Index

A

AlignmentGlobal (relag.kernels.KernelVariant attribute) AlignmentLength (relag.kernels.alignments.GlobalIdentityMode attribute) (relag.kernels.alignments.LocalIdentityMode attribute)

AlignmentLocal (relag.kernels.KernelVariant attribute) args (relag.core.HNSWState attribute)

B

BitFingerprint (class in relag.utils) Blosum100 (relag.kernels.alignments.ScoringMatrix attribute) Blosum30 (relag.kernels.alignments.ScoringMatrix attribute) Blosum35 (relag.kernels.alignments.ScoringMatrix attribute) Blosum40 (relag.kernels.alignments.ScoringMatrix attribute) Blosum45 (relag.kernels.alignments.ScoringMatrix attribute) Blosum50 (relag.kernels.alignments.ScoringMatrix attribute) Blosum55 (relag.kernels.alignments.ScoringMatrix attribute) Blosum60 (relag.kernels.alignments.ScoringMatrix attribute)

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

C

cache_capacity (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) cache_shards (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) call() (relag.kernels.alignments.GlobalAligner method) (relag.kernels.alignments.LocalAligner method) (relag.kernels.molecules.TanimotoBit method) (relag.kernels.molecules.TanimotoReal method) (relag.kernels.protspam.ProtSpamKernel method) (relag.kernels.structures.USAlignKernel method) (relag.kernels.vectors.Cosine method) (relag.kernels.vectors.L1 method) (relag.kernels.vectors.L2 method)

config (relag.core.HNSWIndex attribute) (relag.core.HNSWState attribute) Cosine (class in relag.kernels.vectors) (relag.kernels.KernelVariant attribute) count() (relag.utils.BitFingerprint method) CoverageMode (class in relag.kernels.alignments) CPM (relag.core.LeidenObjective attribute) CsrGraph (class in relag.core)

D

data (relag.core.HNSWState attribute) dataset_size (relag.core.HNSWIndex attribute) DatatypeWidth (class in relag.kernels.alignments) Diag (relag.kernels.alignments.VectorizationStrategy attribute) dict() (relag.core.HNSWConfig method)

Distance (relag.core.INWeightType attribute) distance() (relag.kernels.protspam.ProtSpamKernel method) Dnafull (relag.kernels.alignments.ScoringMatrix attribute) dont_care (relag.utils.SWPattern attribute) (relag.utils.SWPatternSet attribute) dontcare() (relag.utils.SWPattern method)

E

edges (relag.core.CsrGraph attribute) edges() (relag.core.EdgeStore method) (relag.core.HNSWState method) EdgeStore (class in relag.core) ef_construction (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) ef_init (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

entry_point (relag.core.HNSWIndex attribute) Evolutionary (relag.kernels.protspam.ProtSpamDistance attribute) exact_edges() (in module relag.core) exact_nearest_neighbors() (in module relag.core) extend_build() (relag.core.HNSWState method) extend_candidates (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

F

find_communities() (in module relag.core) find_components() (in module relag.core) fp (relag.utils.BitFingerprint attribute) (relag.utils.RealFingerprint attribute) from_list() (relag.utils.BitFingerprint static method) (relag.utils.RealFingerprint static method) (relag.utils.Vector static method)

from_np() (relag.utils.BitFingerprint static method) (relag.utils.RealFingerprint static method) (relag.utils.Vector static method) from_patterns() (relag.utils.SWPatternSet static method) Full (relag.kernels.alignments.DatatypeWidth attribute)

G

get_layer() (relag.core.HNSWState method) GlobalAligner (class in relag.kernels.alignments)

GlobalIdentityMode (class in relag.kernels.alignments) graph() (relag.core.EdgeStore method)

H

Half (relag.kernels.alignments.DatatypeWidth attribute) HNSWConfig (class in relag.core)

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

I

Identity (relag.kernels.alignments.ScoringMatrix attribute) index (relag.core.HNSWState attribute) inweight_type (relag.core.CsrGraph attribute)

INWeightType (class in relag.core) is_built (relag.core.HNSWState attribute) is_match() (relag.utils.SWPattern method)

K

keep_all_edges (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) keep_pruned_connections (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

KernelVariant (class in relag.kernels) key() (relag.utils.SWWord method) kwargs (relag.core.HNSWState attribute)

L

L1 (class in relag.kernels.vectors) (relag.kernels.KernelVariant attribute) L2 (class in relag.kernels.vectors) (relag.kernels.KernelVariant attribute) largest_cluster() (in module relag.utils) layers (relag.core.HNSWIndex attribute) LeidenObjective (class in relag.core)

