aizynthfinder.utils package

Submodules

aizynthfinder.utils.exceptions module

Module containing custom exception classes

exception aizynthfinder.utils.exceptions.CostException

Bases: Exception

Exception raised by molecule cost classes

exception aizynthfinder.utils.exceptions.ExternalModelAPIError

Bases: Exception

Custom error type to signal failure in External model

exception aizynthfinder.utils.exceptions.MoleculeException

Bases: Exception

An exception that is raised by molecule class

exception aizynthfinder.utils.exceptions.NodeUnexpectedBehaviourException

Bases: Exception

Exception that is raised if the tree search is behaving unexpectedly.

exception aizynthfinder.utils.exceptions.PolicyException

Bases: Exception

An exception raised by policy classes

exception aizynthfinder.utils.exceptions.RejectionException

Bases: Exception

An exception raised if a retro action should be rejected

exception aizynthfinder.utils.exceptions.ScorerException

Bases: Exception

Exception raised by scoring classes

exception aizynthfinder.utils.exceptions.StockException

Bases: Exception

An exception raised by stock classes

exception aizynthfinder.utils.exceptions.TreeAnalysisException

Bases: Exception

Exception raised when analysing trees

aizynthfinder.utils.files module

Module containing routines to work with files and processes.

aizynthfinder.utils.files.read_datafile(filename)

Read aizynth output from disc in either .hdf5 or .json format

Parameters

filename (Union[str, Path]) – the path to the data

Returns

the loaded data

Return type

pd.DataFrame

aizynthfinder.utils.files.save_datafile(data, filename)

Save the given data to disc in either .hdf5 or .json format

Parameters

  • data (pd.DataFrame) – the data to save

  • filename (Union[str, Path]) – the path to the data

Return type

None

aizynthfinder.utils.files.cat_hdf_files(input_files, output_name, trees_name=None)

Concatenate hdf5 or json datafiles

Parameters

  • input_files (List[str]) –

  • output_name (str) –

  • trees_name (Optional[str]) –

Return type

None

aizynthfinder.utils.files.cat_datafiles(input_files, output_name, trees_name=None)

Concatenate hdf5 or json datafiles

if tree_name is given, will take out the trees column from the tables and save it to a gzipped-json file.

Parameters

  • input_files (List[str]) – the paths to the files to concatenate

  • output_name (str) – the name of the concatenated file

  • trees_name (Optional[str]) – the name of the concatenated trees

Return type

None

aizynthfinder.utils.files.split_file(filename, nparts)

Split the content of a text file into a given number of temporary files

Parameters

  • filename (str) – the path to the file to split

  • nparts (int) – the number of parts to create

Returns

list of filenames of the parts

Return type

List[str]

aizynthfinder.utils.files.start_processes(inputs, log_prefix, cmd_callback, poll_freq=5)

Start a number of background processes and wait for them to complete.

The standard output and standard error is saved to a log file.

The command to start for each process is given by the cmd_callback function that takes the index of the process and an item of the input as arguments.

Parameters

  • inputs (Sequence[Any]) – a sequence of input to the processes

  • log_prefix (str) – the prefix to the log file of each processes

  • cmd_callback (Callable) – function that creates the process commands

  • poll_freq (int) – the polling frequency for checking if processes are completed

Return type

None

aizynthfinder.utils.image module

This module contains a collection of routines to produce pretty images

aizynthfinder.utils.image.molecule_to_image(mol, frame_color, size=300)

Create a pretty image of a molecule, with a colored frame around it

Parameters

  • mol (Molecule) – the molecule

  • frame_color (PilColor) – the color of the frame

  • size (int) – the size of the image

Returns

the produced image

Return type

PilImage

aizynthfinder.utils.image.molecules_to_images(mols, frame_colors, size=300)

Create pretty images of molecules with a colored frame around each one of them.

The molecules will be resized to be of similar sizes.

