Index

A

APICache (class in drugs.cache)

B

batch_similarity_matrix() (drugs.core.Drug static method)

C

chembl_bioactivities() (in module drugs.data_sources) chembl_id (drugs.core.Drug property) chembl_mechanisms() (in module drugs.data_sources)

chembl_molecules_by_inchikey() (in module drugs.data_sources) chembl_target_detail() (in module drugs.data_sources) chembl_to_pubchem_cid() (in module drugs.id_mapping) clear_expired() (drugs.cache.APICache method)

D

dedupe_preserve_order() (in module drugs.utils) default_embedding_path() (in module drugs.features.embeddings.path) Drug (class in drugs.core) drugs.cache module drugs.chemistry module drugs.core module drugs.data_sources module

drugs.features.embeddings.esm module drugs.features.embeddings.path module drugs.features.embeddings.text module drugs.id_mapping module drugs.utils module

E

esm_inputs() (drugs.core.Drug method)

F

fetch_chembl_bioactivities() (drugs.core.Drug method) fetch_chembl_mechanisms() (drugs.core.Drug method) fetch_drug_interactions() (drugs.core.Drug method) fetch_pubchem_properties() (drugs.core.Drug method) fetch_pubchem_text() (drugs.core.Drug method) fetch_target_details() (drugs.core.Drug method)

fetch_uniprot_sequence() (in module drugs.features.embeddings.esm) fingerprint_similarity() (in module drugs.chemistry) from_batch() (drugs.core.Drug class method) from_chembl_id() (drugs.core.Drug class method) from_inchikey() (drugs.core.Drug class method) from_pubchem_cid() (drugs.core.Drug class method)

G

get() (drugs.cache.APICache method)

get_default_cache() (in module drugs.cache) get_json() (in module drugs.utils)

I

inchikey (drugs.core.Drug property)

invalidate() (drugs.cache.APICache method)

L

lipinski_violations() (in module drugs.chemistry)

list_pubchem_text_headings() (in module drugs.core) (in module drugs.data_sources)

M

make_esm_embed_fn() (in module drugs.features.embeddings.esm) make_text_embed_fn() (in module drugs.features.embeddings.text) map_ids() (drugs.core.Drug method) max_chars_per_chunk (drugs.features.embeddings.text.TextEmbedConfig attribute) metadata (drugs.core.Drug attribute) model (drugs.features.embeddings.text.TextEmbedConfig attribute) module drugs.cache drugs.chemistry drugs.core drugs.data_sources drugs.features.embeddings.esm drugs.features.embeddings.path drugs.features.embeddings.text drugs.id_mapping drugs.utils

mol_from_smiles() (in module drugs.chemistry) molecular_fingerprint() (drugs.core.Drug method) (in module drugs.chemistry) molecular_properties() (drugs.core.Drug method)

N

normalize (drugs.features.embeddings.text.TextEmbedConfig attribute)

O

openai_api_key (drugs.features.embeddings.text.TextEmbedConfig attribute)

P

protein_embedding() (drugs.core.Drug method) protein_embedding_cached() (drugs.core.Drug method) provider (drugs.features.embeddings.text.TextEmbedConfig attribute) pubchem_cid (drugs.core.Drug property) pubchem_cid_from_inchikey() (in module drugs.id_mapping)

pubchem_cid_to_chembl() (in module drugs.id_mapping) pubchem_cid_to_inchikey() (in module drugs.id_mapping) pubchem_properties() (in module drugs.data_sources) pubchem_pug_view_record() (in module drugs.data_sources) pubchem_text_snippets() (in module drugs.data_sources)

R

rdkit_mol() (drugs.core.Drug method) rdkit_properties() (in module drugs.chemistry)

RDKitNotAvailable require_rdkit() (in module drugs.chemistry) rxnav_interactions() (in module drugs.data_sources)

S

selfies() (drugs.core.Drug method) SELFIESNotAvailable set() (drugs.cache.APICache method)

similarity_to() (drugs.core.Drug method) smiles() (drugs.core.Drug method) synonyms (drugs.core.Drug attribute) synthetic_accessibility() (in module drugs.chemistry)

T

target_accessions() (drugs.core.Drug method) target_gene_symbols() (drugs.core.Drug method) text_corpus() (drugs.core.Drug method)

text_embedding() (drugs.core.Drug method) text_embedding_cached() (drugs.core.Drug method) TextEmbedConfig (class in drugs.features.embeddings.text) to_selfies() (in module drugs.chemistry)

U

unichem_sources() (in module drugs.id_mapping)

unichem_src_id() (in module drugs.id_mapping)

V

voyage_api_key (drugs.features.embeddings.text.TextEmbedConfig attribute)

W

write_drug_markdown() (drugs.core.Drug method)