SYMBOL INDEX (377 symbols across 58 files)

FILE: docs/notebooks/scripts/06_hyperparameter_tuning.py
  function report (line 125) | def report(results, n_top=3):

FILE: docs/notebooks/scripts/07_parallel_transforms.py
  function test_transformer (line 72) | def test_transformer(transformer):

FILE: docs/notebooks/scripts/08_external_library_skopt.py
  function objective (line 80) | def objective(**params):

FILE: docs/notebooks/scripts/10_pipeline_pandas_output.py
  function compute_metrics (line 132) | def compute_metrics(y_true, y_pred):
  function combine_datasets (line 201) | def combine_datasets(data, cddd):

FILE: docs/notebooks/scripts/12_custom_fingerprint_transformer.py
  class DummyFingerprintTransformer (line 36) | class DummyFingerprintTransformer(BaseFpsTransformer):
    method __init__ (line 37) | def __init__(self, fpSize=64, n_jobs=1, safe_inference_mode=False):
    method _transform_mol (line 43) | def _transform_mol(self, mol):
  class UnpickableFingerprintTransformer (line 63) | class UnpickableFingerprintTransformer(BaseFpsTransformer):
    method __init__ (line 64) | def __init__(self, fpSize=1024, n_jobs=1, safe_inference_mode=False, *...
    method _transform_mol (line 73) | def _transform_mol(self, mol):
  class BadTransformer (line 85) | class BadTransformer(BaseFpsTransformer):
    method __init__ (line 86) | def __init__(self, generator, n_jobs=1):
    method _transform_mol (line 90) | def _transform_mol(self, mol):
  class NamedTansformer1 (line 117) | class NamedTansformer1(UnpickableFingerprintTransformer):
  class NamedTansformer2 (line 121) | class NamedTansformer2(UnpickableFingerprintTransformer):
    method __init__ (line 122) | def __init__(self):
  class FancyFingerprintTransformer (line 126) | class FancyFingerprintTransformer(UnpickableFingerprintTransformer):

FILE: docs/notebooks/scripts/13_applicability_domain.py
  function check_drug_applicability (line 220) | def check_drug_applicability(smiles, name):

FILE: scikit_mol/applicability/base.py
  class _ADOutputMixin (line 15) | class _ADOutputMixin(_SetOutputMixin):
    method __init_subclass__ (line 18) | def __init_subclass__(cls, **kwargs):
  function _safe_flatten (line 30) | def _safe_flatten(X: Union[ArrayLike, pd.DataFrame]) -> NDArray[np.float...
  class BaseApplicabilityDomain (line 48) | class BaseApplicabilityDomain(BaseEstimator, TransformerMixin, _ADOutput...
    method __init__ (line 82) | def __init__(
    method fit (line 108) | def fit(self, X: ArrayLike, y: Optional[Any] = None) -> "BaseApplicabi...
    method fit_threshold (line 125) | def fit_threshold(
    method transform (line 161) | def transform(
    method _transform (line 188) | def _transform(self, X: NDArray) -> NDArray[np.float64]:
    method predict (line 203) | def predict(
    method score_transform (line 225) | def score_transform(
    method get_feature_names_out (line 253) | def get_feature_names_out(self, input_features=None) -> NDArray[np.str_]:

FILE: scikit_mol/applicability/bounding_box.py
  class BoundingBoxApplicabilityDomain (line 18) | class BoundingBoxApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 73) | def __init__(
    method fit (line 93) | def fit(
    method _transform (line 122) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/convex_hull.py
  class ConvexHullApplicabilityDomain (line 19) | class ConvexHullApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 56) | def __init__(
    method fit (line 62) | def fit(
    method _transform (line 87) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/hotelling.py
  class HotellingT2ApplicabilityDomain (line 20) | class HotellingT2ApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 61) | def __init__(
    method _set_statistical_threshold (line 72) | def _set_statistical_threshold(self, X: NDArray) -> None:
    method fit (line 87) | def fit(
    method _transform (line 118) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/isolation_forest.py
  class IsolationForestApplicabilityDomain (line 20) | class IsolationForestApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 63) | def __init__(
    method fit (line 78) | def fit(
    method _transform (line 114) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/kernel_density.py
  class KernelDensityApplicabilityDomain (line 20) | class KernelDensityApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 64) | def __init__(
    method fit (line 75) | def fit(
    method _transform (line 104) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/knn.py
  class KNNApplicabilityDomain (line 20) | class KNNApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 94) | def __init__(
    method distance_metric (line 110) | def distance_metric(self) -> Union[Callable, str]:
    method distance_metric (line 114) | def distance_metric(self, value: Union[str, Callable]) -> None:
    method fit (line 122) | def fit(self, X: ArrayLike, y=None) -> "KNNApplicabilityDomain":
    method _transform (line 160) | def _transform(self, X: np.ndarray) -> np.ndarray:

FILE: scikit_mol/applicability/leverage.py
  class LeverageApplicabilityDomain (line 19) | class LeverageApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 81) | def __init__(
    method _set_statistical_threshold (line 90) | def _set_statistical_threshold(self, X: NDArray) -> None:
    method fit (line 95) | def fit(
    method _transform (line 123) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/local_outlier.py
  class LocalOutlierFactorApplicabilityDomain (line 20) | class LocalOutlierFactorApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 63) | def __init__(
    method fit (line 76) | def fit(
    method _transform (line 109) | def _transform(self, X: NDArray) -> NDArray[np.float64]:
    method _set_statistical_threshold (line 127) | def _set_statistical_threshold(self, X):

FILE: scikit_mol/applicability/mahalanobis.py
  class MahalanobisApplicabilityDomain (line 15) | class MahalanobisApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 50) | def __init__(
    method _set_statistical_threshold (line 57) | def _set_statistical_threshold(self, X: NDArray) -> None:
    method fit (line 67) | def fit(
    method _transform (line 113) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/standardization.py
  class StandardizationApplicabilityDomain (line 21) | class StandardizationApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 54) | def __init__(
    method _set_statistical_threshold (line 61) | def _set_statistical_threshold(self, X: NDArray) -> None:
    method fit (line 69) | def fit(
    method _transform (line 98) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/applicability/topkat.py
  class TopkatApplicabilityDomain (line 20) | class TopkatApplicabilityDomain(BaseApplicabilityDomain):
    method __init__ (line 62) | def __init__(
    method fit (line 69) | def fit(self, X: ArrayLike, y: Optional[Any] = None) -> "TopkatApplica...
    method _transform (line 113) | def _transform(self, X: NDArray) -> NDArray[np.float64]:

FILE: scikit_mol/conversions.py
  class SmilesToMolTransformer (line 22) | class SmilesToMolTransformer(TransformerMixin, NoFitNeededMixin, BaseEst...
    method __init__ (line 36) | def __init__(
    method get_feature_names_out (line 53) | def get_feature_names_out(self, input_features=None):
    method fit (line 56) | def fit(self, X=None, y=None):
    method transform (line 60) | def transform(
    method _transform (line 85) | def _transform(self, X):
    method inverse_transform (line 110) | def inverse_transform(self, X_mols_list, y=None):

FILE: scikit_mol/core.py
  class NoFitNeededMixin (line 19) | class NoFitNeededMixin:
    method __sklearn_is_fitted__ (line 24) | def __sklearn_is_fitted__(self):
  class InvalidMol (line 29) | class InvalidMol:
    method __bool__ (line 44) | def __bool__(self):
    method __repr__ (line 47) | def __repr__(self):
  function _validate_transform_input (line 51) | def _validate_transform_input(X):
  function check_transform_input (line 71) | def check_transform_input(method):
  function feature_names_default_mol (line 88) | def feature_names_default_mol(method):

