CatLearn
latest
User Guide:
Installation
Changelog
Version 0.6.1 (April 2019)
Version 0.6.0 (January 2019)
Version 0.5.0 (October 2018)
Version 0.4.4 (August 2018)
Version 0.4.3 (May 2018)
Version 0.4.2 (May 2018)
Version 0.4.1 (April 2018)
Version 0.4.0 (April 2018)
Version 0.3.1 (February 2018)
Version 0.3.0 (February 2018)
Version 0.2.1 (February 2018)
Version 0.2.0 (January 2018)
Version 0.1.0 (December 2017)
Contributing
Code:
catlearn.api
catlearn.cross_validation
catlearn.featurize package
catlearn.fingerprint package
catlearn.ga
catlearn.learning_curve
catlearn.preprocess
catlearn.regression
catlearn.active_learning package
catlearn.estimator package
catlearn.optimize package
catlearn.utilities
CatLearn
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Z
A
AA_kernel() (in module catlearn.regression.gpfunctions.kernels)
acquire() (catlearn.active_learning.algorithm.ActiveLearning method)
ActiveLearning (class in catlearn.active_learning.algorithm)
ads_av() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
ads_index() (in module catlearn.featurize.adsorbate_prep)
ads_sum() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
AdsorbateFingerprintGenerator (class in catlearn.fingerprint.adsorbate)
alpha_finder() (catlearn.learning_curve.feature_selection.feature_selection method)
alpha_refinment() (catlearn.learning_curve.feature_selection.feature_selection method)
apply_mask() (in module catlearn.optimize.constraints)
array_to_ase() (in module catlearn.optimize.io)
array_to_atoms() (in module catlearn.optimize.io)
ase_connectivity() (in module catlearn.utilities.neighborlist)
ase_neighborlist() (in module catlearn.utilities.neighborlist)
ase_to_catlearn() (in module catlearn.optimize.io)
ase_to_networkx() (in module catlearn.api.networkx_graph_api)
ASECalc (class in catlearn.optimize.mlneb)
attach_cations() (in module catlearn.featurize.adsorbate_prep)
auto_layers() (in module catlearn.featurize.adsorbate_prep)
AutoCorrelationFingerprintGenerator (class in catlearn.fingerprint.molecule)
autogen_info() (in module catlearn.featurize.adsorbate_prep)
average_nested() (catlearn.learning_curve.data_process.data_process method)
B
backward_selection() (catlearn.regression.gpfunctions.sensitivity.SensitivityAnalysis method)
bag_atoms_ads() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_cn() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_cn_general() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_edges() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
bag_edges_ads() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_edges_all() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_edges_chemi() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bag_edges_cn() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
bag_element_cn() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
bag_elements() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
BaseGenerator (class in catlearn.featurize.base)
bond_count_vec() (catlearn.fingerprint.particle.ParticleFingerprintGenerator method)
bootstrap_calc() (catlearn.regression.ridge_regression.RidgeRegression method)
bulk() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
bulk_average() (catlearn.fingerprint.bulk.BulkFingerprintGenerator method)
bulk_std() (catlearn.fingerprint.bulk.BulkFingerprintGenerator method)
bulk_summation() (catlearn.fingerprint.bulk.BulkFingerprintGenerator method)
BulkFingerprintGenerator (class in catlearn.fingerprint.bulk)
C
calculate() (catlearn.optimize.functions_calc.GoldsteinPrice method)
(catlearn.optimize.functions_calc.Himmelblau method)
(catlearn.optimize.functions_calc.ModifiedHimmelblau method)
(catlearn.optimize.functions_calc.MullerBrown method)
(catlearn.optimize.functions_calc.MultiModal method)
(catlearn.optimize.functions_calc.NoiseHimmelblau method)