LengthRatio (relag.kernels.alignments.CoverageMode attribute) load() (relag.core.EdgeStore static method) (relag.core.HNSWIndex static method) (relag.core.HNSWState static method) (relag.utils.SWPatternSet static method) LocalAligner (class in relag.kernels.alignments) LocalIdentityMode (class in relag.kernels.alignments) Long (relag.kernels.alignments.DatatypeWidth attribute)

M

m (relag.core.CsrGraph attribute) (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) m_l (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) m_max (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) m_max0 (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) match_positions() (relag.utils.SWPattern method) max_layers (relag.core.HNSWIndex attribute) MaxLength (relag.kernels.alignments.GlobalIdentityMode attribute) MaxSeqLength (relag.kernels.alignments.GlobalIdentityMode attribute)

Min (relag.kernels.structures.NormMode attribute) MinSeqLength (relag.kernels.alignments.GlobalIdentityMode attribute) (relag.kernels.alignments.LocalIdentityMode attribute) MismatchRate (relag.kernels.protspam.ProtSpamDistance attribute) Modularity (relag.core.LeidenObjective attribute) module relag.kernels relag.kernels.alignments relag.kernels.molecules relag.kernels.protspam relag.kernels.structures relag.kernels.vectors relag.utils

N

n (relag.core.CsrGraph attribute) (relag.utils.SWPatternSet attribute) n_threads (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

neighbors() (relag.core.CsrGraph method) node_count() (relag.core.EdgeStore method) norm_sq() (relag.utils.RealFingerprint method) NormMode (class in relag.kernels.structures) Nuc44 (relag.kernels.alignments.ScoringMatrix attribute)

O

optimize() (relag.utils.SWPatternSet method)

P

Pam10 (relag.kernels.alignments.ScoringMatrix attribute) Pam100 (relag.kernels.alignments.ScoringMatrix attribute) Pam110 (relag.kernels.alignments.ScoringMatrix attribute) Pam120 (relag.kernels.alignments.ScoringMatrix attribute) Pam130 (relag.kernels.alignments.ScoringMatrix attribute) Pam140 (relag.kernels.alignments.ScoringMatrix attribute) Pam150 (relag.kernels.alignments.ScoringMatrix attribute) Pam160 (relag.kernels.alignments.ScoringMatrix attribute) Pam170 (relag.kernels.alignments.ScoringMatrix attribute) Pam180 (relag.kernels.alignments.ScoringMatrix attribute) Pam190 (relag.kernels.alignments.ScoringMatrix attribute) Pam20 (relag.kernels.alignments.ScoringMatrix attribute) Pam200 (relag.kernels.alignments.ScoringMatrix attribute) Pam210 (relag.kernels.alignments.ScoringMatrix attribute) Pam220 (relag.kernels.alignments.ScoringMatrix attribute) Pam230 (relag.kernels.alignments.ScoringMatrix attribute) Pam240 (relag.kernels.alignments.ScoringMatrix attribute) Pam250 (relag.kernels.alignments.ScoringMatrix attribute) Pam260 (relag.kernels.alignments.ScoringMatrix attribute) Pam270 (relag.kernels.alignments.ScoringMatrix attribute) Pam280 (relag.kernels.alignments.ScoringMatrix attribute) Pam290 (relag.kernels.alignments.ScoringMatrix attribute) Pam30 (relag.kernels.alignments.ScoringMatrix attribute) Pam300 (relag.kernels.alignments.ScoringMatrix attribute) Pam310 (relag.kernels.alignments.ScoringMatrix attribute) Pam320 (relag.kernels.alignments.ScoringMatrix attribute) Pam330 (relag.kernels.alignments.ScoringMatrix attribute) Pam340 (relag.kernels.alignments.ScoringMatrix attribute) Pam350 (relag.kernels.alignments.ScoringMatrix attribute) Pam360 (relag.kernels.alignments.ScoringMatrix attribute) Pam370 (relag.kernels.alignments.ScoringMatrix attribute) Pam380 (relag.kernels.alignments.ScoringMatrix attribute)

