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C
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D
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L
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M
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N
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P
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R
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S
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T
A
algorithms (chembee.config.benchmark.kmeans.KMeansClassifier attribute)
(chembee.config.benchmark.knn.KNNClassifier attribute)
(chembee.config.benchmark.linear_regression.LinearRegressionClassifier attribute)
(chembee.config.benchmark.logistic_regression.LogisticRegressionClassifier attribute)
(chembee.config.benchmark.mlp_classifier.NeuralNetworkClassifier attribute)
(chembee.config.benchmark.naive_bayes.NaiveBayesClassifier attribute)
(chembee.config.benchmark.random_forest.RandomForestClassifier attribute)
(chembee.config.benchmark.restricted_bm.RBMClassifier attribute)
(chembee.config.benchmark.spectral_clustering.SpectralClusteringClassifier attribute)
(chembee.config.benchmark.svc.SVClassifier attribute)
(chembee.config.benchmark.svc_poly.SVCPolyClassifier attribute)
B
benchmark_algorithm() (in module chembee.actions.benchmark_algorithms)
benchmark_algorithm_standard() (in module chembee.actions.benchmark_algorithms)
benchmark_cv_algorithms() (in module chembee.actions.benchmark_algorithms)
benchmark_standard() (in module chembee.actions.benchmark_algorithms)
BenchmarkAlgorithm (class in chembee.config.benchmark.BenchmarkAlgorithm)
BioDegDataSet (class in chembee.datasets.BioDegDataSet)
BreastCancerDataset (class in chembee.datasets.BreastCancer)
C
C (chembee.config.benchmark.spectral_clustering.SpectralClusteringClassifier attribute)
(chembee.config.benchmark.svc.SVClassifier attribute)
(chembee.config.benchmark.svc_poly.SVCPolyClassifier attribute)
calculate_lipinski_desc() (in module chembee.preparation.processing)
calculate_metric() (in module chembee.actions.evaluation)
calculate_metrics_classifier() (in module chembee.actions.evaluation)
calculate_mordred_descriptors() (in module chembee.preparation.processing)
calculate_roc_curve() (in module chembee.actions.evaluation)
check_file_name() (in module chembee.utils.file_utils)
check_make_dir() (in module chembee.utils.file_utils)
chembee
module
chembee.actions
module
chembee.actions.applicability
module
chembee.actions.benchmark_algorithms
module
chembee.actions.calibration
module
chembee.actions.classifier_fit
module
chembee.actions.clf_list
module
chembee.actions.cross_validation
module
chembee.actions.evaluation
module
chembee.actions.feature_extraction
module
chembee.actions.get_false_predictions
module
chembee.actions.get_undersampled_data
module
chembee.actions.save_model
module
chembee.actions.search
module
chembee.config
module
chembee.config.benchmark
module
chembee.config.benchmark.algorithms
module
chembee.config.benchmark.BenchmarkAlgorithm
module
chembee.config.benchmark.grid_search_cv
module
chembee.config.benchmark.kmeans
module
chembee.config.benchmark.knn
module
chembee.config.benchmark.linear_regression
module
chembee.config.benchmark.logistic_regression
module
chembee.config.benchmark.mlp_classifier
module
chembee.config.benchmark.naive_bayes
module
chembee.config.benchmark.random_forest
module
chembee.config.benchmark.restricted_bm
module
chembee.config.benchmark.spectral_clustering
module
chembee.config.benchmark.svc
module
chembee.config.benchmark.svc_poly
module
chembee.config.calibration
module
chembee.config.calibration.kmeans
module
chembee.config.calibration.knn
module
chembee.config.calibration.linear_regression
module
chembee.config.calibration.logistic_regression
module
chembee.config.calibration.mlp_classifier
module
chembee.config.calibration.naive_bayes
module
chembee.config.calibration.random_forest
module
chembee.config.calibration.restricted_bm
module
chembee.config.calibration.spectral_clustering
module
chembee.config.calibration.svc
module
chembee.config.calibration.svc_poly
module
chembee.datasets
module
chembee.datasets.BioDegDataSet
module
chembee.datasets.BreastCancer
module
chembee.datasets.ChemicalDataSet
module
chembee.datasets.DataSet
module
chembee.datasets.IrisDataSet
module
chembee.plotting
module
chembee.plotting.applicability
module
chembee.plotting.benchmarking
