method) from_on_bit_positions() (in module chemfp.encodings) from_query_fp() (chemfp.search.SimarrayProcessor class method) 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 static method) from_smistring() (chemfp.cdk_types.CDKBaseFingerprintType method) (chemfp.openbabel_types.OpenBabelBaseFingerprintType method) (chemfp.rdkit_types.RDKitBaseFingerprintType method) from_source() (chemfp.io.Location class method) from_symmetric() (chemfp.search.SimarrayProcessor class method) from_text_settings() (chemfp.types.FingerprintFamily method)

G

get_all_names() (chemfp.types.FingerprintTypeUnknownError method) get_all_neighbors() (chemfp.diversity.PicksAndNeighbors method) (chemfp.highlevel.diversity.SpherexNeighborSearch method) get_assignments() (chemfp.clustering.ButinaCluster method) get_bit_counts() (chemfp.arena.FingerprintArena method) get_bit_counts_as_numpy() (chemfp.arena.FingerprintArena method) get_butina_clusterer() (in module chemfp.clustering) get_by_id() (chemfp.arena.FingerprintArena method) 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) get_default_writer_args() (chemfp.base_toolkit.Format method) get_defaults() (chemfp.types.FingerprintFamily method) get_description() (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.highlevel.conversion.ConversionInfo method) (chemfp.highlevel.diversity.BaseHeapSweepSearch method) (chemfp.highlevel.diversity.BaseSpherexSearch method) (chemfp.highlevel.simarray.SimarrayResult method) (chemfp.highlevel.similarity.BaseSimsearch method) (chemfp.search.SimarrayMetric 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) get_fingerprint_by_id() (chemfp.arena.FingerprintArena method) get_fingerprint_families() (in module chemfp) get_fingerprint_family() (chemfp.types.BaseFingerprintType method) (chemfp.types.FingerprintTypeParameterError method) (in module chemfp) get_fingerprint_family_names() (in module chemfp) get_fingerprint_type() (chemfp.FingerprintReader 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_heapsweep_picker() (in module chemfp.diversity) get_help() (chemfp.types.FingerprintTypeUnknownError method) 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.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) 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) get_index_by_id() (chemfp.arena.FingerprintArena method) 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) 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)

get_indices_as_numpy_array() (chemfp.highlevel.similarity.SingleQuerySimsearch method) (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_maxmin_picker() (in module chemfp.diversity) get_metadata() (chemfp.clustering.ButinaClusterer method) (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.search.SimarrayContent method) (chemfp.types.FingerprintType method) get_method() (chemfp.search.SimarrayMetric method) get_name() (chemfp.clustering.ButinaAssignmentType static method) get_npz_name() (chemfp.search.MatrixType method) get_npz_names() (chemfp.search.MatrixType static method) get_num_threads() (in module chemfp) get_omp_num_threads() (in module chemfp) get_out_description() (chemfp.search.SimarrayContent method) 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_popcount_offsets() (chemfp.arena.FingerprintArena method) get_ranks() (chemfp.diversity.SphereExclusionCandidates method) get_reader_args_from_text_settings() (chemfp.base_toolkit.Format 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) get_scores_as_numpy_array() (chemfp.highlevel.similarity.SingleQuerySimsearch method) (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_search_results() (in module chemfp.search) get_simarray_dtype() (in module chemfp.search) get_simarray_metric() (in module chemfp.search) get_simarray_metric_names() (in module chemfp.search) get_sphere_exclusion_picker() (in module chemfp.diversity) get_suggestions() (chemfp.types.FingerprintTypeUnknownError method) get_tag() (chemfp.text_records.SDFRecord method) (chemfp.text_records.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_records.SDFRecord method) (chemfp.text_records.TextRecord method) get_tag_pairs() (chemfp.text_records.SDFRecord method) (chemfp.text_records.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_records.SDFRecord method) (chemfp.text_records.TextRecord method) get_tanimoto_precision() (in module chemfp.bitops) get_times_description() (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.highlevel.simarray.SimarrayResult method) get_toolkit() (in module chemfp) get_toolkit_names() (in module chemfp) get_type() (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.types.BaseFingerprintType method) (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) graph_only (in module chemfp.cdk_toolkit)