Pam390 (relag.kernels.alignments.ScoringMatrix attribute) Pam40 (relag.kernels.alignments.ScoringMatrix attribute) Pam400 (relag.kernels.alignments.ScoringMatrix attribute) Pam410 (relag.kernels.alignments.ScoringMatrix attribute) Pam420 (relag.kernels.alignments.ScoringMatrix attribute) Pam430 (relag.kernels.alignments.ScoringMatrix attribute) Pam440 (relag.kernels.alignments.ScoringMatrix attribute) Pam450 (relag.kernels.alignments.ScoringMatrix attribute) Pam460 (relag.kernels.alignments.ScoringMatrix attribute) Pam470 (relag.kernels.alignments.ScoringMatrix attribute) Pam480 (relag.kernels.alignments.ScoringMatrix attribute) Pam490 (relag.kernels.alignments.ScoringMatrix attribute) Pam50 (relag.kernels.alignments.ScoringMatrix attribute) Pam500 (relag.kernels.alignments.ScoringMatrix attribute) Pam60 (relag.kernels.alignments.ScoringMatrix attribute) Pam70 (relag.kernels.alignments.ScoringMatrix attribute) Pam80 (relag.kernels.alignments.ScoringMatrix attribute) Pam90 (relag.kernels.alignments.ScoringMatrix attribute) parse() (relag.utils.SWPattern static method) partition() (in module relag.core) path (relag.utils.PdbStructure attribute) pattern_count() (relag.utils.SWSequence method) patterns (relag.utils.SWSequence attribute) patterns() (relag.kernels.protspam.ProtSpamKernel method) (relag.utils.SWPatternSet method) PdbStructure (class in relag.utils) pos() (relag.utils.SWWord method) ProtSpam (relag.kernels.KernelVariant attribute) ProtSpamDistance (class in relag.kernels.protspam) ProtSpamKernel (class in relag.kernels.protspam) proximity_edges (relag.core.HNSWIndex attribute) proximity_threshold (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

Q

Query (relag.kernels.alignments.CoverageMode attribute) (relag.kernels.structures.NormMode attribute)

R

random() (relag.utils.BitFingerprint static method) (relag.utils.SWPatternSet static method) read_fasta() (in module relag.utils) RealFingerprint (class in relag.utils) relag.kernels module relag.kernels.alignments module relag.kernels.molecules module relag.kernels.protspam module relag.kernels.structures module

relag.kernels.vectors module relag.utils module return (relag.core.CsrGraph attribute) (relag.core.EdgeStore attribute) (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) (relag.utils.BitFingerprint attribute) (relag.utils.PdbStructure attribute) (relag.utils.RealFingerprint attribute) (relag.utils.SWPattern attribute) (relag.utils.SWPatternSet attribute) (relag.utils.SWSequence attribute) (relag.utils.Vector attribute)

S

Sat (relag.kernels.alignments.DatatypeWidth attribute) save() (relag.core.EdgeStore method) (relag.core.HNSWIndex method) (relag.core.HNSWState method) (relag.utils.SWPatternSet method) Scan (relag.kernels.alignments.VectorizationStrategy attribute) ScoringMatrix (class in relag.kernels.alignments) search() (relag.core.HNSWState method) seq() (relag.utils.SWSequence method) Short (relag.kernels.alignments.DatatypeWidth attribute) ShorterSeq (relag.kernels.alignments.CoverageMode attribute) shuffle (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

significance_threshold() (relag.kernels.protspam.ProtSpamKernel method) Similarity (relag.core.INWeightType attribute) SimilarityComplement (relag.core.INWeightType attribute) sorted_words() (relag.utils.SWSequence method) strength() (relag.core.CsrGraph method) strict_ef (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute) Striped (relag.kernels.alignments.VectorizationStrategy attribute) Structure (relag.kernels.KernelVariant attribute) subgraph() (relag.core.CsrGraph method) SWPattern (class in relag.utils) SWPatternSet (class in relag.utils) SWSequence (class in relag.utils) SWWord (class in relag.utils)

T

TanimotoBit (class in relag.kernels.molecules) (relag.kernels.KernelVariant attribute) TanimotoReal (class in relag.kernels.molecules) (relag.kernels.KernelVariant attribute) Target (relag.kernels.alignments.CoverageMode attribute) (relag.kernels.structures.NormMode attribute) threshold_based_neighbourhood (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

to_list() (relag.utils.BitFingerprint method) (relag.utils.RealFingerprint method) (relag.utils.Vector method) to_np() (relag.utils.BitFingerprint method) (relag.utils.RealFingerprint method) (relag.utils.Vector method) to_rdkit() (relag.utils.BitFingerprint method) (relag.utils.RealFingerprint method)

U

Unweighted (relag.core.INWeightType attribute) USAlignKernel (class in relag.kernels.structures)

use_heuristic (relag.core.HNSWConfig attribute) (relag.core.HNSWState attribute)

V

values (relag.utils.Vector attribute) variant (relag.core.HNSWState attribute)

Vector (class in relag.utils) VectorizationStrategy (class in relag.kernels.alignments)

W

weight (relag.utils.SWPatternSet attribute)

weight() (relag.utils.SWPattern method) with_limit() (relag.utils.SWPatternSet static method)

Z

zip_kernel() (in module relag.kernels)