FILE: scikit_mol/descriptors.py
  class MolecularDescriptorTransformer (line 15) | class MolecularDescriptorTransformer(TransformerMixin, NoFitNeededMixin,...
    method __init__ (line 42) | def __init__(
    method _get_desc_calculator (line 54) | def _get_desc_calculator(self) -> MolecularDescriptorCalculator:
    method desc_list (line 67) | def desc_list(self):
    method get_feature_names_out (line 71) | def get_feature_names_out(self, input_features=None):
    method desc_list (line 75) | def desc_list(self, desc_list):
    method available_descriptors (line 80) | def available_descriptors(self) -> List[str]:
    method selected_descriptors (line 85) | def selected_descriptors(self) -> List[str]:
    method start_method (line 90) | def start_method(self):
    method start_method (line 94) | def start_method(self, start_method):
    method _transform_mol (line 103) | def _transform_mol(self, mol: Mol) -> Union[np.ndarray, np.ma.MaskedAr...
    method fit (line 117) | def fit(self, x, y=None):
    method _transform (line 122) | def _transform(self, x: List[Mol]) -> Union[np.ndarray, np.ma.MaskedAr...
    method transform (line 132) | def transform(self, x: List[Mol], y=None) -> Union[np.ndarray, np.ma.M...
  function parallel_helper (line 158) | def parallel_helper(params, mols):

FILE: scikit_mol/fingerprints/atompair.py
  class AtomPairFingerprintTransformer (line 9) | class AtomPairFingerprintTransformer(FpsGeneratorTransformer):
    method __init__ (line 24) | def __init__(
    method _generate_fp_generator (line 86) | def _generate_fp_generator(self):
    method _transform_mol (line 95) | def _transform_mol(self, mol) -> np.array:

FILE: scikit_mol/fingerprints/avalon.py
  class AvalonFingerprintTransformer (line 9) | class AvalonFingerprintTransformer(FpsTransformer):
    method __init__ (line 12) | def __init__(
    method _mol2fp (line 53) | def _mol2fp(self, mol):

FILE: scikit_mol/fingerprints/baseclasses.py
  class BaseFpsTransformer (line 24) | class BaseFpsTransformer(TransformerMixin, NoFitNeededMixin, ABC, BaseEs...
    method __init__ (line 39) | def __init__(
    method nBits (line 51) | def nBits(self):
    method nBits (line 61) | def nBits(self, nBits):
    method _get_column_prefix (line 70) | def _get_column_prefix(self) -> str:
    method _get_n_digits_column_suffix (line 81) | def _get_n_digits_column_suffix(self) -> int:
    method get_display_feature_names_out (line 84) | def get_display_feature_names_out(self, input_features=None):
    method get_feature_names_out (line 97) | def get_feature_names_out(self, input_features=None):
    method _safe_transform_mol (line 106) | def _safe_transform_mol(self, mol):
    method _transform_mol (line 121) | def _transform_mol(self, mol):
    method fit (line 125) | def fit(self, X, y=None):
    method _transform (line 133) | def _transform(self, X):
    method _transform_sparse (line 141) | def _transform_sparse(self, X):
    method transform (line 148) | def transform(self, X, y=None):
  class FpsTransformer (line 176) | class FpsTransformer(BaseFpsTransformer):
    method __init__ (line 179) | def __init__(
    method _transform_mol (line 188) | def _transform_mol(self, mol):
    method _mol2fp (line 194) | def _mol2fp(self, mol):
    method _fp2array (line 201) | def _fp2array(self, fp):
    method _transform (line 211) | def _transform(self, X):
    method _get_param_names (line 222) | def _get_param_names(self):
  class FpsGeneratorTransformer (line 229) | class FpsGeneratorTransformer(BaseFpsTransformer):
    method __getstate__ (line 234) | def __getstate__(self):
    method __setstate__ (line 242) | def __setstate__(self, state):
    method __setattr__ (line 260) | def __setattr__(self, name: str, value):
    method _generate_fp_generator (line 269) | def _generate_fp_generator(self):
    method _transform_mol (line 273) | def _transform_mol(self, mol) -> np.array:
    method dtype (line 282) | def dtype(self):
    method dtype (line 292) | def dtype(self, dtype):
    method _get_param_names (line 302) | def _get_param_names(self):
  function parallel_helper (line 309) | def parallel_helper(X_mols, cls: Type[BaseFpsTransformer], parameters: d...

