Reactions

class hippo.reaction.Reaction(db: Database, id: int, type: str, product: int, product_yield: float)[source]

A Reaction is a simplified representation of a synthetic pathway to create a product Compound. Reactants (also Compound objects) as well as a reaction type are required.

Attention

Reaction objects should not be created directly. Instead use HIPPO.register_reaction() or HIPPO.reactions()

Reaction initialisation

self == other: int | Reaction → bool[source]: compare this reaction to a Reaction object or ID

hash(self) → int[source]: Integer hash from ID

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted string representation

check_chemistry(debug: bool = False) → bool[source]

Sanity check the chemistry of this reaction

Parameters:: debug – increase verbosity (Default value = False)

check_reactant_availability(supplier: None | str = None, debug: bool = False) → bool[source]

Check the availability of reactant compounds

Parameters:

supplier – Limit to quotes from this supplier (Default value = None)
debug – increase verbosity (Default value = False)

property db: Database: Returns a pointer to the parent database

draw() → None[source]: Draw the molecules involved in this reaction

get_dict(smiles: bool = True, mols: bool = True) → dict[str][source]

Returns a dictionary representing this Reaction

Parameters:

smiles – include smiles string (Default value = True)
mols – include rdkit.Chem.Mol (Default value = True)

get_reactant_amount_pairs(compound_object: bool = True) → list[tuple][source]

Returns pairs of reactants and their amounts

Parameters:: compound_object – return Compound object instead of ID, (Default value = True)
Returns:: list of tuples containing Compound ID/object and amount in mg

get_reactant_ids() → list[int][source]

Returns list of reactants Compound IDs

Returns:: list of Compound IDs

get_recipes(amount: float = 1, debug: bool = False, pick_cheapest: bool = False, permitted_reactions: None | ReactionSet = None, supplier: str | None = None) → Recipe | list[Recipe][source]

Get a Recipe describing how to make the product

Parameters:

amount – Amount in mg, defaults to 1
debug – Increase verbosity, (Default value = False)
pick_cheapest – pick the cheapest Recipe, (Default value = False)
permitted_reactions – Limit the reactions to consider to members of this set, (Default value = None)
supplier – Limit to reactants from this supplier (Default value = None)

Returns:

Recipe object or list thereof

property id: int: Returns the Reaction ID

property metadata: MetaData: Returns the compound’s metadata dict

property plain_repr: str: Unformatted long string representation

property price_estimate: float: Estimate the price of this Reaction

property product: Compound: Returns the reaction’s product Compound

property product_id: int: Returns the product Compound ID

property product_mol: Product Compound rdkit.Chem.Mol object

property product_smiles: str: Product Compound SMILES string

property product_yield: float: Returns the reaction’s product yield (fraction)

property reactant_ids: set[int]: Returns a set of reactant ID’s

property reactant_mols: List of reactant Compound rdkit.Chem.Mol object

property reactant_smiles: list[str]: List of reactant Compound SMILES strings

property reactant_str_ids: str: Return an SQL formatted tuple string of the reactant Compound IDs

property reactants: CompoundSet: Returns a CompoundSet of the reactants

property reaction_str: str: Returns a string representing the reaction

summary(draw: bool = True) → None[source]

Print a summary of this reaction’s information

Parameters:: draw – draw the reaction compounds (Default value = True)

property type: str: Returns the Reaction tyoe

class hippo.rset.ReactionSet(db: Database, indices: list = None, *, sort: bool = True, name: str | None = None)[source]

Object representing a subset of the ‘reaction’ table in the Database.

Attention

ReactionSet objects should not be created directly. Instead use the HIPPO.reactions() property. See Getting started with HIPPO and insert_elaborations.

Use as an iterable

Iterate through Reaction objects in the set:

rset = animal.reactions[:100]

for reaction in rset:
        ...

Check membership

To determine if a Reaction is present in the set:

is_member = reaction in cset

Selecting compounds in the set

The ReactionSet can be indexed like standard Python lists by their indices

rset = animal.reactions[1:100]

# indexing individual compounds
reaction = rset[0]  # get the first reaction
reaction = rset[1]  # get the second reaction
reaction = rset[-1] # get the last reaction

# getting a subset of compounds using a slice
rset2 = rset[13:18] # using a slice

ReactionSet initialisation

self + other: ReactionSet → ReactionSet[source]: Add a ReactionSet to this one

self[key] → Reaction | ReactionSet[source]: Get member Reaction object by single, slice or list/set/tuple of ID

iter(self)[source]: Iterate through member Reaction objects

len(self) → int[source]: Number of member Reaction objects

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted string representation

add(r: Reaction) → None[source]

Add a Reaction to this set

Parameters:: r – Reaction to be added

copy() → ReactionSet[source]: Return a copy of this set

property db: Database: Returns the associated Database

get_df(smiles=True, mols=True, **kwargs) → pandas.DataFrame[source]

Construct a pandas.DataFrame of this ReactionSet

Parameters:

smiles – Include smiles column (Default value = True)
mols – Include rdkit.Chem.Mol column (Default value = True)
kwargs – keyword arguments are passed on to :meth:`.Reaction.get_dict:

get_dict() → dict[str][source]: Serializable dictionary

get_recipes(amounts: float | list[float] = 1.0, **kwargs) → Recipe | list[Recipe][source]

Get the Recipe object(s) from this set of recipes

Parameters:

amounts – float or list/generator of product amounts in mg, (Default value = 1.0)
kwargs – keyword arguments are passed on to :meth:`.Recipe.from_reactions:

property ids: list[int]: Returns the ids of reactions in this set

property indices: list[int]: Returns the ids of reactions in this set

interactive()[source]: Creates a ipywidget to interactively navigate this PoseSet.

property intermediates: CompoundSet: Get all intermediate compounds that can be synthesised with these reactions

property name: str | None: Returns the name of set

property num_types: int: Returns the number of reaction types in this set

property products: CompoundSet: Get all product compounds that can be synthesised with these reactions (no intermediates)

property reactants: CompoundSet: Get all reactant compounds that are used by these reactions

reverse() → None[source]: In-place reversal of indices

property str_ids: str: Return an SQL formatted tuple string of the Compound IDs

summary() → None[source]: Print a summary of the Reactions

property table: str: Returns the name of the Database table

property types: list[str]: Returns the types of reactions in this set