Molecule Biochemical Significance Query

Query a molecule's biochemical significance using BioT5 multi-modal model.

When to Use

• User asks about a molecule's biological roles or functions
• User wants to understand what a molecule is used for
• User requests natural language description of molecular properties
• User asks about a molecule's metabolic or chemical significance

Workflow

Step 1: Create Molecule

Create molecule from SMILES string.

from open_biomed.data import Molecule
molecule = Molecule.from_smiles("CCCCCCCc1ccco1")  # Heptylfuran

Step 2: Ask About Biochemical Significance

Use the molecule_question_answering tool with the default question.

from open_biomed.data import Text
from open_biomed.tools.tool_registry import TOOLS

qa_tool = TOOLS["molecule_question_answering"]
question = Text.from_str(
    "I am interested in understanding the molecule biochemical significance; "
    "can you describe its roles in biology and chemistry?"
)
outputs, _ = qa_tool.run(molecule=molecule, text=question)
print(outputs[0])  # Natural language answer

Alternative: Get Molecule by Name

If you have a molecule name instead of SMILES:

from open_biomed.tools.tool_registry import TOOLS

# Get molecule from name
name_tool = TOOLS["molecule_name_request"]
molecules, _ = name_tool.run("aspirin")
molecule = molecules[0]

# Then proceed with QA
qa_tool = TOOLS["molecule_question_answering"]
question = Text.from_str(
    "I am interested in understanding the molecule biochemical significance; "
    "can you describe its roles in biology and chemistry?"
)
outputs, _ = qa_tool.run(molecule=molecule, text=question)

Expected Outputs

Output	Description
Natural language text	Description of biochemical roles, applications, and significance

Example Outputs

Molecule	Output
CCCCCCCc1ccco1 (heptylfuran)	"flavouring agent; fragrance; metabolite"
CC(=O)OC1=CC=CC=C1C(=O)O (aspirin)	"analgesic; anti-inflammatory; antipyretic"

Model Details

• Model: BioT5
• Checkpoint: ./checkpoints/server/molecule_question_answering_biot5.ckpt
• Device: CUDA (default: cuda:0)

Error Handling

Error	Solution
Checkpoint not found	Ensure ./checkpoints/server/molecule_question_answering_biot5.ckpt exists
Invalid SMILES	Validate SMILES format or use molecule name lookup
CUDA out of memory	Set device to "cpu" in the tool configuration

See Also

• examples/basic_example.py - Complete runnable example
• references/custom_questions.md - Other question templates