module
chembee.plotting.calibration
module
chembee.plotting.compounds
module
chembee.plotting.distribution
module
chembee.plotting.evaluation
module
chembee.plotting.feature_extraction
module
chembee.plotting.graphics
module
chembee.plotting.lipinski
module
chembee.preparation
module
chembee.preparation.processing
module
chembee.utils
module
chembee.utils.file_utils
module
chembee.utils.utils
module
clean_data() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
clf_fit() (in module chembee.actions.classifier_fit)
convert_mol_to_inchi() (in module chembee.preparation.processing)
convert_mols_to_morgan_fp() (in module chembee.preparation.processing)
convert_mols_to_rdk_fp() (in module chembee.preparation.processing)
cross_validation_grid_search() (in module chembee.actions.cross_validation)
D
data (chembee.datasets.DataSet.DataSet attribute)
DataSet (class in chembee.datasets.DataSet)
decision_function() (chembee.config.calibration.linear_regression.LinearRegressionClass method)
F
f_score() (in module chembee.actions.evaluation)
filter_importance_by_std() (in module chembee.actions.feature_extraction)
fit() (chembee.config.calibration.linear_regression.LinearRegressionClass method)
(chembee.config.calibration.spectral_clustering.NaivlyCalibratedSpectralClustering method)
(chembee.config.calibration.svc.NaivelyCalibratedLinearSVC method)
(chembee.config.calibration.svc.NaivelyCalibratedSVC method)
G
GaussianNBAlgorithm (class in chembee.config.calibration.naive_bayes)
get_applicability_domain() (in module chembee.actions.applicability)
get_calibration_displays() (in module chembee.actions.calibration)
get_data_impurities() (in module chembee.actions.get_false_predictions)
get_false_predictions() (in module chembee.actions.get_false_predictions)
get_feature_importances() (in module chembee.actions.feature_extraction)
get_feature_names() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
get_grid_positions() (in module chembee.utils.file_utils)
(in module chembee.utils.utils)
get_mols_from_supplier() (in module chembee.preparation.processing)
get_multi_false_predictions() (in module chembee.actions.get_false_predictions)
get_similar_compounds() (in module chembee.actions.search)
get_similar_compounds_structure() (in module chembee.actions.search)
get_split() (chembee.datasets.DataSet.DataSet method)
get_top_n_similar_compounds() (in module chembee.actions.search)
GridSearchCVClassifier (class in chembee.config.benchmark.grid_search_cv)
H
hidden_layer_sizes (chembee.config.benchmark.mlp_classifier.NeuralNetworkClassifier attribute)
hyperparameters (chembee.config.calibration.knn.KNeighborsClassifierAlgorithm attribute)
(chembee.config.calibration.mlp_classifier.MLPClassifierAlgorithm attribute)
(chembee.config.calibration.random_forest.RandomForestClassifierAlgorithm attribute)
(chembee.config.calibration.svc.NaivelyCalibratedSVC attribute)
I
init_collection_plot() (in module chembee.plotting.evaluation)
init_metrics_collection() (in module chembee.actions.evaluation)
insert_string_in_file_name() (in module chembee.utils.file_utils)
IrisDataSet (class in chembee.datasets.IrisDataSet)
K
KMeansClassifier (class in chembee.config.benchmark.kmeans)
KNeighborsClassifierAlgorithm (class in chembee.config.calibration.knn)
KNNClassifier (class in chembee.config.benchmark.knn)
L
LinearRegressionClass (class in chembee.config.calibration.linear_regression)
LinearRegressionClassifier (class in chembee.config.benchmark.linear_regression)
load_data() (in module chembee.preparation.processing)
load_data_set() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
(chembee.datasets.BreastCancer.BreastCancerDataset method)
(chembee.datasets.DataSet.DataSet method)
(chembee.datasets.IrisDataSet.IrisDataSet method)
load_data_set_from_csv() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
load_json_from_file() (in module chembee.utils.file_utils)
LogisticRegressionClassifier (class in chembee.config.benchmark.logistic_regression)
LogisticRegressionClassifierAlgorithm (class in chembee.config.calibration.logistic_regression)
M
make_comparison_plot() (in module chembee.plotting.graphics)
make_date_file_name() (in module chembee.utils.file_utils)
make_full_filename() (in module chembee.utils.file_utils)
make_grouped_bar_chart() (in module chembee.plotting.evaluation)
make_result() (in module chembee.actions.evaluation)
make_train_test_split() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
