chemicalchecker.tool.targetmate.signaturizer.Fingerprinter

class Fingerprinter(**kwargs)

Bases: BaseSignaturizer

Set up a Fingerprinter. This is usually used as a baseline featurizer to compare with CC signatures.

Initialize base signaturizer

Parameters:

• master_sign_paths (dict) – Path to signature files that are not specific to the collection being analysed (default=None).

• cctype (str) – CC signature type to be used (sign0, sign1, sign2, sign3) (default=’sign3’).

Methods

compress_models	Store model in compressed format for persistance
cpu_count
create_models_path
directory_tree
featurizer
func_hpc	Execute the any method on the configured HPC.
get_datasets
get_destination_dir
get_master_idxs
load	Load previously stored TargetMate instance.
load_base_model	Load a base model
load_data
master_key_type	Check master key types
master_mapping
read_data
read_signatures	Read signatures
repath_bases_by_fold	Redefine path of a TargetMate instance.
repath_predictions_by_fold	Redefine path of a TargetMate instance.
repath_predictions_by_fold_and_set
repath_predictions_by_set	Redefine path of a TargetMate instance.
reset_path_bases
reset_path_predictions	Reset predictions path
save	Save TargetMate instance
save_data
signaturize
waiter	Wait for jobs to finish
wipe	Delete temporary data

compress_models()

Store model in compressed format for persistance

func_hpc(func_name, *args, **kwargs)

Execute the any method on the configured HPC.

Parameters:

• args (tuple) – the arguments for of the function method

• kwargs (dict) – arguments for the HPC method.

static load(models_path)

Load previously stored TargetMate instance.

load_base_model(destination_dir, append_pipe=False)

Load a base model

master_key_type()

Check master key types

read_signatures(idxs, smiles, inchikeys, is_tmp, sign_folder)

Read signatures

repath_bases_by_fold(fold_number, is_tmp=True, reset=True, only_train=False)

Redefine path of a TargetMate instance. Used by the Validation class.

repath_predictions_by_fold(fold_number, is_tmp=True, reset=True)

Redefine path of a TargetMate instance. Used by the Validation class.

repath_predictions_by_set(is_train, is_tmp=True, reset=True)

Redefine path of a TargetMate instance. Used by the Validation class.

reset_path_predictions(is_tmp=True)

Reset predictions path

save()

Save TargetMate instance

waiter(jobs, secs=3)

Wait for jobs to finish

wipe()

Delete temporary data