H

has_fingerprint_family() (in module chemfp) has_header (chemfp.csv_readers.CSVFingerprintReader attribute) (chemfp.csv_readers.CSVIdAndMoleculeReader attribute) (chemfp.csv_readers.CSVRowReader attribute) has_toolkit() (in module chemfp) 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) hex_contains_bit() (in module chemfp.bitops) hex_decode() (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) hex_xor() (in module chemfp.bitops) hybridization (in module chemfp.cdk_toolkit)

I

id (chemfp.text_records.BaseSmiRecord attribute) (chemfp.text_records.CanRecord attribute) (chemfp.text_records.CanStringRecord attribute) (chemfp.text_records.SDFRecord property) (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) id_bytes (chemfp.text_records.SDFRecord property) (chemfp.text_records.TextRecord attribute) id_column (chemfp.csv_readers.CSVFingerprintReader attribute) (chemfp.csv_readers.CSVIdAndMoleculeReader attribute) id_title (chemfp.csv_readers.CSVFingerprintReader property) (chemfp.csv_readers.CSVIdAndMoleculeReader property) IdAndMoleculeReader (class in chemfp.base_toolkit) IdAndRecordReader (class in chemfp.base_toolkit) ids (chemfp.arena.FingerprintArena property) import_decoder() (in module chemfp.encodings) include_help() (chemfp.types.FingerprintTypeUnknownError method) InputOrderFPBWriter (class in chemfp.fpb_io) is_available (chemfp.base_toolkit.Format property) (chemfp.openbabel_types.OpenBabelECFP0FingerprintType_v1 attribute) (chemfp.openbabel_types.OpenBabelECFP10FingerprintType_v1 attribute) (chemfp.openbabel_types.OpenBabelECFP8FingerprintType_v1 attribute) (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) is_available() (in module chemfp.jcmapper_types) is_input_format (chemfp.base_toolkit.Format property) is_licensed() (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 property) is_square() (chemfp.search.MatrixType static method) is_valid_aromaticity() (in module chemfp.openeye_toolkit) iter_arenas() (chemfp.arena.FingerprintArena method) (chemfp.FingerprintReader 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) (chemfp.search.SearchResults method) 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) iter_indices() (chemfp.diversity.BaseMaxMinPicker method) (chemfp.diversity.SphereExclusionPicker method) (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method) 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) 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)

J

JCMapper_AP2D_v1 (class in chemfp.jcmapper_types) JCMapper_ASP_v1 (class in chemfp.jcmapper_types) JCMapper_AT2D_v1 (class in chemfp.jcmapper_types) JCMapper_DFS_v1 (class in chemfp.jcmapper_types)

JCMapper_LSTAR_v1 (class in chemfp.jcmapper_types) JCMapper_PH2_v1 (class in chemfp.jcmapper_types) JCMapper_PH3_v1 (class in chemfp.jcmapper_types) JCMapper_RAD2D_v1 (class in chemfp.jcmapper_types)

K

klekota_roth (in module chemfp.cdk_toolkit) knearest_tanimoto_search() (in module chemfp) knearest_tanimoto_search_arena() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (in module chemfp.search) knearest_tanimoto_search_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (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.fps_search) (in module chemfp.search) knearest_tversky_search_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (in module chemfp.search) knearest_tversky_search_symmetric() (in module chemfp) (in module chemfp.search)

L

lineno (chemfp.io.Location property) load() (chemfp.FingerprintReader method) load_fingerprints() (in module chemfp) load_fingerprints_from_string() (in module chemfp) load_npz() (in module chemfp.search) load_output() (chemfp.highlevel.conversion.ConversionInfo method) load_simarray() (in module chemfp)

location (chemfp.base_toolkit.BaseMoleculeReader attribute) (chemfp.base_toolkit.BaseMoleculeWriter attribute) (chemfp.csv_readers.CSVRowReader attribute) (chemfp.fps_io.FPSReader attribute) (chemfp.fps_io.FPSWriter attribute) (chemfp.ParseError attribute) Location (class in chemfp.io)

