Bond Dissociation Energy

BDE workflow - Bond Dissociation Energy calculations.

BDEEntry dataclass

BDEEntry(
    fragment_idxs: tuple[int, ...], energy: float | None = None
)

A bond dissociation energy result.

BDEResult dataclass

BDEResult(
    workflow_data: dict[str, Any],
    workflow_type: str,
    workflow_uuid: str,
    complete: bool = True,
)

Bases: WorkflowResult

Result from a Bond-Dissociation Energy (BDE) workflow.

energy property

energy: float | None

Energy of the molecule (Hartree).

bdes property

bdes: list[BDEEntry]

Bond dissociation energies.

submit_bde_workflow

submit_bde_workflow(
    initial_molecule: StructureInput,
    mode: str = "omol25_conserving_s",
    multistage_opt_settings: MultiStageOptSettings | None = None,
    fragment_indices: list[list[int]] | None = None,
    all_CH: bool = False,
    all_CX: bool = False,
    name: str = "BDE Workflow",
    folder_uuid: str | None = None,
    folder: Folder | None = None,
    max_credits: int | None = None,
    webhook_url: str | None = None,
    is_draft: bool = False,
) -> Workflow

Submits a Bond-Dissociation Energy (BDE) workflow to the API.

Parameters:

Name	Type	Description	Default
initial_molecule	StructureInput	Molecule to calculate BDEs for.	required
mode	str	Level of theory to run the calculation at, given as a method string: - omol25_conserving_s — neural network potential (default) - g_xtb//gfn2_xtb — semiempirical - r2scan3c//gfn2_xtb — DFT single point on a semiempirical geometry	'omol25_conserving_s'
multistage_opt_settings	MultiStageOptSettings | None	Explicit method sequence to use instead of the one mode would pick — the optimization stage(s) followed by a final singlepoint, given as a MultiStageOptSettings. When omitted, the sequence is built automatically from mode. When supplied, it replaces that sequence.	None
fragment_indices	list[list[int]] | None	1-indexed atoms of each fragment to dissociate. Each fragment must connect to the rest of the molecule by a single bond.	None
all_CH	bool	Whether to dissociate all C-H bonds.	False
all_CX	bool	Whether to dissociate all C-X bonds (X = halogen).	False
name	str	Name of the workflow.	'BDE Workflow'
folder_uuid	str | None	UUID of the folder to place the workflow in.	None
folder	Folder | None	Folder object to store the workflow in.	None
max_credits	int | None	Maximum number of credits to use for the workflow.	None
webhook_url	str | None	URL that Rowan will POST to when the workflow completes.	None
is_draft	bool	If True, submit the workflow as a draft without starting execution.	False

Returns:

Type	Description
Workflow	Workflow object representing the submitted workflow.

Raises:

Type	Description
requests.HTTPError	if the request to the API fails.

find_ch_bonds

find_ch_bonds(
    molecule: StructureInput, distance_max: float = 1.2
) -> list[tuple[int, int]]

Find all C-H bonds in a molecule.

Parameters:

Name	Type	Description	Default
molecule	StructureInput	Molecule to search (Molecule, stjames.Molecule, or dict).	required
distance_max	float	Maximum C-H distance to consider a bond (A).	1.2

Returns:

Type	Description
list[tuple[int, int]]	List of (carbon_index, hydrogen_index) tuples (1-based indices). Example:: mol = Molecule.from_smiles("CCO") # ethanol bonds = find_ch_bonds(mol) # [(1, 4), (1, 5), (1, 6), (2, 7), (2, 8)]

find_cx_bonds

find_cx_bonds(molecule: StructureInput) -> list[tuple[int, int]]

Find all C-X bonds in a molecule (X = F, Cl, Br, I, At, Ts).

Parameters:

Name	Type	Description	Default
molecule	StructureInput	Molecule to search (Molecule, stjames.Molecule, or dict).	required

Returns:

Type	Description
list[tuple[int, int]]	List of (carbon_index, halogen_index) tuples (1-based indices). Example:: mol = Molecule.from_smiles("CCCl") # chloroethane bonds = find_cx_bonds(mol) # [(2, 3)]

find_bonds

find_bonds(
    molecule: StructureInput,
    element_a: int,
    element_b: int,
    distance_max: float,
) -> list[tuple[int, int]]

Find all bonds between two element types in a molecule.

Parameters:

Name	Type	Description	Default
molecule	StructureInput	Molecule to search (Molecule, stjames.Molecule, or dict).	required
element_a	int	Atomic number of first element.	required
element_b	int	Atomic number of second element.	required
distance_max	float	Maximum distance to consider a bond (A).	required

Returns:

Type	Description
list[tuple[int, int]]	List of (atom_a_index, atom_b_index) tuples (1-based indices). Example:: mol = Molecule.from_smiles("O") # water bonds = find_bonds(mol, 8, 1, 1.1) # O-H bonds # [(1, 2), (1, 3)]