(chembee.datasets.BreastCancer.BreastCancerDataset method)
(chembee.datasets.DataSet.DataSet method)
max_iter (chembee.config.benchmark.mlp_classifier.NeuralNetworkClassifier attribute)
MLPClassifierAlgorithm (class in chembee.config.calibration.mlp_classifier)
module
chembee
chembee.actions
chembee.actions.applicability
chembee.actions.benchmark_algorithms
chembee.actions.calibration
chembee.actions.classifier_fit
chembee.actions.clf_list
chembee.actions.cross_validation
chembee.actions.evaluation
chembee.actions.feature_extraction
chembee.actions.get_false_predictions
chembee.actions.get_undersampled_data
chembee.actions.save_model
chembee.actions.search
chembee.config
chembee.config.benchmark
chembee.config.benchmark.algorithms
chembee.config.benchmark.BenchmarkAlgorithm
chembee.config.benchmark.grid_search_cv
chembee.config.benchmark.kmeans
chembee.config.benchmark.knn
chembee.config.benchmark.linear_regression
chembee.config.benchmark.logistic_regression
chembee.config.benchmark.mlp_classifier
chembee.config.benchmark.naive_bayes
chembee.config.benchmark.random_forest
chembee.config.benchmark.restricted_bm
chembee.config.benchmark.spectral_clustering
chembee.config.benchmark.svc
chembee.config.benchmark.svc_poly
chembee.config.calibration
chembee.config.calibration.kmeans
chembee.config.calibration.knn
chembee.config.calibration.linear_regression
chembee.config.calibration.logistic_regression
chembee.config.calibration.mlp_classifier
chembee.config.calibration.naive_bayes
chembee.config.calibration.random_forest
chembee.config.calibration.restricted_bm
chembee.config.calibration.spectral_clustering
chembee.config.calibration.svc
chembee.config.calibration.svc_poly
chembee.datasets
chembee.datasets.BioDegDataSet
chembee.datasets.BreastCancer
chembee.datasets.ChemicalDataSet
chembee.datasets.DataSet
chembee.datasets.IrisDataSet
chembee.plotting
chembee.plotting.applicability
chembee.plotting.benchmarking
chembee.plotting.calibration
chembee.plotting.compounds
chembee.plotting.distribution
chembee.plotting.evaluation
chembee.plotting.feature_extraction
chembee.plotting.graphics
chembee.plotting.lipinski
chembee.preparation
chembee.preparation.processing
chembee.utils
chembee.utils.file_utils
chembee.utils.utils
N
n_neighbors (chembee.config.benchmark.knn.KNNClassifier attribute)
NaiveBayesClassifier (class in chembee.config.benchmark.naive_bayes)
NaivelyCalibratedLinearSVC (class in chembee.config.calibration.svc)
NaivelyCalibratedSVC (class in chembee.config.calibration.svc)
NaivlyCalibratedSpectralClustering (class in chembee.config.calibration.spectral_clustering)
name (chembee.config.benchmark.grid_search_cv.GridSearchCVClassifier attribute)
(chembee.config.benchmark.kmeans.KMeansClassifier attribute)
(chembee.config.benchmark.knn.KNNClassifier attribute)
(chembee.config.benchmark.linear_regression.LinearRegressionClassifier attribute)
(chembee.config.benchmark.logistic_regression.LogisticRegressionClassifier attribute)
(chembee.config.benchmark.mlp_classifier.NeuralNetworkClassifier attribute)
(chembee.config.benchmark.naive_bayes.NaiveBayesClassifier attribute)
(chembee.config.benchmark.random_forest.RandomForestClassifier attribute)
(chembee.config.benchmark.restricted_bm.RBMClassifier attribute)
(chembee.config.benchmark.spectral_clustering.SpectralClusteringClassifier attribute)
(chembee.config.benchmark.svc.SVClassifier attribute)
(chembee.config.benchmark.svc_poly.SVCPolyClassifier attribute)
(chembee.config.calibration.knn.KNeighborsClassifierAlgorithm attribute)
(chembee.config.calibration.linear_regression.LinearRegressionClass attribute)
(chembee.config.calibration.logistic_regression.LogisticRegressionClassifierAlgorithm attribute)
(chembee.config.calibration.mlp_classifier.MLPClassifierAlgorithm attribute)
(chembee.config.calibration.naive_bayes.GaussianNBAlgorithm attribute)
(chembee.config.calibration.random_forest.RandomForestClassifierAlgorithm attribute)
(chembee.config.calibration.spectral_clustering.NaivlyCalibratedSpectralClustering attribute)
(chembee.config.calibration.svc.NaivelyCalibratedLinearSVC attribute)
(chembee.config.calibration.svc.NaivelyCalibratedSVC attribute)
(chembee.datasets.BioDegDataSet.BioDegDataSet attribute)
(chembee.datasets.BreastCancer.BreastCancerDataset attribute)
(chembee.datasets.DataSet.DataSet attribute)
(chembee.datasets.IrisDataSet.IrisDataSet attribute)