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) (chemfp.types.ThreadsafeFingerprinterMixin method) make_id_and_molecule_fingerprint_parser() (chemfp.types.BaseFingerprintType method) (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) matrix (chemfp.highlevel.clustering.ButinaClusters attribute) matrix_filename (chemfp.highlevel.clustering.ButinaClusters attribute) matrix_type (chemfp.highlevel.simarray.SimarrayResult attribute) (chemfp.highlevel.similarity.BaseSimsearch property) (chemfp.search.SearchResults property) (chemfp.search.SimarrayContent attribute) (chemfp.search.SimarrayProcessor property) (chemfp.simarray_io.SimarrayFileContent property) matrix_type_name (chemfp.highlevel.similarity.BaseSimsearch property) (chemfp.search.SearchResults property) 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) MEMBER (chemfp.clustering.ButinaAssignmentType attribute) members (chemfp.clustering.ButinaCluster attribute) MERGED (chemfp.clustering.ButinaAssignmentType attribute) metadata (chemfp.arena.FingerprintArena attribute) (chemfp.base_toolkit.BaseMoleculeReader attribute) (chemfp.base_toolkit.BaseMoleculeWriter attribute) (chemfp.FingerprintWriter attribute) (chemfp.fpb_io.InputOrderFPBWriter attribute) (chemfp.fpb_io.OrderedFPBWriter attribute) (chemfp.fps_io.FPSReader attribute) (chemfp.fps_io.FPSWriter attribute) Metadata (class in chemfp) metric (chemfp.highlevel.simarray.SimarrayResult attribute) (chemfp.search.SimarrayContent attribute) (chemfp.search.SimarrayProcessor property) (chemfp.simarray_io.SimarrayFileContent property) metric_name (chemfp.search.DTypeValueError property) min() (chemfp.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) module chemfp chemfp.arena chemfp.base_toolkit chemfp.bitops chemfp.cdk_toolkit chemfp.cdk_types chemfp.clustering chemfp.csv_readers chemfp.diversity chemfp.encodings chemfp.fpb_io chemfp.fps_io chemfp.fps_search chemfp.highlevel.clustering chemfp.highlevel.conversion chemfp.highlevel.diversity chemfp.highlevel.simarray chemfp.highlevel.similarity chemfp.io chemfp.jcmapper_types chemfp.openbabel_toolkit chemfp.openbabel_types chemfp.openeye_toolkit chemfp.openeye_types chemfp.rdkit_toolkit chemfp.rdkit_types chemfp.search chemfp.simarray_io chemfp.text_records chemfp.text_toolkit chemfp.toolkit chemfp.types

module (chemfp.cdk_types.CDKBaseFingerprintType attribute) (chemfp.openbabel_types.OpenBabelBaseFingerprintType attribute) (chemfp.rdkit_types.RDKitBaseFingerprintType attribute) mol (chemfp.io.Location property) mol_column (chemfp.csv_readers.CSVIdAndMoleculeReader attribute) mol_title (chemfp.csv_readers.CSVIdAndMoleculeReader property) molecule_screen (in module chemfp.openeye_toolkit) MoleculeReader (class in chemfp.base_toolkit) MoleculeStringWriter (class in chemfp.base_toolkit) MoleculeWriter (class in chemfp.base_toolkit) morgan (in module chemfp.rdkit_toolkit) morgan1 (in module chemfp.rdkit_toolkit) morgan1_v1 (in module chemfp.rdkit_toolkit) morgan1_v2 (in module chemfp.rdkit_toolkit) morgan2 (in module chemfp.rdkit_toolkit) morgan2_v1 (in module chemfp.rdkit_toolkit) morgan2_v2 (in module chemfp.rdkit_toolkit) morgan3 (in module chemfp.rdkit_toolkit) morgan3_v1 (in module chemfp.rdkit_toolkit) morgan3_v2 (in module chemfp.rdkit_toolkit) morgan4 (in module chemfp.rdkit_toolkit) morgan4_v1 (in module chemfp.rdkit_toolkit) morgan4_v2 (in module chemfp.rdkit_toolkit) morgan_v1 (in module chemfp.rdkit_toolkit) morgan_v2 (in module chemfp.rdkit_toolkit) move_false_singletons_to_nearest_center() (chemfp.clustering.ButinaClusterer method) move_members() (chemfp.clustering.ButinaCluster method) move_pick_index_to_first() (chemfp.diversity.PicksAndScores method) MOVED_FALSE_SINGLETON (chemfp.clustering.ButinaAssignmentType attribute) msg (chemfp.csv_readers.CSVColumnError attribute) (chemfp.ParseError attribute) 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.CDKPubchemFingerprintType_v29 attribute) (chemfp.cdk_types.CDKShortestPathFingerprintType_v20 attribute) (chemfp.cdk_types.CDKShortestPathFingerprintType_v27 attribute) (chemfp.cdk_types.CDKSubstructureFingerprintType_v20 attribute) (chemfp.jcmapper_types.JCMapper_AP2D_v1 attribute) (chemfp.jcmapper_types.JCMapper_ASP_v1 attribute) (chemfp.jcmapper_types.JCMapper_AT2D_v1 attribute) (chemfp.jcmapper_types.JCMapper_DFS_v1 attribute) (chemfp.jcmapper_types.JCMapper_LSTAR_v1 attribute) (chemfp.jcmapper_types.JCMapper_PH2_v1 attribute) (chemfp.jcmapper_types.JCMapper_PH3_v1 attribute) (chemfp.jcmapper_types.JCMapper_RAD2D_v1 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.RDKitFingerprintType_v3 attribute) (chemfp.rdkit_types.RDKitMACCSFingerprintType_v1 attribute) (chemfp.rdkit_types.RDKitMACCSFingerprintType_v2 attribute) (chemfp.rdkit_types.RDKitMorganFingerprintType_v1 attribute) (chemfp.rdkit_types.RDKitMorganFingerprintType_v2 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.rdkit_types.RDKitTorsionFingerprintType_v4 attribute) (chemfp.search.SimarrayDType attribute) (chemfp.types.BaseFingerprintType attribute) (chemfp.types.FingerprintFamily property) (chemfp.types.FingerprintTypeError attribute) (chemfp.types.FingerprintUnavailableError attribute) (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit)

