Index

Symbols

--adjusttext asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option --algo <algorithm> asap-select command line option --algorithm asap-select command line option --algorithm <algorithm> asap-kde-kde_sklearn command line option --annotate <annotate> asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option --aspect_ratio <aspect_ratio> asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option --atom-gaussian-width <atom_gaussian_width> asap-gen_desc-soap command line option --axes <axes> asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map-pca command line option asap-map-raw command line option asap-map-skpca command line option asap-map-tsne command line option asap-map-umap command line option --bandwidth <bandwidth> asap-kde-kde_sklearn command line option --bw_method <bw_method> asap-kde-kde_scipy command line option --color <color> asap-map command line option --color_column <color_column> asap-map command line option --color_from_zero asap-map command line option --color_label <color_label> asap-map command line option --colormap <colormap> asap-map command line option --crossover asap-gen_desc-soap command line option --cutoff <cutoff> asap-gen_desc-acsf command line option asap-gen_desc-soap command line option --design_matrix <design_matrix> asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option asap-select command line option --dimension <dimension> asap-cluster-plot_pca command line option asap-kde-kde_internal command line option asap-kde-kde_scipy command line option asap-kde-kde_sklearn command line option asap-kde-plot_pca command line option asap-map-pca command line option asap-map-raw command line option asap-map-skpca command line option asap-map-tsne command line option asap-map-umap command line option --early_exaggeration <early_exaggeration> asap-map-tsne command line option --element_wise asap-gen_desc-acsf command line option asap-gen_desc-soap command line option --eps <eps> asap-cluster-dbscan command line option --extra-properties <extra_properties> asap-map command line option --fxyz <fxyz> asap-cluster command line option asap-fit command line option asap-gen_desc command line option asap-kde command line option asap-map command line option asap-select command line option --fxyz_format <fxyz_format> asap-gen_desc command line option --in <in_file> asap-gen_desc command line option --in_file asap-gen_desc command line option --keepraw asap-map command line option --kernel <kernel> asap-fit-kernelridge command line option asap-kde-kde_sklearn command line option asap-map-skpca command line option --kernel_matrix <kernel_matrix> asap-cluster command line option --kernel_parameter <kernel_parameter> asap-fit-kernelridge command line option asap-map-skpca command line option --lc_points <lc_points> asap-fit command line option --learning_curve <learning_curve> asap-fit command line option --learning_rate <learning_rate> asap-map-tsne command line option --lmax <lmax> asap-gen_desc-soap command line option --metric <metric> asap-cluster-dbscan command line option asap-kde-kde_sklearn command line option asap-map-tsne command line option asap-map-umap command line option --min_dist <min_dist> asap-map-umap command line option --min_samples <min_samples> asap-cluster-dbscan command line option --n_neighbors <n_neighbors> asap-map-umap command line option --n_sparse <n_sparse> asap-fit-kernelridge command line option asap-map-skpca command line option --nkeep <nkeep> asap-select command line option --nmax <nmax> asap-gen_desc-soap command line option --no-adjusttext asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option --no-crossover asap-gen_desc-soap command line option --no-keepraw asap-map command line option --no-pca asap-map-tsne command line option --no-periodic asap-gen_desc command line option --no-savetxt asap-cluster command line option asap-kde command line option asap-select command line option --no-savexyz asap-cluster command line option asap-kde command line option asap-select command line option --no-scale asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map-pca command line option asap-map-raw command line option asap-map-skpca command line option asap-map-tsne command line option asap-map-umap command line option --normalized_by_size asap-fit command line option asap-map command line option --nprocess <number_processes> asap-gen_desc command line option --number_processes asap-gen_desc command line option --only_use_species <only_use_species> asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option --output <output> asap-map command line option --pca asap-map-tsne command line option --peratom asap-cluster-plot_pca command line option asap-gen_desc-acsf command line option asap-gen_desc-soap command line option asap-kde-plot_pca command line option asap-map command line option --periodic asap-gen_desc command line option --perplexity <perplexity> asap-map-tsne command line option --prefix <prefix> asap-cluster command line option asap-cluster-plot_pca command line option asap-fit command line option asap-gen_desc command line option asap-kde command line option asap-kde-plot_pca command line option asap-map command line option asap-select command line option --rbf <rbf> asap-gen_desc-soap command line option --reducer_type <reducer_type> asap-gen_desc-acsf command line option asap-gen_desc-soap command line option

