When to Use

Convert drug name to molecular structure (SMILES, SDF)
Find similar compounds for lead optimization
Query bioactivity data against protein targets
Get compounds active in specific assays

Workflow

Use Case 1: Name/ID to Structure

from open_biomed.tools.tool_registry import TOOLS

tool = TOOLS["molecule_name_request"]
molecules, _ = tool.run("aspirin")
mol = molecules[0]
print(f"SMILES: {mol.smiles}")

Use Case 2: Similarity Search

from open_biomed.data import Molecule

query = Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O")  # aspirin
tool = TOOLS["molecule_structure_request"]
molecules, _ = tool.run(molecule=query, threshold=0.85, max_records=10)
for mol in molecules:
    print(mol.smiles)

Query PubChem database for drug discovery and chemistry applications.

When to Use

Convert drug name to molecular structure (SMILES, SDF)
Find similar compounds for lead optimization
Query bioactivity data against protein targets
Get compounds active in specific assays

Workflow

Use Case 1: Name/ID to Structure

from open_biomed.tools.tool_registry import TOOLS

tool = TOOLS["molecule_name_request"]
molecules, _ = tool.run("aspirin")
mol = molecules[0]
print(f"SMILES: {mol.smiles}")

Use Case 2: Similarity Search

from open_biomed.data import Molecule

query = Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O")  # aspirin
tool = TOOLS["molecule_structure_request"]
molecules, _ = tool.run(molecule=query, threshold=0.85, max_records=10)
for mol in molecules:
    print(mol.smiles)

Query Type	Output
Name to Structure	`Molecule` object with SMILES, SDF file saved
Similarity Search	List of similar `Molecule` objects
Bioactivity (compound)	List of AIDs where compound was active/inactive
Bioactivity (assay)	List of CIDs active/inactive in the assay
Bioactivity (target)	List of AIDs targeting the gene

Similarity Threshold	Interpretation
> 0.90	Very similar, likely same scaffold
0.80-0.90	Similar, potential analogs
0.70-0.80	Moderately similar, scaffold hops possible

Error	Solution
Compound not found	Try alternative names or SMILES
No similar compounds	Lower threshold (min 0.70)
No bioactivity data	Compound may not be tested; try related compounds
Timeout	Reduce max_records or retry

Tool Name	Purpose
`molecule_name_request`	Name/CID to structure
`molecule_structure_request`	Similarity search
`pubchem_bioactivity`	Bioactivity queries

Pubchem Query

When to Use

Workflow

Use Case 1: Name/ID to Structure

Use Case 2: Similarity Search

Pubchem Query

When to Use

Workflow

Use Case 1: Name/ID to Structure

Use Case 2: Similarity Search

Use Case 3: Bioactivity Query

Expected Outputs

Score Interpretation

Error Handling

Available Tools

Healthcare Cdss Patterns

Drug Discovery

Qmd

Attack Tree Construction

Azure Ai Anomalydetector Java

Viboscope