name_table (chemfp.clustering.ButinaAssignmentType attribute) Neighbors (class in chemfp.diversity) next() (chemfp.fps_io.FPSReader method) (chemfp.search.SimarrayProcessor method) NoFingerprintParametersMixin (class in chemfp.types) num_bits (chemfp.arena.FingerprintArena attribute) (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.CDKPubchemFingerprintType_v29 attribute) (chemfp.cdk_types.CDKSubstructureFingerprintType_v20 attribute) (chemfp.highlevel.simarray.SimarrayResult attribute) (chemfp.Metadata 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.search.SimarrayContent attribute) (chemfp.simarray_io.SimarrayFileContent property) (chemfp.types.FingerprintType attribute) num_butina_clusters (chemfp.highlevel.clustering.ButinaClusters attribute) num_bytes (chemfp.arena.FingerprintArena attribute) (chemfp.Metadata attribute) num_columns (chemfp.search.SearchResults attribute) num_initial_picks (chemfp.highlevel.diversity.BaseSpherexSearch attribute) num_input_records (chemfp.highlevel.conversion.ConversionInfo property) num_output_records (chemfp.highlevel.conversion.ConversionInfo property) num_picked (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) num_remaining (chemfp.clustering.ButinaClusterer attribute) num_rows (chemfp.search.SearchResults attribute) num_threshold_hits (chemfp.clustering.ButinaRanking attribute) numpy_dtype (chemfp.search.SimarrayDType attribute) NxN_threshold (chemfp.highlevel.clustering.ButinaClusters attribute) NxNSimsearch (class in chemfp.highlevel.similarity)

O

ob2fps() (in module chemfp) obj (chemfp.io.Location attribute) object (chemfp.csv_readers.CSVUnicodeDecodeError attribute) oe2fps() (in module chemfp) offsets (chemfp.io.Location property) open() (in module chemfp) open_fasta_writer() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) open_fasta_writer_to_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) open_fingerprint_writer() (in module chemfp) 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) (in module chemfp.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) (in module chemfp.toolkit) open_inchikey_writer() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.toolkit) 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) 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) (in module chemfp.toolkit) open_pdb_writer_to_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit)

open_sdf3k_writer() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.toolkit) openbabel (in module chemfp) OpenBabelBaseFingerprintType (class in chemfp.openbabel_types) OpenBabelBaseMACCSFingerprintType (class in chemfp.openbabel_types) 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) OpenBabelECFPBaseFingerprintType (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_v2 (class in chemfp.openbabel_types) openeye (in module chemfp) 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) out (chemfp.highlevel.simarray.SimarrayResult attribute) (chemfp.highlevel.similarity.BaseSimsearch property) (chemfp.search.SimarrayContent attribute) output_filename (chemfp.highlevel.conversion.ConversionInfo attribute) output_format (chemfp.highlevel.conversion.ConversionInfo attribute) output_recno (chemfp.io.Location property)