Parameters

  • mols (Sequence[Molecule]) – the molecules

  • frame_colors (Sequence[PilColor]) – the color of the frame for each molecule

  • size (int) – the sub-image size

Returns

the produced images

Return type

List[PilImage]

aizynthfinder.utils.image.crop_image(img, margin=20)

Crop an image by removing white space around it

Parameters

  • img (PilImage) – the image to crop

  • margin (int) – padding, defaults to 20

Returns

the cropped image

Return type

PilImage

aizynthfinder.utils.image.draw_rounded_rectangle(img, color, arc_size=20)

Draw a rounded rectangle around an image

Parameters

  • img (PilImage) – the image to draw upon

  • color (PilColor) – the color of the rectangle

  • arc_size (int) – the size of the corner, defaults to 20

Returns

the new image

Return type

PilImage

aizynthfinder.utils.image.save_molecule_images(molecules, frame_colors, size=300)

Create images of a list of molecules and save them to disc a globally managed folder.

Parameters

  • molecules (Sequence[Molecule]) – the molecules to save as images

  • frame_colors (Sequence[PilColor]) – the color of the frame around each image

  • size (int) – the sub-image size for each molecule

Returns

the filename of the created images

Return type

Dict[Molecule, str]

aizynthfinder.utils.image.make_visjs_page(filename, molecules, reactions, edges, frame_colors, hierarchical=False)

Create HTML code of a bipartite graph of molecules and reactions using the vis.js network library.

Package the created HTML page and all images as tar-ball.

Parameters

  • filename (str) – the basename of the archive

  • molecules (Sequence[Molecule]) – the molecules nodes

  • reactions (Sequence[FixedRetroReaction]) – the reaction nodes

  • edges (Union[Sequence[Tuple[Any, Any]], nx.digraph.OutEdgeView]) – the edges of the graph

  • frame_colors (Sequence[PilColor]) – the color of the frame around each image

  • hierarchical (bool) – if True, will produce a hierarchical layout

Return type

None

class aizynthfinder.utils.image.RouteImageFactory(route, in_stock_colors=None, show_all=True, margin=100)

Bases: object

Factory class for drawing a route

Parameters

  • route (StrDict) – the dictionary representation of the route

  • in_stock_colors (FrameColors) – the colors around molecules, defaults to {True: “green”, False: “orange”}

  • show_all (bool) – if True, also show nodes that are marked as hidden

  • margin (int) – the margin between images

Return type

None

aizynthfinder.utils.loading module

Module containing routine to dynamically load a class from a specification

aizynthfinder.utils.loading.load_dynamic_class(name_spec, default_module=None, exception_cls=<class 'ValueError'>)

Load an object from a dynamic specification.

The specification can be either:

ClassName, in-case the module name is taken from the default_module argument

or

package_name.module_name.ClassName, in-case the module is taken as package_name.module_name

Parameters

  • name_spec (str) – the class specification

  • default_module (Optional[str]) – the default module

  • exception_cls (Any) – the exception class to raise on exception

Returns

the loaded class

Return type

Any

aizynthfinder.utils.logging module

Module containing routines to setup proper logging

aizynthfinder.utils.logging.logger()

Returns the logger that should be used by all classes

Returns

the logger object

Return type

logging.Logger

aizynthfinder.utils.logging.setup_logger(console_level, file_level=None)

Setup the logger that should be used by all classes

The logger configuration is read from the logging.yml file.

Parameters

  • console_level (int) – the level of logging to the console

  • file_level (Optional[int]) – the level of logging to file, if not set logging to file is disabled, default to None

Returns

the logger object

Return type

logging.Logger

aizynthfinder.utils.math module

Module containing diverse math functions, including neural network-related functions.

aizynthfinder.utils.math.softmax(x)

Compute softmax values for each sets of scores in x.

Parameters

x (numpy.ndarray) –

Return type

numpy.ndarray

aizynthfinder.utils.models module

Module containing helper routines for using Keras, Tensorflow and Onnx models

aizynthfinder.utils.models.load_model(source, key, use_remote_models)

Load model from a configuration specification.