FILE: scikit_mol/fingerprints/maccs.py
  class MACCSKeysFingerprintTransformer (line 9) | class MACCSKeysFingerprintTransformer(FpsTransformer):
    method __init__ (line 12) | def __init__(
    method fpSize (line 49) | def fpSize(self):
    method fpSize (line 53) | def fpSize(self, fpSize):
    method _mol2fp (line 60) | def _mol2fp(self, mol):

FILE: scikit_mol/fingerprints/minhash.py
  class MHFingerprintTransformer (line 11) | class MHFingerprintTransformer(FpsTransformer):
    method __init__ (line 14) | def __init__(
    method __getstate__ (line 66) | def __getstate__(self):
    method __setstate__ (line 73) | def __setstate__(self, state):
    method _mol2fp (line 79) | def _mol2fp(self, mol):
    method _fp2array (line 85) | def _fp2array(self, fp):
    method _recreate_encoder (line 88) | def _recreate_encoder(self):
    method seed (line 94) | def seed(self):
    method seed (line 98) | def seed(self, seed):
    method n_permutations (line 104) | def n_permutations(self):
    method n_permutations (line 112) | def n_permutations(self, n_permutations):
  class SECFingerprintTransformer (line 123) | class SECFingerprintTransformer(FpsTransformer):
    method __init__ (line 125) | def __init__(
    method __getstate__ (line 166) | def __getstate__(self):
    method __setstate__ (line 173) | def __setstate__(self, state):
    method _mol2fp (line 179) | def _mol2fp(self, mol):
    method _recreate_encoder (line 190) | def _recreate_encoder(self):
    method seed (line 196) | def seed(self):
    method seed (line 200) | def seed(self, seed):
    method n_permutations (line 206) | def n_permutations(self):
    method n_permutations (line 210) | def n_permutations(self, n_permutations):
    method length (line 216) | def length(self):

FILE: scikit_mol/fingerprints/morgan.py
  class MorganFingerprintTransformer (line 12) | class MorganFingerprintTransformer(FpsGeneratorTransformer):
    method __init__ (line 28) | def __init__(
    method _generate_fp_generator (line 78) | def _generate_fp_generator(self):
    method _transform_mol (line 92) | def _transform_mol(self, mol) -> np.array:

FILE: scikit_mol/fingerprints/rdkitfp.py
  class RDKitFingerprintTransformer (line 9) | class RDKitFingerprintTransformer(FpsGeneratorTransformer):
    method __init__ (line 22) | def __init__(
    method _transform_mol (line 83) | def _transform_mol(self, mol) -> np.array:
    method _generate_fp_generator (line 89) | def _generate_fp_generator(self):

FILE: scikit_mol/fingerprints/topologicaltorsion.py
  class TopologicalTorsionFingerprintTransformer (line 9) | class TopologicalTorsionFingerprintTransformer(FpsGeneratorTransformer):
    method __init__ (line 16) | def __init__(
    method _generate_fp_generator (line 69) | def _generate_fp_generator(self):
    method _transform_mol (line 79) | def _transform_mol(self, mol) -> np.array:

FILE: scikit_mol/parallel.py
  function parallelized_with_batches (line 9) | def parallelized_with_batches(

FILE: scikit_mol/plotting.py
  class ParallelTester (line 17) | class ParallelTester:
    method __init__ (line 22) | def __init__(
    method _test_single (line 60) | def _test_single(self, mols, n_jobs):
    method test (line 66) | def test(self) -> pd.DataFrame:
  function get_processor_name (line 81) | def get_processor_name() -> str:
  function plot_heatmap (line 113) | def plot_heatmap(

FILE: scikit_mol/safeinference.py
  class MaskedArrayError (line 21) | class MaskedArrayError(ValueError):
  function filter_invalid_rows (line 27) | def filter_invalid_rows(warn_on_invalid=False, replace_value=np.nan):
  class SafeInferenceWrapper (line 118) | class SafeInferenceWrapper(TransformerMixin, BaseEstimator):
    method __init__ (line 130) | def __init__(
    method n_features_in_ (line 155) | def n_features_in_(self):
    method fit (line 159) | def fit(self, X, y=None, **fit_params):
    method predict (line 164) | def predict(self, X, y=None):
    method predict_proba (line 169) | def predict_proba(self, X, y=None):
    method decision_function (line 174) | def decision_function(self, X, y=None):
    method transform (line 179) | def transform(self, X, y=None):
    method fit_transform (line 184) | def fit_transform(self, X, y=None, **fit_params):
    method score (line 189) | def score(self, X, y=None):
    method get_feature_names_out (line 194) | def get_feature_names_out(self, *args, **kwargs):
    method __sklearn_is_fitted__ (line 197) | def __sklearn_is_fitted__(self):