(catlearn.optimize.functions_calc.Rosenbrock method)
(catlearn.optimize.mlneb.ASECalc method)
catalysis_hub_to_info() (in module catlearn.featurize.adsorbate_prep)
catlearn (module)
catlearn.active_learning (module)
catlearn.active_learning.acquisition_functions (module)
catlearn.active_learning.algorithm (module)
catlearn.api (module)
catlearn.api.ase_atoms_api (module)
catlearn.api.ase_data_setup (module)
catlearn.api.networkx_graph_api (module)
catlearn.cross_validation (module)
catlearn.cross_validation.hierarchy_cv (module)
catlearn.cross_validation.k_fold_cv (module)
catlearn.estimator (module)
catlearn.estimator.general_gp (module)
catlearn.estimator.general_kernel (module)
catlearn.estimator.general_preprocess (module)
catlearn.featurize (module)
catlearn.featurize.adsorbate_prep (module)
catlearn.featurize.base (module)
catlearn.featurize.neighbor_matrix (module)
catlearn.featurize.periodic_table_data (module)
catlearn.featurize.setup (module)
catlearn.featurize.slab_utilities (module)
catlearn.fingerprint (module)
catlearn.fingerprint.adsorbate (module)
catlearn.fingerprint.bulk (module)
catlearn.fingerprint.chalcogenide (module)
catlearn.fingerprint.convoluted (module)
catlearn.fingerprint.graph (module)
catlearn.fingerprint.molecule (module)
catlearn.fingerprint.particle (module)
catlearn.fingerprint.prototype (module)
catlearn.fingerprint.standard (module)
catlearn.fingerprint.voro (module)
catlearn.ga (module)
catlearn.ga.algorithm (module)
catlearn.ga.convergence (module)
catlearn.ga.initialize (module)
catlearn.ga.io (module)
catlearn.ga.mating (module)
catlearn.ga.mutate (module)
catlearn.ga.natural_selection (module)
catlearn.ga.predictors (module)
catlearn.learning_curve (module)
catlearn.learning_curve.data_process (module)
catlearn.learning_curve.feature_selection (module)
catlearn.learning_curve.learning_curve (module)
catlearn.learning_curve.placeholder (module)
catlearn.optimize (module)
catlearn.optimize.constraints (module)
catlearn.optimize.functions_calc (module)
catlearn.optimize.io (module)
catlearn.optimize.mlneb (module)
catlearn.optimize.tools (module)
catlearn.preprocess (module)
catlearn.preprocess.clean_data (module)
catlearn.preprocess.feature_elimination (module)
catlearn.preprocess.feature_engineering (module)
catlearn.preprocess.feature_extraction (module)
catlearn.preprocess.greedy_elimination (module)
catlearn.preprocess.importance_testing (module)
catlearn.preprocess.scaling (module)
catlearn.regression (module)
catlearn.regression.cost_function (module)
catlearn.regression.gaussian_process (module)
catlearn.regression.gpfunctions (module)
catlearn.regression.gpfunctions.covariance (module)
catlearn.regression.gpfunctions.default_scale (module)
catlearn.regression.gpfunctions.hyperparameter_scaling (module)
catlearn.regression.gpfunctions.io (module)
catlearn.regression.gpfunctions.kernel_scaling (module)
catlearn.regression.gpfunctions.kernel_setup (module)
catlearn.regression.gpfunctions.kernels (module)
catlearn.regression.gpfunctions.log_marginal_likelihood (module)
catlearn.regression.gpfunctions.sensitivity (module)
catlearn.regression.gpfunctions.uncertainty (module)
catlearn.regression.ridge_regression (module)
catlearn.regression.scikit_wrapper (module)
catlearn.utilities (module)
catlearn.utilities.clustering (module)
catlearn.utilities.database_functions (module)
catlearn.utilities.distribution (module)
catlearn.utilities.neighborlist (module)
catlearn.utilities.penalty_functions (module)
catlearn.utilities.sammon (module)
catlearn.utilities.utilities (module)
catlearn_neighborlist() (in module catlearn.utilities.neighborlist)
catlearn_pca() (in module catlearn.preprocess.feature_extraction)
ChalcogenideFingerprintGenerator (class in catlearn.fingerprint.chalcogenide)
check_labels() (in module catlearn.featurize.base)
