aizynthfinder.context.stock package¶

Submodules¶

aizynthfinder.context.stock.queries module¶

Module containing classes that interfaces different stocks query classes

class aizynthfinder.context.stock.queries.StockQueryMixin¶

Bases: object

Mixin class for all query classes, providing a default interface to some methods that might not be possible to implement for each query class.

amount(mol)¶

Returns the maximum amount of the molecule in stock

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Raises: StockException – if the amount cannot be computed
Returns: the amount
Return type: float

availability_string(mol)¶

Returns the sources of the molecule

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Raises: StockException – if the string cannot be computed
Returns: a comma-separated list of sources
Return type: str

cached_search(mol)¶

Finds the entries of the molecule in the stock and cache them if necessary.

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Returns: if the molecule is in stock
Return type: bool

clear_cache()¶

Clear the internal search cache if available

Return type: None

price(mol)¶

Returns the minimum price of the molecule in stock

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Raises: StockException – if the price cannot be computed
Return type: float

class aizynthfinder.context.stock.queries.InMemoryInchiKeyQuery(path, inchi_key_col='inchi_key', price_col=None)¶

Bases: aizynthfinder.context.stock.queries.StockQueryMixin

A stock query class that is based on an in-memory list of pre-computed inchi-keys.

This list can be instantiated from

A Pandas dataframe in HDF5 or CSV format
A text file with an inchi key on each row

The dataframe must have a column with InChIkeys that by default is “inchi_key”. The HDF5 file must have a dataset called “table”.

If the source is a dataframe, then optionally it can contain prices and this columns can be specified with the “price_column” argument.

Parameters

path (str) – the path to the file with inchi-keys
inchi_key_col (str) – the name of the column of the InChI keys
path –
inchi_key_col –
price_col (Optional[str]) –

Paramater price_col

the name of the column with the optional prices

Return type

None

property stock_inchikeys: Set[str]¶: Return the InChiKeys in this stock

price(mol)¶

Returns the minimum price of the molecule in stock

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Raises: StockException – if the price cannot be computed
Return type: float

class aizynthfinder.context.stock.queries.MongoDbInchiKeyQuery(host=None, database='stock_db', collection='molecules')¶

Bases: aizynthfinder.context.stock.queries.StockQueryMixin

A stock query class that is looking up inchi keys in a Mongo database.

The documents in the database collection should have at least 2 fields:

inchi_key: the inchi key of the molecule
source: the original source of the molecule

Variables

client – the Mongo client
database – the database instance
molecules – the collection of documents

Parameters

host (Optional[str]) – the database host, defaults to None
database (str) – the database name, defaults to “stock_db”
collection (str) – the database collection, defaults to “molecules”
host –
database –
collection –

Return type

None

availability_string(mol)¶

Returns the sources of the molecule

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the query molecule
Raises: StockException – if the string cannot be computed
Returns: a comma-separated list of sources
Return type: str

class aizynthfinder.context.stock.queries.MolbloomFilterQuery(path, smiles_based=False)¶

Bases: aizynthfinder.context.stock.queries.StockQueryMixin

A stock query class that is based on an a molbloom filter for SMILES strings or InChI keys

Parameters

path (str) – the path to the saved bloom filter
smiles_based (bool) – if True will use SMILES for lookup instead of InChI keys
path –
smiles_based –

Return type

None

aizynthfinder.context.stock.stock module¶

Module containing classes that interfaces different stock classes

class aizynthfinder.context.stock.stock.Stock¶

Bases: aizynthfinder.context.collection.ContextCollection

A collection of molecules that are in stock

A molecule can be queried on the stock with:

my_mol = Molecule(smiles="CCO")
my_mol in stock

One can obtain individual stocks with:

sub_stock = stock["key"]

One can obtain the number of molecules in the selected stock with:

number_of_molecules = len(stock)

Return type: None

property stop_criteria: dict¶: Return a copy of the stop criteria used by the stock

amount(mol)¶

Calculate the maximum amount of a molecule in stock

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the molecule to query
Raises: StockException – if the amount could not be computed
Returns: the maximum amount
Return type: float

availability_list(mol)¶

Return a list of what stocks a given mol is available

If the molecule is not in stock it will return any empty list

Parameters: mol (Molecule) – The molecule to query
Returns: string with a list of stocks that mol was found in
Return type: List[str]

availability_string(mol)¶

Return a string of what stocks a given mol is available

If the molecule is not in stock it will return “Not in stock”

Parameters: mol (aizynthfinder.chem.mol.Molecule) – The molecule to query
Returns: string with a list of stocks that mol was found in
Return type: str

exclude(mol)¶

Exclude a molecule from the stock. When this molecule is queried it will return False, regardless if the molecule is in the stock.

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the molecule to exclude
Return type: None

load(source, key)¶

Add a pre-initialized stock query object to the stock

Parameters

source (aizynthfinder.context.stock.queries.StockQueryMixin) – the item to add
key (str) – The key that will be used to select the stock

Return type

None

load_from_config(**config)¶

Load one or more stock queries from a configuration

The key can be “stop_criteria” in case the config is given to the set_stop_criteria method

The format should be key:

type: name of the stock class or custom_package.custom_model.CustomClass path: path to the stock file other settings or params

or key: path_to_model

Parameters: config (Any) – the configuration
Return type: None

price(mol)¶

Calculate the minimum price of a molecule in stock

Parameters: mol (aizynthfinder.chem.mol.Molecule) – the molecule to query
Raises: StockException – if the price could not be computed
Returns: the minimum price
Return type: float

reset_exclusion_list()¶

Remove all molecules in the exclusion list

Return type: None

select(value, append=False)¶

Select one or more stock queries

Parameters

value (Union[str, List[str]]) – the key of the stocks to select
append (bool) – if True and value is a single key append it to the current selection

Return type

None

set_stop_criteria(criteria=None)¶

Set criteria that stop the search

The keys of the criteria can be “price” or “amount” which accepts numerical settings, or “counts” that should be dictionary of maximum allowed count for each atomic symbol.

Example:

criteria = {
    "price": 5,
    "amount": 100,
    "counts": {
        "C": 6,
        "O": 4
    }
}

Parameters: criteria (Optional[Dict]) – the criteria settings
Return type: None

smiles_in_stock(smiles)¶

Check if the SMILES is in the currently selected stocks

Parameters: smiles (str) – SMILES string (must be RDKit sanitizable)
Returns: if the SMILES was on stock
Return type: bool

Module contents¶

Sub-package containing stock routines

aizynthfinder

Navigation

Related Topics

aizynthfinder.context.stock package¶

Submodules¶

aizynthfinder.context.stock.queries module¶

aizynthfinder.context.stock.stock module¶

Module contents¶