Query a molecule's biochemical significance and roles in biology and chemistry using BioT5 multi-modal model. Use this skill when: (1) Understanding a molecule's biological roles and functions, (2) Describing a molecule's chemical significance and applications, (3) Getting natural language explanations of molecular properties, (4) Summarizing what a molecule is used for or its metabolic relevance.
Query a molecule's biochemical significance using BioT5 multi-modal model.
Create molecule from SMILES string.
from open_biomed.data import Molecule
molecule = Molecule.from_smiles("CCCCCCCc1ccco1") # Heptylfuran
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
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)
| Output | Description |
|---|---|
| Natural language text | Description of biochemical roles, applications, and significance |
| Molecule | Output |
|---|---|
CCCCCCCc1ccco1 (heptylfuran) | "flavouring agent; fragrance; metabolite" |
CC(=O)OC1=CC=CC=C1C(=O)O (aspirin) | "analgesic; anti-inflammatory; antipyretic" |
./checkpoints/server/molecule_question_answering_biot5.ckpt| 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 |
examples/basic_example.py - Complete runnable examplereferences/custom_questions.md - Other question templates