check_length() (in module catlearn.fingerprint.convoluted)
check_reconstructions() (in module catlearn.featurize.adsorbate_prep)
classify() (in module catlearn.active_learning.acquisition_functions)
clean_infinite() (in module catlearn.preprocess.clean_data)
clean_skewness() (in module catlearn.preprocess.clean_data)
clean_variance() (in module catlearn.preprocess.clean_data)
cluster() (in module catlearn.active_learning.acquisition_functions)
cluster_features() (in module catlearn.utilities.clustering)
compare_slab_connectivity() (in module catlearn.featurize.adsorbate_prep)
composition_vec() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
connection_dict() (in module catlearn.featurize.neighbor_matrix)
connection_matrix() (in module catlearn.featurize.neighbor_matrix)
connections_vec() (catlearn.fingerprint.particle.ParticleFingerprintGenerator method)
connectivity2ads_index() (in module catlearn.featurize.adsorbate_prep)
connectivity_termination() (in module catlearn.featurize.adsorbate_prep)
constant_kernel() (in module catlearn.regression.gpfunctions.kernels)
constant_multi_kernel() (in module catlearn.regression.gpfunctions.kernels)
constraints_termination() (in module catlearn.featurize.adsorbate_prep)
conv_bulk() (catlearn.fingerprint.convoluted.ConvolutedFingerprintGenerator method)
conv_term() (catlearn.fingerprint.convoluted.ConvolutedFingerprintGenerator method)
Convergence (class in catlearn.ga.convergence)
ConvolutedFingerprintGenerator (class in catlearn.fingerprint.convoluted)
count_chemisorbed_fragment() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
create_column() (catlearn.utilities.database_functions.DescriptorDatabase method)
create_db() (catlearn.utilities.database_functions.DescriptorDatabase method)
create_mask() (in module catlearn.optimize.constraints)
create_ml_neb() (in module catlearn.optimize.mlneb)
create_table() (catlearn.utilities.database_functions.FingerprintDB method)
ctime() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
cut_and_splice() (in module catlearn.ga.mating)
D
data_process (class in catlearn.learning_curve.data_process)
database_to_list() (in module catlearn.api.ase_atoms_api)
db_size() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
dbid() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
default_catlearn_radius() (in module catlearn.featurize.periodic_table_data)
default_fingerprinters() (in module catlearn.featurize.setup)
default_lengthscale() (in module catlearn.estimator.general_kernel)
default_parameters (catlearn.optimize.functions_calc.MullerBrown attribute)
delta_energy() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
DescriptorDatabase (class in catlearn.utilities.database_functions)
detect_adsorbate() (in module catlearn.featurize.adsorbate_prep)
detect_termination() (in module catlearn.featurize.adsorbate_prep)
distance_vec() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
distribution_vec() (catlearn.fingerprint.particle.ParticleFingerprintGenerator method)
dK_dtheta_j() (in module catlearn.regression.gpfunctions.log_marginal_likelihood)
E
EI() (in module catlearn.active_learning.acquisition_functions)
eigenspectrum_vec() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
element_mass_vec() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
element_parameter_vec() (catlearn.fingerprint.standard.StandardFingerprintGenerator method)
eliminate_features() (catlearn.preprocess.feature_elimination.FeatureScreening method)
en_difference_active() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
en_difference_ads() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
en_difference_chemi() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
ensemble_test() (catlearn.active_learning.algorithm.ActiveLearning method)
eval_and_append() (in module catlearn.optimize.mlneb)
