chemicalchecker.tool.targetmate.signaturizer.SignaturizerSetup

class SignaturizerSetup(**kwargs)

Bases: Signaturizer, Fingerprinter

Set up a signaturizer

Set up a Signaturizer

Parameters:

• datasets (list) – CC datasets (A1.001-E5.999). By default, all datasets having a SMILES-to-sign predictor are used.

• sign_predict_paths (dict) – pre-loaded predict_fn, keys are dataset codes, values are tuples of (sign, predict_fn)

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
read_signatures_ensemble	Return signatures as an ensemble
read_signatures_prestacked	Return signatures in a stacked form from an already prestacked file
read_signatures_stacked	Return signatures in a stacked form
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(datasets=None, idxs=None, smiles=None, inchikeys=None, is_tmp=None, sign_folder=None)

Read signatures

read_signatures_ensemble(datasets, smiles, inchikeys, idxs, is_tmp, sign_folder)

Return signatures as an ensemble

read_signatures_prestacked(mask, datasets, smiles, inchikeys, idxs, is_tmp, sign_folder)

Return signatures in a stacked form from an already prestacked file

read_signatures_stacked(datasets, smiles, inchikeys, idxs, is_tmp, sign_folder)

Return signatures in a stacked form

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