FILE: scikit_mol/standardizer.py
  class Standardizer (line 24) | class Standardizer(TransformerMixin, NoFitNeededMixin, BaseEstimator):
    method __init__ (line 32) | def __init__(
    method fit (line 54) | def fit(self, X, y=None):
    method _standardize_mol (line 57) | def _standardize_mol(self, mol):
    method _transform (line 88) | def _transform(self, X):
    method get_feature_names_out (line 92) | def get_feature_names_out(self, input_features=None):
    method transform (line 96) | def transform(self, X, y=None):
  function parallel_helper (line 104) | def parallel_helper(classname, parameters, X_mols):

FILE: scikit_mol/utilities.py
  class CheckSmilesSanitization (line 12) | class CheckSmilesSanitization:
    method __init__ (line 13) | def __init__(self, return_mol=False):
    method sanitize (line 17) | def sanitize(self, X_smiles_list, y=None):
  function set_safe_inference_mode (line 76) | def set_safe_inference_mode(estimator: BaseEstimator, value: bool) -> Ba...

FILE: tests/applicability/conftest.py
  function ad_estimator (line 54) | def ad_estimator(request):
  function reduced_fingerprints (line 61) | def reduced_fingerprints(mols_list):
  function binary_fingerprints (line 71) | def binary_fingerprints(mols_list):
  function ad_test_data (line 77) | def ad_test_data():

FILE: tests/applicability/test_base.py
  function test_basic_functionality (line 9) | def test_basic_functionality(ad_estimator, reduced_fingerprints):
  function test_predict_functionality (line 17) | def test_predict_functionality(ad_estimator, ad_test_data):
  function test_score_transform (line 34) | def test_score_transform(ad_estimator, ad_test_data):
  function test_threshold_setting (line 54) | def test_threshold_setting(ad_estimator, reduced_fingerprints):
  function test_feature_names (line 74) | def test_feature_names(ad_estimator, reduced_fingerprints):
  function test_pandas_output (line 84) | def test_pandas_output(ad_estimator, reduced_fingerprints):
  function test_input_validation (line 101) | def test_input_validation(ad_estimator):
  function test_refit_consistency (line 117) | def test_refit_consistency(ad_estimator, reduced_fingerprints):

FILE: tests/applicability/test_bounding_box.py
  function test_bounding_box_bounds (line 12) | def test_bounding_box_bounds(ad_test_data):
  function test_bounding_box_violations (line 26) | def test_bounding_box_violations():
  function test_bounding_box_percentile_validation (line 46) | def test_bounding_box_percentile_validation():
  function test_bounding_box_pipeline (line 61) | def test_bounding_box_pipeline():

FILE: tests/applicability/test_convex_hull.py
  function test_convex_hull_simple (line 13) | def test_convex_hull_simple():
  function test_convex_hull_pipeline (line 32) | def test_convex_hull_pipeline():
  function test_convex_hull_numerical_stability (line 52) | def test_convex_hull_numerical_stability():
  function test_convex_hull_single_point (line 71) | def test_convex_hull_single_point():

FILE: tests/applicability/test_hotelling.py
  function test_hotelling_threshold (line 12) | def test_hotelling_threshold():
  function test_hotelling_scores (line 28) | def test_hotelling_scores():
  function test_hotelling_significance_validation (line 50) | def test_hotelling_significance_validation():
  function test_hotelling_pipeline (line 62) | def test_hotelling_pipeline():
  function test_hotelling_threshold_fitting (line 77) | def test_hotelling_threshold_fitting():

FILE: tests/applicability/test_isolation_forest.py
  function test_refit_consistency (line 8) | def test_refit_consistency():

FILE: tests/applicability/test_kernel_density.py
  function ad_estimator (line 9) | def ad_estimator():
  function test_kernel_parameter (line 14) | def test_kernel_parameter():
  function test_bandwidth_effect (line 29) | def test_bandwidth_effect():