extend_atoms_class() (in module catlearn.api.ase_atoms_api)
F
feature_frequency() (in module catlearn.learning_curve.learning_curve)
feature_inspection() (catlearn.learning_curve.feature_selection.feature_selection method)
feature_invariance() (in module catlearn.preprocess.importance_testing)
feature_randomize() (in module catlearn.preprocess.importance_testing)
feature_select() (catlearn.regression.scikit_wrapper.RegressionFit method)
feature_selection (class in catlearn.learning_curve.feature_selection)
feature_shuffle() (in module catlearn.preprocess.importance_testing)
FeatureGenerator (class in catlearn.featurize.setup)
FeatureScreening (class in catlearn.preprocess.feature_elimination)
featurize_atomic_pairs() (catlearn.featurize.setup.FeatureGenerator method)
fill_db() (catlearn.utilities.database_functions.DescriptorDatabase method)
find_optimal_regularization() (catlearn.regression.ridge_regression.RidgeRegression method)
fingerprint_entry() (catlearn.utilities.database_functions.FingerprintDB method)
FingerprintDB (class in catlearn.utilities.database_functions)
fitness (catlearn.ga.algorithm.GeneticAlgorithm attribute)
formal_charges() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
(in module catlearn.utilities.utilities)
formula2ads_index() (in module catlearn.featurize.adsorbate_prep)
G
gaussian_dk_dwidth() (in module catlearn.regression.gpfunctions.kernels)
gaussian_kernel() (in module catlearn.regression.gpfunctions.kernels)
gaussian_process_predict() (catlearn.estimator.general_gp.GeneralGaussianProcess method)
gaussian_xx_gradients() (in module catlearn.regression.gpfunctions.kernels)
gaussian_xxp_gradients() (in module catlearn.regression.gpfunctions.kernels)
GaussianProcess (class in catlearn.regression.gaussian_process)
general_kernel() (in module catlearn.estimator.general_kernel)
GeneralGaussianProcess (class in catlearn.estimator.general_gp)
generalized_cn() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
GeneralPrepreprocess (class in catlearn.estimator.general_preprocess)
generate() (catlearn.fingerprint.prototype.PrototypeFingerprintGenerator method)
(catlearn.fingerprint.voro.VoronoiFingerprintGenerator method)
generate_all() (catlearn.fingerprint.prototype.PrototypeFingerprintGenerator method)
generate_features() (in module catlearn.preprocess.feature_engineering)
generate_positive_features() (in module catlearn.preprocess.feature_engineering)
GeneticAlgorithm (class in catlearn.ga.algorithm)
geometry_hash() (in module catlearn.utilities.utilities)
get_ablog() (in module catlearn.preprocess.feature_engineering)
get_all_distances() (catlearn.featurize.base.BaseGenerator method)
get_atomic_numbers() (catlearn.featurize.base.BaseGenerator method)
get_autocorrelation() (catlearn.fingerprint.molecule.AutoCorrelationFingerprintGenerator method)
get_coefficients() (catlearn.regression.ridge_regression.RidgeRegression method)
get_column_names() (catlearn.utilities.database_functions.DescriptorDatabase method)
get_covariance() (in module catlearn.regression.gpfunctions.covariance)
get_data_scale() (catlearn.learning_curve.placeholder.placeholder method)
get_dataframe() (catlearn.featurize.setup.FeatureGenerator method)
get_div_order_2() (in module catlearn.preprocess.feature_engineering)
get_energy_catlearn() (in module catlearn.optimize.mlneb)
get_error() (in module catlearn.regression.cost_function)
get_features() (in module catlearn.api.ase_atoms_api)
get_fingerprints() (catlearn.utilities.database_functions.FingerprintDB method)
get_fmax() (in module catlearn.optimize.mlneb)
get_forces_catlearn() (in module catlearn.optimize.mlneb)
get_graph() (in module catlearn.api.ase_atoms_api)
get_labels_ablog() (in module catlearn.preprocess.feature_engineering)
get_labels_order_2() (in module catlearn.preprocess.feature_engineering)