P

parse_fasta() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) parse_helm() (in module chemfp.rdkit_toolkit) 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.BaseFingerprintType method) (chemfp.types.FingerprintType method) parse_inchi() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) parse_inchistring() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) 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.BaseFingerprintType method) (chemfp.types.FingerprintType method) parse_molfile() (in module chemfp.cdk_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (in module chemfp.toolkit) parse_sequence() (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.toolkit) parsed (chemfp.types.FingerprintTypeParameterError attribute) ParseError 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) 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) picker (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) picks (chemfp.diversity.BaseMaxMinPicker attribute) (chemfp.diversity.SphereExclusionPicker attribute) (chemfp.highlevel.diversity.BaseHeapSweepSearch property) 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 property) position_units (chemfp.io.Location property) prefix (chemfp.base_toolkit.Format property) print_report() (in module chemfp.bitops) process() (chemfp.clustering.ButinaClusterer method) process_all() (chemfp.search.SimarrayProcessor method) processor (chemfp.highlevel.simarray.SimarrayResult attribute) progress_bar() (chemfp.io.Location method) ProgressBar (class in chemfp.io) prune_clusters() (chemfp.clustering.ButinaClusterer method) pubchem (in module chemfp.cdk_toolkit) Python Enhancement Proposals PEP 343

Q

queries (chemfp.highlevel.simarray.SimarrayResult property) query_fp (chemfp.highlevel.simarray.SimarrayResult attribute) query_id (chemfp.fps_search.FPSSearchResult attribute) (chemfp.highlevel.similarity.SingleQuerySimsearch property) (chemfp.search.SearchResult property) query_ids (chemfp.fps_search.FPSSearchResults attribute) (chemfp.highlevel.simarray.SimarrayResult property) (chemfp.highlevel.similarity.MultiQuerySimsearch property) (chemfp.highlevel.similarity.NxNSimsearch property) (chemfp.search.SearchResults attribute) (chemfp.search.SimarrayContent attribute) (chemfp.search.SimarrayProcessor property)

R

random_choice() (chemfp.arena.FingerprintArena method) (chemfp.arena.FingerprintList method) rank_arena() (chemfp.diversity.DISERanker method) rank_index (chemfp.clustering.ButinaRankings attribute) rdk (in module chemfp.rdkit_toolkit) rdk_v2 (in module chemfp.rdkit_toolkit) rdk_v3 (in module chemfp.rdkit_toolkit) rdkit (in module chemfp) rdkit2fps() (in module chemfp) RDKitAtomPairFingerprint_v1 (class in chemfp.rdkit_types) RDKitAtomPairFingerprint_v2 (class in chemfp.rdkit_types) RDKitAvalonFingerprintType_v1 (class in chemfp.rdkit_types) 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) RDKitFingerprintType_v2 (class in chemfp.rdkit_types) RDKitFingerprintType_v3 (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) RDKitMorganFingerprintType_v2 (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) RDKitPatternFingerprint_v4 (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) RDKitTorsionFingerprintType_v3 (class in chemfp.rdkit_types) RDKitTorsionFingerprintType_v4 (class in chemfp.rdkit_types) read_csv_ids_and_fingerprints() (in module chemfp.csv_readers) read_csv_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_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) (in module chemfp.toolkit) read_fasta_ids_and_molecules_from_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) read_fasta_molecules() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) read_fasta_molecules_from_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) 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_inchi_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.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) (in module chemfp.toolkit) read_inchi_molecules() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.toolkit) read_molecule_fingerprints() (chemfp.types.BaseFingerprintType method) (chemfp.types.FingerprintType method) (in module chemfp) read_molecule_fingerprints_from_string() (chemfp.types.BaseFingerprintType method) (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_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) (in module chemfp.toolkit)

