"""
Rowan v2 API: Bond Dissociation Energy (BDE) Workflow
Calculate bond dissociation energies for molecular bonds.
"""
from typing import Annotated
import rowan
import stjames
import json
def submit_bde_workflow(
initial_molecule: Annotated[str, "SMILES string of the molecule for BDE calculations"],
optimize_fragments: Annotated[bool, "Whether to optimize the resulting fragments after bond cleavage"] = True,
atoms: Annotated[str, "JSON string list of atom indices to calculate BDEs for. Empty string for automatic selection"] = "",
fragment_indices: Annotated[str, "JSON string list of lists specifying fragment atom groups. Empty string for automatic"] = "",
all_CH: Annotated[bool, "Calculate BDEs for all C-H bonds in the molecule"] = False,
all_CX: Annotated[bool, "Calculate BDEs for all C-X bonds where X is any heavy atom"] = False,
name: Annotated[str, "Workflow name for identification and tracking"] = "BDE Workflow",
folder_uuid: Annotated[str, "UUID of folder to organize this workflow. Empty string uses default folder"] = "",
max_credits: Annotated[int, "Maximum credits to spend on this calculation. 0 for no limit"] = 0,
):
"""Submit a bond dissociation energy (BDE) workflow.
Args:
initial_molecule: SMILES string representing the molecule
optimize_fragments: Optimize fragment geometries after bond cleavage (default: True)
atoms: JSON string list of atom indices (0-based) to calculate BDEs for (default: automatic)
fragment_indices: JSON string list of lists defining fragment atom groups (default: automatic)
all_CH: Calculate BDEs for all C-H bonds (default: False)
all_CX: Calculate BDEs for all C-X bonds where X is a heavy atom (default: False)
name: Workflow name for identification and tracking
folder_uuid: UUID of folder to organize this workflow. Empty string uses default folder.
max_credits: Maximum credits to spend on this calculation. 0 for no limit.
Bond dissociation energy (BDE) measures the strength of chemical bonds and is crucial for
understanding reactivity, stability, and reaction mechanisms.
Returns:
Workflow object representing the submitted workflow
Examples:
# Calculate BDEs for all C-H bonds in butane
result = submit_bde_workflow(
initial_molecule="CCCC",
all_CH=True,
name="Butane BDE"
)
"""
import logging
logger = logging.getLogger(__name__)
# Build workflow_data
workflow_data = {
"mode": "rapid",
"optimize_fragments": optimize_fragments,
"all_CH": all_CH,
"all_CX": all_CX
}
# Parse atoms if provided
if atoms:
try:
parsed_atoms = json.loads(atoms)
workflow_data["atoms"] = parsed_atoms
except json.JSONDecodeError:
logger.warning(f"Invalid atoms JSON: {atoms}. Skipping atoms parameter.")
# Parse fragment_indices if provided
if fragment_indices:
try:
parsed_fragments = json.loads(fragment_indices)
workflow_data["fragment_indices"] = parsed_fragments
except json.JSONDecodeError:
logger.warning(f"Invalid fragment_indices JSON: {fragment_indices}. Skipping fragment_indices parameter.")
# Submit the workflow
logger.info(f"Submitting BDE workflow: {name}")
workflow = rowan.submit_workflow(
workflow_type="bde",
initial_molecule=stjames.Molecule.from_smiles(initial_molecule),
workflow_data=workflow_data,
name=name,
folder_uuid=folder_uuid if folder_uuid else None,
max_credits=max_credits if max_credits > 0 else None
)
# Make workflow publicly viewable
workflow.update(public=True)
logger.info(f"BDE workflow submitted with UUID: {workflow.uuid}")
return workflow