FILE: tests/applicability/test_knn.py
  function binary_fingerprints (line 11) | def binary_fingerprints(mols_list):
  function test_knn_tanimoto (line 16) | def test_knn_tanimoto(binary_fingerprints):

FILE: tests/applicability/test_leverage.py
  function test_leverage_statistical_threshold (line 13) | def test_leverage_statistical_threshold(ad_test_data):
  function test_leverage_pipeline (line 25) | def test_leverage_pipeline(reduced_fingerprints):
  function test_leverage_threshold_factor (line 41) | def test_leverage_threshold_factor():
  function test_leverage_var_covar_matrix (line 55) | def test_leverage_var_covar_matrix(ad_test_data):

FILE: tests/applicability/test_local_outlier.py
  function ad_estimator (line 10) | def ad_estimator():
  function test_n_neighbors_effect (line 15) | def test_n_neighbors_effect():
  function test_metric_parameter (line 37) | def test_metric_parameter():
  function test_contamination_effect (line 49) | def test_contamination_effect():

FILE: tests/applicability/test_mahalanobis.py
  function ad_estimator (line 11) | def ad_estimator():
  function test_statistical_threshold (line 16) | def test_statistical_threshold():
  function test_mean_covariance (line 35) | def test_mean_covariance():
  function test_distance_properties (line 50) | def test_distance_properties():

FILE: tests/applicability/test_standardization.py
  function ad_estimator (line 11) | def ad_estimator():
  function test_statistical_threshold (line 16) | def test_statistical_threshold():
  function test_standardization (line 33) | def test_standardization():
  function test_max_absolute_score (line 47) | def test_max_absolute_score():
  function test_outlier_detection (line 64) | def test_outlier_detection():

FILE: tests/applicability/test_topkat.py
  function ad_estimator (line 11) | def ad_estimator():
  function test_ops_transformation (line 16) | def test_ops_transformation():
  function test_fixed_threshold (line 32) | def test_fixed_threshold():
  function test_eigendecomposition (line 43) | def test_eigendecomposition():

FILE: tests/conftest.py
  function pytest_configure (line 14) | def pytest_configure(config):
  function md5 (line 25) | def md5(fn):
  function data_pth (line 34) | def data_pth(tmp_path_factory) -> Path:
  function data (line 54) | def data(data_pth) -> pd.DataFrame:
  function pandas_output (line 59) | def pandas_output():
  function setup_random (line 68) | def setup_random():

FILE: tests/fixtures.py
  function smiles_list (line 49) | def smiles_list():
  function smiles_container (line 76) | def smiles_container(
  function chiral_smiles_list (line 83) | def chiral_smiles_list():  # Need to be a certain size, so the fingerpri...
  function smiles_list_with_invalid (line 95) | def smiles_list_with_invalid(smiles_list):
  function invalid_smiles_list (line 102) | def invalid_smiles_list():
  function mols_list (line 110) | def mols_list():
  function mols_container (line 115) | def mols_container(request):
  function chiral_mols_list (line 120) | def chiral_mols_list(chiral_smiles_list):
  function mols_with_invalid_container (line 125) | def mols_with_invalid_container(smiles_list_with_invalid):
  function fingerprint (line 137) | def fingerprint(mols_list):
  function SLC6A4_subset (line 147) | def SLC6A4_subset():
  function SLC6A4_subset_with_cddd (line 153) | def SLC6A4_subset_with_cddd(SLC6A4_subset):
  function featurizer (line 185) | def featurizer(request):
  function combined_transformer (line 190) | def combined_transformer(featurizer):
  function morgan_transformer (line 210) | def morgan_transformer():
  function rdkit_transformer (line 215) | def rdkit_transformer():
  function atompair_transformer (line 220) | def atompair_transformer():
  function topologicaltorsion_transformer (line 225) | def topologicaltorsion_transformer():