NeuralNetworkClassifier (class in chembee.config.benchmark.mlp_classifier)
P
parse_metrics_output() (in module chembee.plotting.evaluation)
parse_multi_output() (in module chembee.actions.evaluation)
plot_applicability_domain() (in module chembee.plotting.applicability)
plot_bar_chart() (in module chembee.plotting.evaluation)
plot_bar_chart_collection() (in module chembee.plotting.evaluation)
plot_bar_chart_collection_strat() (in module chembee.plotting.evaluation)
plot_calibration() (in module chembee.plotting.calibration)
plot_collection() (in module chembee.plotting.evaluation)
plot_collection_stratified() (in module chembee.plotting.evaluation)
plot_combined_bar_chart() (in module chembee.plotting.evaluation)
plot_comparison_1() (in module chembee.plotting.graphics)
plot_comparison_2() (in module chembee.plotting.graphics)
plot_comparison_3() (in module chembee.plotting.graphics)
plot_comparison_4() (in module chembee.plotting.graphics)
plot_compound_list() (in module chembee.plotting.compounds)
plot_data_set_distribution_by_col() (in module chembee.plotting.distribution)
plot_feature_importances() (in module chembee.plotting.feature_extraction)
plot_grouped_bar_chart() (in module chembee.plotting.evaluation)
plot_heat_map() (in module chembee.plotting.evaluation)
plot_heat_map_collection() (in module chembee.plotting.evaluation)
plot_roc_chart() (in module chembee.plotting.evaluation)
plot_roc_chart_collection() (in module chembee.plotting.evaluation)
plot_roc_chart_collection_strat() (in module chembee.plotting.evaluation)
plot_roc_chart_strat() (in module chembee.plotting.evaluation)
polar_plot() (in module chembee.plotting.lipinski)
precision() (in module chembee.actions.evaluation)
predict_proba() (chembee.config.calibration.linear_regression.LinearRegressionClass method)
(chembee.config.calibration.spectral_clustering.NaivlyCalibratedSpectralClustering method)
(chembee.config.calibration.svc.NaivelyCalibratedLinearSVC method)
(chembee.config.calibration.svc.NaivelyCalibratedSVC method)
prepare_data_decicion_lib() (in module chembee.utils.file_utils)
(in module chembee.utils.utils)
prepare_file_name_saving() (in module chembee.utils.file_utils)
R
RandomForestClassifier (class in chembee.config.benchmark.random_forest)
RandomForestClassifierAlgorithm (class in chembee.config.calibration.random_forest)
RBMClassifier (class in chembee.config.benchmark.restricted_bm)
recall() (in module chembee.actions.evaluation)
S
save_data_csv() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
(chembee.datasets.DataSet.DataSet method)
save_data_npy() (chembee.datasets.BreastCancer.BreastCancerDataset method)
save_data_sdf() (chembee.datasets.BioDegDataSet.BioDegDataSet method)
save_fig() (in module chembee.plotting.graphics)
save_json_to_file() (in module chembee.utils.file_utils)
save_model() (in module chembee.actions.save_model)
screen_calibration() (in module chembee.actions.calibration)
screen_classifier_for_metrics() (in module chembee.actions.evaluation)
screen_classifier_for_metrics_stratified() (in module chembee.actions.evaluation)
screen_cross_validation_grid_search() (in module chembee.actions.cross_validation)
screen_fingerprints_against_data() (in module chembee.actions.search)
specificity() (in module chembee.actions.evaluation)
SpectralClusteringClassifier (class in chembee.config.benchmark.spectral_clustering)
stratified_n_fold() (in module chembee.actions.cross_validation)
stratified_n_fold_filter() (in module chembee.actions.cross_validation)
SVClassifier (class in chembee.config.benchmark.svc)
SVCPolyClassifier (class in chembee.config.benchmark.svc_poly)
T
titles (chembee.config.benchmark.kmeans.KMeansClassifier attribute)
(chembee.config.benchmark.knn.KNNClassifier attribute)
(chembee.config.benchmark.linear_regression.LinearRegressionClassifier attribute)
(chembee.config.benchmark.logistic_regression.LogisticRegressionClassifier attribute)
(chembee.config.benchmark.mlp_classifier.NeuralNetworkClassifier attribute)
(chembee.config.benchmark.naive_bayes.NaiveBayesClassifier attribute)
(chembee.config.benchmark.random_forest.RandomForestClassifier attribute)
(chembee.config.benchmark.restricted_bm.RBMClassifier attribute)
(chembee.config.benchmark.spectral_clustering.SpectralClusteringClassifier attribute)
(chembee.config.benchmark.svc.SVClassifier attribute)
(chembee.config.benchmark.svc_poly.SVCPolyClassifier attribute)
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