If use_remote_models is True, tries to load:

  1. A Tensorflow server through gRPC

  2. A Tensorflow server through REST API

  3. A local Keras model

otherwise it just loads the local model.

Parameters

  • source (str) – if fallbacks to a local model, this is the filename

  • key (str) – when connecting to Tensorflow server this is the model name

  • use_remote_models (bool) – if True will try to connect to remote model server

Returns

a model object with a predict object

Return type

Union[‘LocalKerasModel’, ‘LocalOnnxModel’, ‘ExternalModelViaGRPC’, ‘ExternalModelViaREST’]

class aizynthfinder.utils.models.LocalKerasModel(filename)

Bases: object

A keras policy model that is executed locally.

The size of the input vector can be determined with the len() method.

Variables

  • model – the compiled model

  • output_size – the length of the output vector

Parameters

filename (str) – the path to a Keras checkpoint file

Return type

None

predict(*args, **_)

Perform a forward pass of the neural network.

Parameters

  • args (numpy.ndarray) – the input vectors

  • _ (numpy.ndarray) –

Returns

the vector of the output layer

Return type

numpy.ndarray

class aizynthfinder.utils.models.LocalOnnxModel(filename)

Bases: object

An Onnx model that is executed locally.

The size of the input vector can be determined with the len() method.

Variables

  • model – the compiled Onnx model

  • output_size – the length of the output vector

Parameters

filename (str) – the path to a Onnx model checkpoint file

Return type

None

predict(*args, **_)

Perform a prediction run on the onnx model.

Parameters

  • args (numpy.ndarray) – the input vectors

  • _ (numpy.ndarray) –

Returns

the vector of the output layer

Return type

numpy.ndarray

class aizynthfinder.utils.models.ExternalModelViaREST(name)

Bases: object

A neural network model implementation using TF Serving via REST API.

Parameters

name (str) – the name of model

Return type

None

predict(*args, **kwargs)

Get prediction from model.

If the keys in kwargs agree with the model input names, they will be used in stead of arg

Parameters

  • args (numpy.ndarray) – the input vectors

  • kwargs (numpy.ndarray) – the named input vectors

Returns

the vector of the output layer

Return type

numpy.ndarray

class aizynthfinder.utils.models.ExternalModelViaGRPC(name)

Bases: object

A neural network model implementation using TF Serving via gRPC.

Parameters

name (str) – the name of model

Return type

None

predict(*args, **kwargs)

Get prediction from model.

If the keys in kwargs agree with the model input names, they will be used in stead of arg

Parameters

  • args (numpy.ndarray) – the input vectors

  • kwargs (numpy.ndarray) – the named input vectors

Returns

the vector of the output layer

Return type

numpy.ndarray

aizynthfinder.utils.mongo module

Module containing routines to obtain a MongoClient instance

aizynthfinder.utils.mongo.get_mongo_client(host='localhost', port=27017, user=None, password=None, tls_certs_path='')

A helper function to create and reuse MongoClient

The client is only setup once. Therefore if this function is called a second time with different parameters, it would still return the first client.

Parameters

  • host (str) – the host

  • port (int) – the host port

  • user (Optional[str]) – username, defaults to None

  • password (Optional[str]) – password, defaults to None

  • tls_certs_path (str) – the path to TLS certificates if to be used, defaults to “”

Raises

ValueError – if host and port is not given first time

Returns

the MongoDB client

Return type

Optional[pymongo.mongo_client.MongoClient]

aizynthfinder.utils.paths module

Module containing routines for returning package paths

aizynthfinder.utils.paths.package_path()

Return the path to the package

Return type

str

aizynthfinder.utils.paths.data_path()

Return the path to the data directory of the package

Return type

str

aizynthfinder.utils.type_utils module

Module containing all types and type imports

Module contents