FILE: tests/test_desctransformer.py
  function default_descriptor_transformer (line 30) | def default_descriptor_transformer():
  function selected_descriptor_transformer (line 35) | def selected_descriptor_transformer():
  function test_descriptor_transformer_clonability (line 41) | def test_descriptor_transformer_clonability(default_descriptor_transform...
  function test_descriptor_transformer_set_params (line 52) | def test_descriptor_transformer_set_params(default_descriptor_transformer):
  function test_descriptor_transformer_available_descriptors (line 65) | def test_descriptor_transformer_available_descriptors(
  function test_descriptor_transformer_transform (line 82) | def test_descriptor_transformer_transform(
  function test_descriptor_transformer_wrong_descriptors (line 90) | def test_descriptor_transformer_wrong_descriptors():
  function test_descriptor_transformer_parallel (line 103) | def test_descriptor_transformer_parallel(mols_list, default_descriptor_t...
  function test_transform_with_safe_inference_mode (line 134) | def test_transform_with_safe_inference_mode(mols_with_invalid_container):
  function test_transform_without_safe_inference_mode (line 148) | def test_transform_without_safe_inference_mode(mols_with_invalid_contain...
  function test_transform_parallel_with_safe_inference_mode (line 156) | def test_transform_parallel_with_safe_inference_mode(mols_with_invalid_c...
  function test_transform_parallel_without_safe_inference_mode (line 170) | def test_transform_parallel_without_safe_inference_mode(mols_with_invali...
  function test_safe_inference_mode_setting (line 178) | def test_safe_inference_mode_setting():
  function test_descriptor_transformer_pandas_output (line 191) | def test_descriptor_transformer_pandas_output(
  function test_descriptor_transformer_pandas_output_pipeline (line 208) | def test_descriptor_transformer_pandas_output_pipeline(

FILE: tests/test_fptransformers.py
  function maccs_transformer (line 31) | def maccs_transformer():
  function secfp_transformer (line 36) | def secfp_transformer():
  function mhfp_transformer (line 41) | def mhfp_transformer():
  function avalon_transformer (line 46) | def avalon_transformer():
  function test_clonability (line 50) | def test_clonability(
  function test_set_params (line 71) | def test_set_params(
  function test_transform (line 94) | def test_transform(
  function test_transform_parallel (line 120) | def test_transform_parallel(
  function test_picklable (line 146) | def test_picklable(
  function assert_transformer_set_params (line 164) | def assert_transformer_set_params(tr_class, new_params, mols_list):
  function test_SECFingerprintTransformer (line 197) | def test_SECFingerprintTransformer(chiral_mols_list):
  function test_MHFingerprintTransformer (line 213) | def test_MHFingerprintTransformer(chiral_mols_list):
  function test_AvalonFingerprintTransformer (line 228) | def test_AvalonFingerprintTransformer(chiral_mols_list):
  function test_transform_with_safe_inference_mode (line 240) | def test_transform_with_safe_inference_mode(
  function test_transform_without_safe_inference_mode (line 264) | def test_transform_without_safe_inference_mode(
  function test_transform_parallel_with_safe_inference_mode (line 285) | def test_transform_parallel_with_safe_inference_mode(

FILE: tests/test_fptransformersgenerator.py
  function test_fpstransformer_transform_mol (line 34) | def test_fpstransformer_transform_mol(transformer_class, mols_list):
  function test_clonability (line 55) | def test_clonability(transformer_class):
  function test_set_params (line 68) | def test_set_params(transformer_class):
  function test_transform (line 81) | def test_transform(mols_container, transformer_class):
  function test_transform_parallel (line 95) | def test_transform_parallel(mols_container, transformer_class):
  function test_picklable (line 109) | def test_picklable(transformer_class):
  function assert_transformer_set_params (line 125) | def assert_transformer_set_params(transfomer, new_params, mols_list):
  function test_morgan_set_params (line 159) | def test_morgan_set_params(chiral_mols_list):
  function test_atompairs_set_params (line 174) | def test_atompairs_set_params(chiral_mols_list):
  function test_topologicaltorsion_set_params (line 194) | def test_topologicaltorsion_set_params(chiral_mols_list):
  function test_RDKitFPTransformer (line 210) | def test_RDKitFPTransformer(chiral_mols_list):

FILE: tests/test_parameter_types.py
  function test_Transformer_exotic_types (line 18) | def test_Transformer_exotic_types(
  function test_RDKFp_exotic_types (line 49) | def test_RDKFp_exotic_types(mols_list, rdkit_transformer):

