rdmc.reaction#

Module for Reaction

class rdmc.reaction.Reaction(reactant: List[RDKitMol] | RDKitMol, product: List[RDKitMol] | RDKitMol, ts: RDKitMol | None = None)#

Bases: object

The Reaction class that stores the reactant, product, and transition state information.

property active_atoms#
property active_bonds#
apply_resonance_correction(inplace: bool = True) → Reaction#

Apply resonance correction to the reactant and product complexes.

bond_analysis()#

Perform bond analysis on the reaction.

property broken_bonds#
property changed_bonds#
draw_2d(figsize: Tuple[int, int] = (800, 300), font_scale: float = 1.0, highlight_by_reactant: bool = True) → str#

This is a modified version of the drawReaction2D function in RDKit.

Parameters:

  • font_scale (float, optional) – The font scale for the atom map number. Defaults to 1.0.

  • highlightByReactant (bool, optional) – Whether to highlight the reactant(s) or product(s). Defaults to True.

Returns:

str – The SVG string. To display the SVG, use IPython.display.SVG(svg_string).

draw_3d(**kwargs)#

Display the reaction in 3D.

property formed_bonds#
classmethod from_reactant_and_product_smiles(rsmi: List[str] | str, psmi: List[str] | str)#

Initialize the Reaction class from reactant and product smile(s).

Args:

classmethod from_reaction_smiles(smiles: str)#

Initialize the Reaction class from reaction SMILES.

Parameters:

smiles (str) – The reaction SMILES.

Returns:

Reaction – The Reaction class.

get_fingerprint(mode: str = 'REAC_DIFF', fp_type: str = 'morgan', count: bool = False, num_bits: int = 2048, **kwargs) → np.array#

Get the fingerprint of the reaction.

Parameters:

  • mode (str) – The fingerprint combination of 'REAC' (reactant), 'PROD' (product), 'DIFF' (reactant - product), 'REVD' (product - reactant), 'SUM' (reactant + product), separated by '_'. Defaults to REAC_DIFF, with the fingerprint to be a concatenation of reactant fingerprint and the difference between the reactant complex and the product complex.

  • fp_type (str, optional) – The type of fingerprint to generate. Options are: 'atom_pair', 'morgan' (default), 'rdkit', 'topological_torsion', 'avalon', and 'maccs'.

  • num_bits (int, optional) – The length of the molecular fingerprint. For a mode with N blocks, the eventual length is num_bits * N. Default is 2048. It has no effect on 'maccs' generator.

  • dtype (str, optional) – The data type of the output numpy array. Defaults to 'int32'.

get_reverse_reaction()#

Get the reverse reaction.

has_same_products(other: Reaction, resonance: bool = False) → bool#

Check if the reaction has the same products as the other reaction.

Parameters:

other (Reaction) – The other reaction to compare.

Returns:

bool – Whether the reaction has the same products as the other reaction.

has_same_reactants(other: Reaction, resonance: bool = False) → bool#

Check if the reaction has the same reactants as the other reaction.

Parameters:

other (Reaction) – The other reaction to compare.

Returns:

bool – Whether the reaction has the same reactants as the other reaction.

init_reactant_product(reactant: List[RDKitMol] | RDKitMol, product: List[RDKitMol] | RDKitMol)#
property involved_atoms#
property involved_bonds#
property is_charge_balanced: bool#

Whether the charge in the reactant(s) and product(s) are balanced.

property is_element_balanced: bool#

Whether the elements in the reactant(s) and product(s) are balanced.

is_equivalent(reaction: Reaction, resonance: bool = False, both_directions: bool = False) → bool#

Check if the reaction is equivalent to the given reaction.

Parameters:

  • reaction (Reaction) – The reaction to compare.

  • resonance (bool, optional) – Whether to consider resonance structures. Defaults to False.

  • both_directions (bool, optional) – Whether to check both directions. Defaults to False.

Returns:

bool – Whether the reaction is equivalent to the given reaction.

property is_mult_equal: bool#

Whether the spin multiplicity in the reactant(s) and product(s) are equal.

property is_num_atoms_balanced: bool#

Whether the number of atoms in the reactant(s) and product(s) are balanced.

property is_resonance_corrected: bool#

Whether the reaction is resonance corrected.

is_same_products(products: List[RDKitMol] | RDKitMol, resonance: bool = False)#

Check if the reaction has the same products as the given products or product complex.

Parameters:

  • product (Union[List[RDKitMol], RDKitMol]) – The products or product complex to compare.

  • resonance (bool, optional) – Whether to consider resonance structures. Defaults to False.

Returns:

bool – Whether the reaction has the same products as the given products or product complex.

is_same_reactants(reactants: List[RDKitMol] | RDKitMol, resonance: bool = False) → bool#

Check if the reaction has the same reactants as the given reactants or reactant complex.

Parameters:

  • reactant (Union[List[RDKitMol], RDKitMol]) – The reactants or reactant complex to compare.

  • resonance (bool, optional) – Whether to consider resonance structures. Defaults to False.

Returns:

bool – Whether the reaction has the same reactants as the given reactants or reactant complex.

make_ts()#

Make the transition state of the reaction based on the reactant and product. This method assumes that the reactant complex and product complex are atom-mapped already.

map_h_atoms(add_hs: bool = False) → Reaction#

Atom map H atoms. This is useful if the reactions are initialized with only heavy atoms or the reactant and product complex only has heavy atom mapped.

Parameters:

add_hs (bool, optional) – If the reaction is initialized with only heavy atoms presenting, set it to True. Defaults to False.

Returns:

Reaction – a new reaction instance with h atoms mapped.

property num_atoms: bool#

The number of atoms involved in the reactant(s) and product(s).

property num_broken_bonds#
property num_changed_bonds#
property num_formed_bonds#
property num_heavy_atoms: bool#

The number of heavy atoms involved in the reaction.

property num_products: int#

The number of products.

property num_reactants: int#

The number of reactants.

property product_element_count: dict#

The element count in the reactant(s) and product(s).

property reactant_element_count: dict#

The element count in the reactant(s) and product(s).

require_bond_analysis()#

Timer decorator for recording the time of a function.

Parameters:

func (function) – The function to be decorated.

Returns:

function – The decorated function.

to_rdkit_reaction() → ChemicalReaction#

Convert the reaction to RDKit ChemicalReaction.

to_smiles(remove_hs: bool = False, remove_atom_map: bool = False, **kwargs) → str#

Convert the reaction to reaction SMILES.

property ts#

The transition state of the reaction.

rdmc.reaction.is_equivalent_reaction(rxn1: Reaction, rxn2: Reaction) → bool#

If two reactions has equivalent transformation regardless of atom mapping. This can be useful when filtering out duplicate reactions that are generated from different atom mapping.

Parameters:

  • rxn1 (Reaction) – The first reaction.

  • rxn2 (Reaction) – The second reaction.

Returns:

bool – Whether the two reactions are equivalent.