get_labels_order_2ab() (in module catlearn.preprocess.feature_engineering)
get_masses() (catlearn.featurize.base.BaseGenerator method)
get_mendeleev_params() (in module catlearn.featurize.periodic_table_data)
get_neighborlist() (catlearn.featurize.base.BaseGenerator method)
(in module catlearn.api.ase_atoms_api)
get_order_2() (in module catlearn.preprocess.feature_engineering)
get_order_2ab() (in module catlearn.preprocess.feature_engineering)
get_parameters() (catlearn.utilities.database_functions.FingerprintDB method)
get_positions() (catlearn.featurize.base.BaseGenerator method)
get_radius() (in module catlearn.featurize.periodic_table_data)
get_results_predicted_path() (in module catlearn.optimize.mlneb)
get_statistic() (catlearn.learning_curve.data_process.data_process method)
get_subset_data() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
get_train() (in module catlearn.api.ase_data_setup)
get_uncertainty() (in module catlearn.regression.gpfunctions.uncertainty)
get_unique() (in module catlearn.api.ase_data_setup)
getstats() (catlearn.learning_curve.placeholder.placeholder method)
globalscaledata() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
globalscaling() (catlearn.learning_curve.data_process.data_process method)
GoldsteinPrice (class in catlearn.optimize.functions_calc)
GraphFingerprintGenerator (class in catlearn.fingerprint.graph)
greedy_elimination() (catlearn.preprocess.greedy_elimination.GreedyElimination method)
GreedyElimination (class in catlearn.preprocess.greedy_elimination)
H
Hierarchy (class in catlearn.cross_validation.hierarchy_cv)
hierarchy() (in module catlearn.learning_curve.learning_curve)
Himmelblau (class in catlearn.optimize.functions_calc)
holdout_set() (in module catlearn.utilities.utilities)
hyperparameters() (in module catlearn.regression.gpfunctions.hyperparameter_scaling)
I
image_entry() (catlearn.utilities.database_functions.FingerprintDB method)
images_connectivity() (in module catlearn.api.ase_atoms_api)
images_pair_distances() (in module catlearn.api.ase_atoms_api)
implemented_properties (catlearn.optimize.functions_calc.GoldsteinPrice attribute)
(catlearn.optimize.functions_calc.Himmelblau attribute)
(catlearn.optimize.functions_calc.ModifiedHimmelblau attribute)
(catlearn.optimize.functions_calc.MullerBrown attribute)
(catlearn.optimize.functions_calc.MultiModal attribute)
(catlearn.optimize.functions_calc.NoiseHimmelblau attribute)
(catlearn.optimize.functions_calc.Rosenbrock attribute)
(catlearn.optimize.mlneb.ASECalc attribute)
importance_elimination() (catlearn.preprocess.importance_testing.ImportanceElimination method)
ImportanceElimination (class in catlearn.preprocess.importance_testing)
info2primary_index() (in module catlearn.featurize.adsorbate_prep)
initialize_population() (in module catlearn.ga.initialize)
interval_modifier() (catlearn.learning_curve.feature_selection.feature_selection method)
is_metal() (in module catlearn.featurize.slab_utilities)
is_oxide() (in module catlearn.featurize.slab_utilities)
iterative_screen() (catlearn.preprocess.feature_elimination.FeatureScreening method)
K
k_fold() (in module catlearn.cross_validation.k_fold_cv)
kdict2list() (in module catlearn.regression.gpfunctions.kernel_setup)
kdicts2list() (in module catlearn.regression.gpfunctions.kernel_setup)
kernel_scaling() (in module catlearn.regression.gpfunctions.kernel_scaling)
L
laplacian_dk_dwidth() (in module catlearn.regression.gpfunctions.kernels)
laplacian_kernel() (in module catlearn.regression.gpfunctions.kernels)
last2ads_index() (in module catlearn.featurize.adsorbate_prep)
layers2ads_index() (in module catlearn.featurize.adsorbate_prep)
layers_termination() (in module catlearn.featurize.adsorbate_prep)
LearningCurve (class in catlearn.learning_curve.learning_curve)
