PubChmAPI 0.0.45

Simplifies interaction with the PubChem database via PUG-REST API.

PubChmAPI Library

Overview

Introduction

The PubChmAPI Python package simplifies interaction with the PubChem database via the PUG-REST API. Unlike traditional wrappers with hard-coded functions, PubChmAPI uses dynamic metaprogramming to generate endpoints, ensuring full coverage of the PubChem schema. It handles URL generation, automatic batching, and throttling to provide a seamless data retrieval experience.

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Naming Convention

Functions in PubChmAPI follow a strict semantic naming convention to eliminate ambiguity:

domain_identifier_get_operation_option

• Domain: The primary database being queried (e.g., compound, substance, assay, gene).
• Identifier: The input type provided (e.g., cid, name, smiles, geneid).
• Operation: The specific data to retrieve (e.g., properties, aids, synonyms).
• Option (Optional): Filters or variants (e.g., active, inactive, 2d).

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Functions

Compound Property Functions (By Name)

Retrieve calculated properties using a compound name (e.g., "Aspirin"). Format: compound_name_get_[Property](identifier)

• compound_name_get_Title(identifier)
• compound_name_get_MolecularFormula(identifier)
• compound_name_get_MolecularWeight(identifier)
• compound_name_get_CanonicalSMILES(identifier)
• compound_name_get_IsomericSMILES(identifier)
• compound_name_get_InChI(identifier)
• compound_name_get_InChIKey(identifier)
• compound_name_get_IUPACName(identifier)
• compound_name_get_XLogP(identifier)
• compound_name_get_ExactMass(identifier)
• compound_name_get_MonoisotopicMass(identifier)
• compound_name_get_TPSA(identifier)
• compound_name_get_Complexity(identifier)
• compound_name_get_Charge(identifier)
• compound_name_get_HBondDonorCount(identifier)
• compound_name_get_HBondAcceptorCount(identifier)
• compound_name_get_RotatableBondCount(identifier)
• compound_name_get_HeavyAtomCount(identifier)
• compound_name_get_IsotopeAtomCount(identifier)
• compound_name_get_AtomStereoCount(identifier)
• compound_name_get_DefinedAtomStereoCount(identifier)
• compound_name_get_UndefinedAtomStereoCount(identifier)
• compound_name_get_BondStereoCount(identifier)
• compound_name_get_DefinedBondStereoCount(identifier)
• compound_name_get_UndefinedBondStereoCount(identifier)
• compound_name_get_CovalentUnitCount(identifier)
• compound_name_get_Volume3D(identifier)
• compound_name_get_ConformerModelRMSD3D(identifier)
• compound_name_get_EffectiveRotorCount3D(identifier)
• compound_name_get_ConformerCount3D(identifier)
• compound_name_get_Fingerprint2D(identifier)
• compound_name_get_FeatureCount3D(identifier)
• compound_name_get_FeatureAcceptorCount3D(identifier)
• compound_name_get_FeatureDonorCount3D(identifier)
• compound_name_get_FeatureAnionCount3D(identifier)
• compound_name_get_FeatureCationCount3D(identifier)
• compound_name_get_FeatureRingCount3D(identifier)
• compound_name_get_FeatureHydrophobeCount3D(identifier)
• compound_name_get_XStericQuadrupole3D(identifier)
• compound_name_get_YStericQuadrupole3D(identifier)
• compound_name_get_ZStericQuadrupole3D(identifier)

Compound CID Functions

Retrieve data using a Compound Identifier (CID). Format: compound_cid_get_[Operation](identifier)

General & Conversion

• compound_cid_get_description(identifier)
• compound_cid_get_synonyms(identifier)
• compound_cid_get_sids(identifier) (Get Substance IDs)
• compound_cid_get_cids(identifier) (Self-retrieval/Verification)
• compound_cid_get_conformers(identifier)

Images

• compound_cid_get_png(identifier) (Default)
• compound_cid_get_png_2d(identifier)
• compound_cid_get_png_3d(identifier)

Assays (Biological Activity)

• compound_cid_get_aids(identifier) (All associated Assays)
• compound_cid_get_aids_active(identifier) (Only Active Assays)
• compound_cid_get_aids_inactive(identifier) (Only Inactive Assays)
• compound_cid_get_assaysummary(identifier)

Structural & Isotopic Variants

• compound_cid_get_cids_same_isotopes(identifier)
• compound_cid_get_cids_same_connectivity(identifier)
• compound_cid_get_cids_same_tautomer(identifier)
• compound_cid_get_cids_same_stereo(identifier)
• compound_cid_get_cids_parent(identifier)
• compound_cid_get_cids_original(identifier)
• compound_cid_get_cids_component(identifier)
• compound_cid_get_cids_preferred(identifier)

Properties (Batch)

• compound_cid_get_all_properties(identifier) (Retrieves all properties as CSV)
• compound_cid_get_properties(identifier, properties=[...]) (Retrieve specific list)

Note: All single property functions listed under "Compound Name" are also available for CIDs (e.g., compound_cid_get_MolecularWeight).

Structural Search Functions

Retrieve CIDs based on structural similarity or substructures. Format: compound_[Method]_[InputType]_get_cids(identifier)

• compound_fastsimilarity_2d_cid_get_cids(cid)
• compound_fastsubstructure_smiles_get_cids(smiles)
• compound_fastidentity_smiles_get_cids(smiles)
• compound_similarity_3d_cid_get_cids(cid)

Biological Domain Functions

Retrieve data related to proteins, genes, taxonomy, and cell lines.

Protein Functions

Format: protein_[Identifier]_get_[Operation]

• protein_accession_get_summary(accession)
• protein_accession_get_aids(accession)
• protein_gi_get_summary(gi)
• protein_synonym_get_aids(synonym)

Gene Functions

Format: gene_[Identifier]_get_[Operation]

• gene_geneid_get_summary(geneid)
• gene_geneid_get_aids(geneid)
• gene_genesymbol_get_summary(symbol)
• gene_genesymbol_get_aids(symbol)

Taxonomy Functions

Format: taxonomy_[Identifier]_get_[Operation]

• taxonomy_taxid_get_summary(taxid)
• taxonomy_taxid_get_aids(taxid)
• taxonomy_synonym_get_aids(synonym)

Cell Line Functions

Format: cell_[Identifier]_get_[Operation]

• cell_cellacc_get_summary(cellacc)
• cell_cellacc_get_aids(cellacc)
• cell_synonym_get_summary(synonym)

Ahmed Alhilal

0.0.42 (12/12/2025)

• First Release