read_pdb_ids_and_molecules_from_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) read_pdb_molecules() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) read_pdb_molecules_from_string() (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.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) (in module chemfp.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) (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_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_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) (in module chemfp.toolkit) read_sdf_records() (in module chemfp.text_toolkit) read_sdf_records_from_string() (in module chemfp.text_toolkit) 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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.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) (in module chemfp.toolkit) reason (chemfp.csv_readers.CSVUnicodeDecodeError attribute) (chemfp.types.FingerprintTypeError attribute) (chemfp.types.FingerprintTypeParameterError attribute) (chemfp.types.FingerprintUnavailableError attribute) recno (chemfp.io.Location property) record (chemfp.io.Location property) (chemfp.text_records.BaseSmiRecord attribute) (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) record_format (chemfp.base_toolkit.FormatMetadata attribute) (chemfp.io.Location property) (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) record_id (chemfp.csv_readers.CSVColumnError attribute) RecordReader (class in chemfp.base_toolkit) reference_popcount (chemfp.diversity.Candidate attribute) references (chemfp.highlevel.diversity.BaseSpherexSearch attribute) rename_table (chemfp.clustering.ButinaAssignmentType attribute) reorder() (chemfp.diversity.Neighbors method) (chemfp.diversity.PicksAndScores method) (chemfp.fps_search.FPSSearchResult method) (chemfp.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) reorder_all() (chemfp.fps_search.FPSSearchResults method) (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method) rescore (chemfp.highlevel.clustering.ButinaClusters attribute) rescore_moved() (chemfp.clustering.ButinaClusterer method) result (chemfp.highlevel.clustering.ButinaClusters attribute) (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) (chemfp.highlevel.diversity.HeapSweepScoreSearch attribute) (chemfp.highlevel.diversity.HeapSweepSearch attribute) (chemfp.highlevel.diversity.MaxMinScoreSearch attribute) (chemfp.highlevel.diversity.MaxMinSearch attribute) row (chemfp.csv_readers.CSVColumnError attribute) (chemfp.io.Location property)

S

sample() (chemfp.arena.FingerprintArena method) save() (chemfp.arena.FingerprintArena method) (chemfp.clustering.ButinaClusterer method) (chemfp.FingerprintReader method) (chemfp.highlevel.clustering.ButinaClusters method) (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.highlevel.similarity.SingleQuerySimsearch method) (chemfp.search.SearchResult method) (chemfp.search.SearchResults method) (chemfp.search.SimarrayContent method) save_npz() (in module chemfp.search) score (chemfp.clustering.ButinaAssignment attribute) (chemfp.diversity.PickAndScore attribute) scores (chemfp.fps_search.FPSSearchResult attribute) sdf2fps() (in module chemfp) SDFRecord (class in chemfp.text_records) SearchResult (class in chemfp.search) SearchResults (class in chemfp.search) secfp (in module chemfp.rdkit_toolkit) seed (chemfp.highlevel.clustering.ButinaClusters attribute) (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) set_default_progressbar() (in module chemfp) 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) set_toolkit_name() (chemfp.types.FingerprintTypeUnknownError method) severity (chemfp.ChemFPProblem attribute) shape (chemfp.highlevel.similarity.MultiQuerySimsearch property) (chemfp.highlevel.similarity.NxNSimsearch property) (chemfp.highlevel.similarity.SingleQuerySimsearch property) (chemfp.search.SearchResults property) shortest_path (in module chemfp.cdk_toolkit) simarray() (in module chemfp) SimarrayContent (class in chemfp.search) SimarrayDType (class in chemfp.search) SimarrayFileContent (class in chemfp.simarray_io) SimarrayMetric (class in chemfp.search) SimarrayProcessor (class in chemfp.search) SimarrayResult (class in chemfp.highlevel.simarray) simsearch() (in module chemfp)

SingleQuerySimsearch (class in chemfp.highlevel.similarity) smarts_screen (in module chemfp.openeye_toolkit) smiles (chemfp.text_records.BaseSmiRecord attribute) (chemfp.text_records.CanRecord attribute) (chemfp.text_records.CanStringRecord 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) SmiRecord (class in chemfp.text_records) SmiStringRecord (class in chemfp.text_records) software (chemfp.cdk_types.CDKBaseFingerprintType attribute) (chemfp.Metadata attribute) (chemfp.openbabel_types.OpenBabelBaseFingerprintType attribute) (chemfp.rdkit_types.RDKitBaseFingerprintType attribute) (chemfp.types.BaseFingerprintType attribute) (chemfp.types.FingerprintType attribute) SOFTWARE (in module chemfp) software (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) source_locations (chemfp.highlevel.conversion.ConversionInfo attribute) sources (chemfp.Metadata attribute) 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 (chemfp.arena.FingerprintArena attribute) (chemfp.csv_readers.CSVUnicodeDecodeError attribute) start_in_file (chemfp.csv_readers.CSVUnicodeDecodeError property) start_padding (chemfp.arena.FingerprintArena attribute) start_position (chemfp.io.Location property) (chemfp.io.ProgressBar attribute) storage_size (chemfp.arena.FingerprintArena attribute) substructure (in module chemfp.cdk_toolkit) supported_dtypes (chemfp.search.DTypeValueError property) (chemfp.search.SimarrayMetric property) supports_io (chemfp.base_toolkit.Format property) suppress_log_output() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit)

