Index

A

AlignmentLength (refnd.kernels.protein.sequence.GlobalIdentityMode attribute) (refnd.kernels.protein.sequence.LocalIdentityMode attribute)

B

BitFingerprint (class in refnd.utils) Blosum100 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum30 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum35 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum40 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum45 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum50 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum55 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum60 (refnd.kernels.protein.sequence.ScoringMatrix attribute)

Blosum62 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum65 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum70 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum75 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum80 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum85 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum90 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Blosum95 (refnd.kernels.protein.sequence.ScoringMatrix attribute) BothQueryTarget (refnd.kernels.protein.sequence.CoverageMode attribute) build() (refnd.core.HNSWState method)

C

cache_capacity (refnd.core.HNSWConfig attribute) cache_shards (refnd.core.HNSWConfig attribute) call() (refnd.kernels.molecules.TanimotoBit method) (refnd.kernels.molecules.TanimotoReal method) (refnd.kernels.protein.sequence.GlobalAligner method) (refnd.kernels.protein.sequence.LocalAligner method)

config (refnd.core.HNSWIndex attribute) (refnd.core.HNSWState attribute) count() (refnd.utils.BitFingerprint method) CoverageMode (class in refnd.kernels.protein.sequence) CPM (refnd.core.LeidenObjective attribute) CsrGraph (class in refnd.core)

D

dataset_size (refnd.core.HNSWIndex attribute) DatatypeWidth (class in refnd.kernels.protein.sequence)

Diag (refnd.kernels.protein.sequence.VectorizationStrategy attribute) dict() (refnd.core.HNSWConfig method)

E

edges() (refnd.core.EdgeStore method) (refnd.core.HNSWState method) EdgeStore (class in refnd.core) ef_construction (refnd.core.HNSWConfig attribute)

ef_init (refnd.core.HNSWConfig attribute) entry_point (refnd.core.HNSWIndex attribute) exact_edges() (in module refnd.core) exact_nearest_neighbors() (in module refnd.core) extend_candidates (refnd.core.HNSWConfig attribute)

F

find_communities() (in module refnd.core) find_components() (in module refnd.core) from_list() (refnd.utils.BitFingerprint static method) (refnd.utils.RealFingerprint static method)

from_np() (refnd.utils.BitFingerprint static method) (refnd.utils.RealFingerprint static method) Full (refnd.kernels.protein.sequence.DatatypeWidth attribute)

G

get_layer() (refnd.core.HNSWState method) GlobalAligner (class in refnd.kernels.protein.sequence)

GlobalIdentityMode (class in refnd.kernels.protein.sequence) graph() (refnd.core.EdgeStore method)

H

Half (refnd.kernels.protein.sequence.DatatypeWidth attribute) HNSWConfig (class in refnd.core)

HNSWIndex (class in refnd.core) HNSWState (class in refnd.core)

I

index (refnd.core.HNSWState attribute)

is_built (refnd.core.HNSWState attribute)

K

keep_pruned_connections (refnd.core.HNSWConfig attribute)

KernelVariant (class in refnd.kernels)

L

largest_cluster() (in module refnd.utils) layers (refnd.core.HNSWIndex attribute) LeidenObjective (class in refnd.core) LengthRatio (refnd.kernels.protein.sequence.CoverageMode attribute) load() (refnd.core.EdgeStore static method) (refnd.core.HNSWIndex static method) (refnd.core.HNSWState static method)

LocalAligner (class in refnd.kernels.protein.sequence) LocalIdentityMode (class in refnd.kernels.protein.sequence) Long (refnd.kernels.protein.sequence.DatatypeWidth attribute)

M

m (refnd.core.CsrGraph attribute) (refnd.core.HNSWConfig attribute) m_l (refnd.core.HNSWConfig attribute) m_max (refnd.core.HNSWConfig attribute) m_max0 (refnd.core.HNSWConfig attribute) max_layers (refnd.core.HNSWIndex attribute) MaxLength (refnd.kernels.protein.sequence.GlobalIdentityMode attribute) MaxSeqLength (refnd.kernels.protein.sequence.GlobalIdentityMode attribute)

MinSeqLength (refnd.kernels.protein.sequence.GlobalIdentityMode attribute) (refnd.kernels.protein.sequence.LocalIdentityMode attribute) Modularity (refnd.core.LeidenObjective attribute) module refnd.kernels refnd.kernels.molecules refnd.kernels.protein.sequence refnd.utils

N

n (refnd.core.CsrGraph attribute) n_threads (refnd.core.HNSWConfig attribute)

neighbors() (refnd.core.CsrGraph method) node_count() (refnd.core.EdgeStore method) norm_sq() (refnd.utils.RealFingerprint method)

P

Pam10 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam100 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam110 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam120 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam130 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam140 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam150 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam160 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam170 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam180 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam190 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam20 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam200 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam210 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam220 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam230 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam240 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam250 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam260 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam270 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam280 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam290 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam30 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam300 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam310 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam320 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam330 (refnd.kernels.protein.sequence.ScoringMatrix attribute)

Pam340 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam350 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam360 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam370 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam380 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam390 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam40 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam400 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam410 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam420 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam430 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam440 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam450 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam460 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam470 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam480 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam490 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam50 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam500 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam60 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam70 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam80 (refnd.kernels.protein.sequence.ScoringMatrix attribute) Pam90 (refnd.kernels.protein.sequence.ScoringMatrix attribute) partition() (in module refnd.core) ProteinGlobal (refnd.kernels.KernelVariant attribute) ProteinLocal (refnd.kernels.KernelVariant attribute) proximity_edges (refnd.core.HNSWIndex attribute) proximity_threshold (refnd.core.HNSWConfig attribute)

Q

Query (refnd.kernels.protein.sequence.CoverageMode attribute)

R

read_fasta() (in module refnd.utils) RealFingerprint (class in refnd.utils) refnd.kernels module refnd.kernels.molecules module

refnd.kernels.protein.sequence module refnd.utils module

S

Sat (refnd.kernels.protein.sequence.DatatypeWidth attribute) save() (refnd.core.EdgeStore method) (refnd.core.HNSWIndex method) (refnd.core.HNSWState method) Scan (refnd.kernels.protein.sequence.VectorizationStrategy attribute) ScoringMatrix (class in refnd.kernels.protein.sequence)

search() (refnd.core.HNSWState method) Short (refnd.kernels.protein.sequence.DatatypeWidth attribute) ShorterSeq (refnd.kernels.protein.sequence.CoverageMode attribute) shuffle (refnd.core.HNSWConfig attribute) strength() (refnd.core.CsrGraph method) strict_ef (refnd.core.HNSWConfig attribute) Striped (refnd.kernels.protein.sequence.VectorizationStrategy attribute)

T

TanimotoBit (class in refnd.kernels.molecules) (refnd.kernels.KernelVariant attribute) TanimotoReal (class in refnd.kernels.molecules) (refnd.kernels.KernelVariant attribute) Target (refnd.kernels.protein.sequence.CoverageMode attribute) threshold_based_neighbourhood (refnd.core.HNSWConfig attribute)

to_list() (refnd.utils.BitFingerprint method) (refnd.utils.RealFingerprint method) to_np() (refnd.utils.BitFingerprint method) (refnd.utils.RealFingerprint method) to_rdkit() (refnd.utils.BitFingerprint method) (refnd.utils.RealFingerprint method)

U

use_heuristic (refnd.core.HNSWConfig attribute)

V

VectorizationStrategy (class in refnd.kernels.protein.sequence)