linear_kernel() (in module catlearn.regression.gpfunctions.kernels)
list2kdict() (in module catlearn.regression.gpfunctions.kernel_setup)
list_mendeleev_params() (in module catlearn.featurize.periodic_table_data)
load_split() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
log_marginal_likelihood() (in module catlearn.regression.gpfunctions.log_marginal_likelihood)
M
make_labels() (in module catlearn.featurize.periodic_table_data)
make_neighborlist() (catlearn.featurize.base.BaseGenerator method)
matrix_to_nl() (in module catlearn.api.networkx_graph_api)
max_cation() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
max_site() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
mean_cation() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
mean_chemisorbed_atoms() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
mean_site() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
mean_surf_ligands() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
median_cation() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
median_site() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
min_cation() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
min_max() (in module catlearn.preprocess.scaling)
min_site() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
minimize_error() (in module catlearn.ga.predictors)
minimize_error_descriptors() (in module catlearn.ga.predictors)
minimize_error_time() (in module catlearn.ga.predictors)
MLNEB (class in catlearn.optimize.mlneb)
ModifiedHimmelblau (class in catlearn.optimize.functions_calc)
MullerBrown (class in catlearn.optimize.functions_calc)
MultiModal (class in catlearn.optimize.functions_calc)
N
n_outer() (in module catlearn.featurize.periodic_table_data)
nearestneighbour_vec() (catlearn.fingerprint.particle.ParticleFingerprintGenerator method)
neighbor_features() (in module catlearn.featurize.neighbor_matrix)
neighbor_mean_vec() (catlearn.fingerprint.graph.GraphFingerprintGenerator method)
neighbor_sum_vec() (catlearn.fingerprint.graph.GraphFingerprintGenerator method)
networkx_to_adjacency() (in module catlearn.api.networkx_graph_api)
no_progress() (catlearn.ga.convergence.Convergence method)
noise_multi_kernel() (in module catlearn.regression.gpfunctions.kernels)
NoiseHimmelblau (class in catlearn.optimize.functions_calc)
nolabel (catlearn.optimize.functions_calc.GoldsteinPrice attribute)
(catlearn.optimize.functions_calc.Himmelblau attribute)
(catlearn.optimize.functions_calc.ModifiedHimmelblau attribute)
(catlearn.optimize.functions_calc.MullerBrown attribute)
(catlearn.optimize.functions_calc.MultiModal attribute)
(catlearn.optimize.functions_calc.NoiseHimmelblau attribute)
(catlearn.optimize.functions_calc.Rosenbrock attribute)
(catlearn.optimize.mlneb.ASECalc attribute)
normalize() (in module catlearn.preprocess.scaling)
normalize_features() (catlearn.featurize.setup.FeatureGenerator method)
O
optimistic() (in module catlearn.active_learning.acquisition_functions)
optimistic_proximity() (in module catlearn.active_learning.acquisition_functions)
optimize_hyperparameters() (catlearn.regression.gaussian_process.GaussianProcess method)
P
pair_deviation() (in module catlearn.utilities.distribution)
pair_distribution() (in module catlearn.utilities.distribution)
parameter_entry() (catlearn.utilities.database_functions.FingerprintDB method)
ParticleFingerprintGenerator (class in catlearn.fingerprint.particle)
pca() (in module catlearn.preprocess.feature_extraction)
penalty_close() (catlearn.utilities.penalty_functions.PenaltyFunctions method)
penalty_far() (catlearn.utilities.penalty_functions.PenaltyFunctions method)
PenaltyFunctions (class in catlearn.utilities.penalty_functions)
PI() (in module catlearn.active_learning.acquisition_functions)
placeholder (class in catlearn.learning_curve.placeholder)