T

target_arena_ids (chemfp.search.SearchResults attribute) target_ids (chemfp.highlevel.simarray.SimarrayResult property) (chemfp.highlevel.similarity.BaseSimsearch property) (chemfp.search.SearchResult property) (chemfp.search.SearchResults property) (chemfp.search.SimarrayContent attribute) (chemfp.search.SimarrayProcessor property) target_start (chemfp.search.SearchResult property) targets (chemfp.highlevel.simarray.SimarrayResult property) TextRecord (class in chemfp.text_records) ThreadsafeFingerprinterMixin (class in chemfp.types) threshold (chemfp.diversity.SphereExclusionPicker attribute) (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) threshold_tanimoto_search() (in module chemfp) threshold_tanimoto_search_arena() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (in module chemfp.search) threshold_tanimoto_search_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (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.fps_search) (in module chemfp.search) threshold_tversky_search_fp() (chemfp.arena.FingerprintArena method) (chemfp.fps_io.FPSReader method) (in module chemfp.fps_search) (in module chemfp.search) threshold_tversky_search_symmetric() (in module chemfp) (in module chemfp.search) tiebreaker (chemfp.highlevel.clustering.ButinaClusters attribute) times (chemfp.highlevel.clustering.ButinaClusters attribute) (chemfp.highlevel.conversion.ConversionInfo attribute) (chemfp.highlevel.diversity.BaseHeapSweepSearch attribute) (chemfp.highlevel.diversity.BaseSpherexSearch attribute) (chemfp.highlevel.simarray.SimarrayResult attribute) title (chemfp.csv_readers.CSVColumnError attribute) titles (chemfp.csv_readers.CSVColumnError attribute) (chemfp.csv_readers.CSVFingerprintReader attribute) (chemfp.csv_readers.CSVIdAndMoleculeReader attribute) (chemfp.csv_readers.CSVRowReader attribute) to_csr() (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method)

to_dict() (chemfp.search.SimarrayMetric method) to_numpy_array() (chemfp.arena.FingerprintArena method) (chemfp.highlevel.similarity.MultiQuerySimsearch method) (chemfp.highlevel.similarity.NxNSimsearch method) (chemfp.search.SearchResults method) to_numpy_bitarray() (chemfp.arena.FingerprintArena method) to_pandas() (chemfp.clustering.ButinaAssignments method) (chemfp.clustering.ButinaCluster method) (chemfp.clustering.ButinaClusterer method) (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 property) (chemfp.types.FingerprintType attribute) toolkit_name (chemfp.base_toolkit.Format attribute) (chemfp.types.FingerprintUnavailableError attribute) torsion (in module chemfp.rdkit_toolkit) torsion_v3 (in module chemfp.rdkit_toolkit) torsion_v4 (in module chemfp.rdkit_toolkit) tqdm (chemfp.io.ProgressBar attribute) train_test_split() (chemfp.arena.FingerprintArena method) translate_record() (in module chemfp.cdk_toolkit) (in module chemfp.openbabel_toolkit) (in module chemfp.openeye_toolkit) (in module chemfp.rdkit_toolkit) (in module chemfp.toolkit) tree (in module chemfp.openeye_toolkit) type (chemfp.Metadata attribute) (chemfp.types.FingerprintTypeParameterError attribute)

U

UNASSIGNED (chemfp.clustering.ButinaAssignmentType attribute) UnsupportedMetricValueError update() (chemfp.io.ProgressBar method)

use_environment_variables() (in module chemfp.bitops) UsmRecord (class in chemfp.text_records) UsmStringRecord (class in chemfp.text_records)

V

VariableSizeFingerprint (class in chemfp.rdkit_types) version (chemfp.types.BaseFingerprintType attribute) (chemfp.types.FingerprintFamily property) (chemfp.types.FingerprintUnavailableError 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)