FILE: tests/test_safeinferencemode.py
  function equal_val (line 20) | def equal_val(value, expected_value):
  function transformer (line 31) | def transformer(request):
  function smiles_pipeline (line 36) | def smiles_pipeline(request, transformer):
  function smiles_pipeline_trained (line 53) | def smiles_pipeline_trained(smiles_pipeline, SLC6A4_subset):
  function test_safeinference_wrapper_basic (line 61) | def test_safeinference_wrapper_basic(smiles_pipeline, SLC6A4_subset):
  function test_safeinference_wrapper_with_single_invalid_smiles (line 80) | def test_safeinference_wrapper_with_single_invalid_smiles(smiles_pipelin...
  function test_safeinference_wrapper_with_invalid_smiles (line 89) | def test_safeinference_wrapper_with_invalid_smiles(
  function test_safeinference_wrapper_without_safe_mode (line 111) | def test_safeinference_wrapper_without_safe_mode(
  function test_safeinference_wrapper_pandas_output (line 132) | def test_safeinference_wrapper_pandas_output(
  function test_safeinference_wrapper_get_feature_names_out (line 148) | def test_safeinference_wrapper_get_feature_names_out(smiles_pipeline):

FILE: tests/test_sanitizer.py
  function sanitizer (line 12) | def sanitizer():
  function return_mol_sanitizer (line 17) | def return_mol_sanitizer():
  function test_checksmilessanitation (line 21) | def test_checksmilessanitation(smiles_list, smiles_list_with_invalid, sa...
  function test_checksmilessanitation_x_and_y (line 28) | def test_checksmilessanitation_x_and_y(
  function test_checksmilessanitation_np (line 42) | def test_checksmilessanitation_np(smiles_list, smiles_list_with_invalid,...
  function test_checksmilessanitation_numpy (line 51) | def test_checksmilessanitation_numpy(smiles_list, smiles_list_with_inval...
  function test_checksmilessanitation_return_mol (line 60) | def test_checksmilessanitation_return_mol(

FILE: tests/test_scikit_mol.py
  function test_load_data (line 2) | def test_load_data(data):

FILE: tests/test_smilestomol.py
  function smilestomol_transformer (line 25) | def smilestomol_transformer():
  function test_smilestomol (line 29) | def test_smilestomol(smiles_container, smilestomol_transformer):
  function test_smilestomol_transform (line 39) | def test_smilestomol_transform(smilestomol_transformer, smiles_container):
  function test_smilestomol_fit (line 45) | def test_smilestomol_fit(smilestomol_transformer, smiles_container):
  function test_smilestomol_clone (line 50) | def test_smilestomol_clone(smilestomol_transformer):
  function test_smilestomol_unsanitzable (line 57) | def test_smilestomol_unsanitzable(smiles_list_with_invalid, smilestomol_...
  function test_descriptor_transformer_parallel (line 62) | def test_descriptor_transformer_parallel(smiles_container, smilestomol_t...
  function test_smilestomol_inverse_transform (line 79) | def test_smilestomol_inverse_transform(smilestomol_transformer, smiles_c...
  function test_smilestomol_inverse_transform_with_invalid (line 86) | def test_smilestomol_inverse_transform_with_invalid(
  function test_smilestomol_get_feature_names_out (line 110) | def test_smilestomol_get_feature_names_out(smilestomol_transformer):
  function test_smilestomol_safe_inference (line 115) | def test_smilestomol_safe_inference(smiles_list_with_invalid, smilestomo...
  function test_smilestomol_safe_inference_pandas_output (line 140) | def test_smilestomol_safe_inference_pandas_output(
  function test_pandas_output (line 165) | def test_pandas_output(smiles_container, smilestomol_transformer, pandas...

FILE: tests/test_transformers.py
  function test_transformer (line 42) | def test_transformer(SLC6A4_subset):
  function test_transformer_pandas_output (line 114) | def test_transformer_pandas_output(SLC6A4_subset, pandas_output):
  function test_pandas_out_same_values (line 184) | def test_pandas_out_same_values(featurizer, mols_container):
  function test_combined_transformer_pandas_out (line 209) | def test_combined_transformer_pandas_out(