plotneb() (in module catlearn.optimize.tools)
pls() (in module catlearn.preprocess.feature_extraction)
population (catlearn.ga.algorithm.GeneticAlgorithm attribute)
population_reduction() (in module catlearn.ga.natural_selection)
predict() (catlearn.regression.gaussian_process.GaussianProcess method)
(catlearn.regression.ridge_regression.RidgeRegression method)
predict_subsets() (catlearn.learning_curve.placeholder.placeholder method)
predict_uncertainty() (catlearn.regression.gaussian_process.GaussianProcess method)
prediction_error() (catlearn.learning_curve.data_process.data_process method)
prepare_kernels() (in module catlearn.regression.gpfunctions.kernel_setup)
print_cite_mlmin() (in module catlearn.optimize.io)
print_cite_mlneb() (in module catlearn.optimize.io)
print_info() (in module catlearn.optimize.io)
print_info_neb() (in module catlearn.optimize.io)
print_time() (in module catlearn.optimize.io)
print_version() (in module catlearn.optimize.io)
probability_density() (in module catlearn.active_learning.acquisition_functions)
probability_include() (in module catlearn.ga.mutate)
probability_remove() (in module catlearn.ga.mutate)
process() (catlearn.estimator.general_preprocess.GeneralPrepreprocess method)
property_matrix() (in module catlearn.featurize.neighbor_matrix)
PrototypeFingerprintGenerator (class in catlearn.fingerprint.prototype)
PrototypeSites (class in catlearn.fingerprint.prototype)
proximity() (in module catlearn.active_learning.acquisition_functions)
Q
quadratic_dk_ddegree() (in module catlearn.regression.gpfunctions.kernels)
quadratic_dk_dslope() (in module catlearn.regression.gpfunctions.kernels)
quadratic_kernel() (in module catlearn.regression.gpfunctions.kernels)
query_db() (catlearn.utilities.database_functions.DescriptorDatabase method)
R
random_acquisition() (in module catlearn.active_learning.acquisition_functions)
random_permutation() (in module catlearn.ga.mutate)
rank() (in module catlearn.active_learning.acquisition_functions)
rdf_vec() (catlearn.fingerprint.particle.ParticleFingerprintGenerator method)
read() (in module catlearn.regression.gpfunctions.io)
read_data() (in module catlearn.ga.io)
read_split() (in module catlearn.cross_validation.k_fold_cv)
read_train_data() (in module catlearn.regression.gpfunctions.io)
reg_data_var() (catlearn.learning_curve.placeholder.placeholder method)
reg_feat_var() (catlearn.learning_curve.placeholder.placeholder method)
RegressionFit (class in catlearn.regression.scikit_wrapper)
regularization() (catlearn.regression.ridge_regression.RidgeRegression method)
remove_duplicates() (in module catlearn.ga.natural_selection)
remove_outliers() (in module catlearn.preprocess.clean_data)
rescale_hyperparameters() (in module catlearn.regression.gpfunctions.hyperparameter_scaling)
rescale_targets() (catlearn.regression.gpfunctions.default_scale.ScaleData method)
return_names() (catlearn.featurize.setup.FeatureGenerator method)
return_vec() (catlearn.featurize.setup.FeatureGenerator method)
RidgeRegression (class in catlearn.regression.ridge_regression)
Rosenbrock (class in catlearn.optimize.functions_calc)
RR() (catlearn.regression.ridge_regression.RidgeRegression method)
run() (catlearn.learning_curve.learning_curve.LearningCurve method)
(catlearn.optimize.mlneb.MLNEB method)
run_proto() (catlearn.fingerprint.prototype.PrototypeFingerprintGenerator method)
run_voro() (catlearn.fingerprint.voro.VoronoiFingerprintGenerator method)
S
sammons_error() (in module catlearn.utilities.sammon)
scaled_sqe_kernel() (in module catlearn.regression.gpfunctions.kernels)
ScaleData (class in catlearn.regression.gpfunctions.default_scale)
scaling_data() (catlearn.learning_curve.data_process.data_process method)
screen() (catlearn.preprocess.feature_elimination.FeatureScreening method)
search() (catlearn.ga.algorithm.GeneticAlgorithm method)
