Chemeagle Guide

Chemistry Paper (PDF/text)
         ↓
   Document Parser Agent (section identification)
         ↓
   Chemical NER Agent
   ├── Compound names → SMILES/InChI
   ├── Reagents and catalysts
   ├── Solvents and conditions
   └── Product identification
         ↓
   Reaction Extraction Agent
   ├── Reactants → Products mapping
   ├── Reaction conditions (T, P, time)
   ├── Yields and selectivity
   └── Procedure steps
         ↓
   Validation Agent (cross-check extracted data)
         ↓
   Structured Output (JSON, CSV, database)

from chemeagle import ChemEagle

eagle = ChemEagle(llm_provider="anthropic")

# Extract from a chemistry paper
result = eagle.extract("paper.pdf")

# Extracted reactions
for rxn in result.reactions:
    print(f"\nReaction {rxn.id}:")
    print(f"  Reactants: {rxn.reactants}")
    print(f"  Products: {rxn.products}")
    print(f"  Catalyst: {rxn.catalyst}")
    print(f"  Solvent: {rxn.solvent}")
    print(f"  Temperature: {rxn.temperature}")
    print(f"  Time: {rxn.time}")
    print(f"  Yield: {rxn.yield_percent}%")
    print(f"  SMILES: {rxn.product_smiles}")

# Extracted compounds
for compound in result.compounds:
    print(f"{compound.name}: {compound.smiles}")

# Process multiple papers
results = eagle.extract_batch(
    input_dir="chemistry_papers/",
    output_format="csv",
    output_file="reactions_database.csv",
)

print(f"Papers processed: {results.papers_processed}")
print(f"Reactions extracted: {results.total_reactions}")
print(f"Unique compounds: {results.unique_compounds}")

# Standalone NER
entities = eagle.recognize_entities(
    "The Suzuki coupling of 4-bromoanisole with phenylboronic "
    "acid using Pd(PPh3)4 catalyst in THF/water at 80°C "
    "gave 4-methoxybiphenyl in 95% yield."
)

for entity in entities:
    print(f"  [{entity.type}] {entity.text}")
    if entity.smiles:
        print(f"    SMILES: {entity.smiles}")

# Output:
# [REACTANT] 4-bromoanisole — SMILES: COc1ccc(Br)cc1
# [REACTANT] phenylboronic acid — SMILES: OB(O)c1ccccc1
# [CATALYST] Pd(PPh3)4
# [SOLVENT] THF/water
# [CONDITION] 80°C
# [PRODUCT] 4-methoxybiphenyl — SMILES: COc1ccc(-c2ccccc2)cc1
# [YIELD] 95%

# Build a searchable reaction database
from chemeagle import ReactionDatabase

db = ReactionDatabase("reactions.db")

# Add extracted reactions
db.add_from_extraction(result)

# Search by substrate
hits = db.search(reactant="bromoanisole", reaction_type="coupling")
for hit in hits:
    print(f"{hit.reactants} → {hit.products} ({hit.yield_percent}%)")
    print(f"  Source: {hit.paper_doi}")

# Search by conditions
hits = db.search(catalyst="palladium", temperature_max=100)

# Export
db.export_csv("all_reactions.csv")
db.export_json("all_reactions.json")