selection() (catlearn.learning_curve.feature_selection.feature_selection method)
SensitivityAnalysis (class in catlearn.regression.gpfunctions.sensitivity)
set_features() (in module catlearn.api.ase_atoms_api)
set_graph() (in module catlearn.api.ase_atoms_api)
set_neighborlist() (in module catlearn.api.ase_atoms_api)
single_transform() (in module catlearn.preprocess.feature_engineering)
slab_index() (in module catlearn.featurize.adsorbate_prep)
slab_layers() (in module catlearn.featurize.slab_utilities)
slab_positions2ads_index() (in module catlearn.featurize.adsorbate_prep)
smooth_kernel() (in module catlearn.estimator.general_kernel)
spca() (in module catlearn.preprocess.feature_extraction)
split_index() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
split_predict() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
sqe_kernel() (in module catlearn.regression.gpfunctions.kernels)
stagnation() (catlearn.ga.convergence.Convergence method)
StandardFingerprintGenerator (class in catlearn.fingerprint.standard)
standardize() (in module catlearn.preprocess.scaling)
stat_mendeleev_params() (in module catlearn.featurize.periodic_table_data)
stoichiometry() (in module catlearn.featurize.slab_utilities)
store_results_neb() (in module catlearn.optimize.io)
store_trajectory_neb() (in module catlearn.optimize.io)
strain() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
sum_cation() (catlearn.fingerprint.chalcogenide.ChalcogenideFingerprintGenerator method)
sum_site() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
sym2ads_index() (in module catlearn.featurize.adsorbate_prep)
T
tags2ads_index() (in module catlearn.featurize.adsorbate_prep)
tags_termination() (in module catlearn.featurize.adsorbate_prep)
target_center() (in module catlearn.preprocess.scaling)
target_correlation() (in module catlearn.utilities.utilities)
target_normalize() (in module catlearn.preprocess.scaling)
target_standardize() (in module catlearn.preprocess.scaling)
term() (catlearn.fingerprint.adsorbate.AdsorbateFingerprintGenerator method)
termination_info() (in module catlearn.featurize.adsorbate_prep)
test() (catlearn.regression.gpfunctions.default_scale.ScaleData method)
test_acquisition() (catlearn.active_learning.algorithm.ActiveLearning method)
todb() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
train() (catlearn.regression.gpfunctions.default_scale.ScaleData method)
train_gaussian_process() (catlearn.estimator.general_gp.GeneralGaussianProcess method)
train_gp_model() (in module catlearn.optimize.mlneb)
transform() (catlearn.estimator.general_preprocess.GeneralPrepreprocess method)
transform_output() (catlearn.cross_validation.hierarchy_cv.Hierarchy method)
U
UCB() (in module catlearn.active_learning.acquisition_functions)
unit_length() (in module catlearn.preprocess.scaling)
unmask_geometry() (in module catlearn.optimize.constraints)
update_data() (catlearn.regression.gaussian_process.GaussianProcess method)
update_descriptor() (catlearn.utilities.database_functions.DescriptorDatabase method)
update_gp() (catlearn.regression.gaussian_process.GaussianProcess method)
update_str() (catlearn.fingerprint.prototype.PrototypeFingerprintGenerator method)
V
VoronoiFingerprintGenerator (class in catlearn.fingerprint.voro)
W
write() (in module catlearn.regression.gpfunctions.io)
write_proto_input() (catlearn.fingerprint.prototype.PrototypeFingerprintGenerator method)
write_split() (in module catlearn.cross_validation.k_fold_cv)
write_train_data() (in module catlearn.regression.gpfunctions.io)
write_voro_input() (catlearn.fingerprint.voro.VoronoiFingerprintGenerator method)
X
xyz_id() (catlearn.fingerprint.bulk.BulkFingerprintGenerator method)
Z
z2ads_index() (in module catlearn.featurize.adsorbate_prep)
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