--savetxt asap-cluster command line option asap-kde command line option asap-select command line option --savexyz asap-cluster command line option asap-kde command line option asap-select command line option --scale asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map-pca command line option asap-map-raw command line option asap-map-skpca command line option asap-map-tsne command line option asap-map-umap command line option --sigma <sigma> asap-fit-kernelridge command line option asap-fit-ridge command line option --sparse_mode <sparse_mode> asap-fit-kernelridge command line option asap-map-skpca command line option --stride <stride> asap-gen_desc command line option --style <style> asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option --tag <tag> asap-gen_desc-acsf command line option asap-gen_desc-cm command line option asap-gen_desc-soap command line option --test <test_ratio> asap-fit command line option --test_ratio asap-fit command line option --uacsf <universal_acsf> asap-gen_desc-acsf command line option --universal_acsf asap-gen_desc-acsf command line option --universal_soap asap-gen_desc-soap command line option --use_atomic asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option --use_atomic_descriptors asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option --usoap <universal_soap> asap-gen_desc-soap command line option --y <y> asap-fit command line option --zeta <zeta> asap-gen_desc-acsf command line option asap-gen_desc-soap command line option -a asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option asap-select command line option -ar asap-cluster-plot_pca command line option asap-kde-plot_pca command line option asap-map command line option -bw asap-kde-kde_scipy command line option asap-kde-kde_sklearn command line option -c asap-gen_desc-acsf command line option asap-gen_desc-soap command line option asap-map command line option -c0 asap-map command line option -ccol asap-map command line option -clab asap-map command line option -cmap asap-map command line option -d asap-cluster-plot_pca command line option asap-kde-kde_internal command line option asap-kde-kde_scipy command line option asap-kde-kde_sklearn command line option asap-kde-plot_pca command line option asap-map-pca command line option asap-map-raw command line option asap-map-skpca command line option asap-map-tsne command line option asap-map-umap command line option -dm asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option asap-select command line option -e asap-cluster-dbscan command line option asap-gen_desc-acsf command line option asap-gen_desc-soap command line option asap-map-tsne command line option -ep asap-map command line option -f asap-cluster command line option asap-fit command line option asap-gen_desc command line option asap-kde command line option asap-map command line option asap-select command line option -g asap-gen_desc-soap command line option -i asap-gen_desc command line option -k asap-fit-kernelridge command line option asap-map-skpca command line option -km asap-cluster command line option -kp asap-fit-kernelridge command line option asap-map-skpca command line option -l asap-gen_desc-soap command line option asap-map-tsne command line option -lc asap-fit command line option -lcp asap-fit command line option -md asap-map-umap command line option -ms asap-cluster-dbscan command line option -n asap-fit-kernelridge command line option asap-gen_desc-soap command line option asap-map-skpca command line option asap-select command line option -nbs asap-fit command line option asap-map command line option -nn asap-map-umap command line option -np asap-gen_desc command line option -o asap-map command line option -p asap-cluster command line option asap-cluster-plot_pca command line option asap-fit command line option asap-gen_desc command line option asap-kde command line option asap-kde-plot_pca command line option asap-map command line option asap-map-tsne command line option asap-select command line option -pa asap-gen_desc-acsf command line option asap-gen_desc-soap command line option -r asap-gen_desc-acsf command line option asap-gen_desc-soap command line option -s asap-cluster-plot_pca command line option asap-fit-kernelridge command line option asap-gen_desc command line option asap-kde-plot_pca command line option asap-map command line option asap-map-skpca command line option -sigma asap-gen_desc-soap command line option -t asap-fit command line option -u asap-gen_desc-acsf command line option asap-gen_desc-soap command line option -ua asap-cluster command line option asap-fit command line option asap-kde command line option asap-map command line option -y asap-fit command line option -z asap-gen_desc-acsf command line option asap-gen_desc-soap command line option

A

abc2h() (in module asaplib.io.io_cell) add() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptors method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Descriptors method) (asaplib.descriptors.global_descriptors.Global_Descriptors method) (asaplib.kernel.kernel_transforms.Descriptors_to_Kernels method) (asaplib.plot.plotters.Plotters method) (asaplib.reducedim.dim_reducer.Dimension_Reducers method) add_score() (asaplib.fit.getscore.LC_SCOREBOARD method) add_subplot_axes() (in module asaplib.plot.plot_styles) array_handling() (in module asaplib.cluster.ml_cluster_tools) asap-cluster command line option --design_matrix <design_matrix> --fxyz <fxyz> --kernel_matrix <kernel_matrix> --no-savetxt --no-savexyz --only_use_species <only_use_species> --prefix <prefix> --savetxt --savexyz --use_atomic --use_atomic_descriptors -dm -f -km -p -ua asap-cluster-dbscan command line option --eps <eps> --metric <metric> --min_samples <min_samples> -e -ms asap-cluster-plot_pca command line option --adjusttext --annotate <annotate> --aspect_ratio <aspect_ratio> --axes <axes> --dimension <dimension> --no-adjusttext --no-scale --peratom --prefix <prefix> --scale --style <style> -a -ar -d -p -s asap-fit command line option --design_matrix <design_matrix> --fxyz <fxyz> --lc_points <lc_points> --learning_curve <learning_curve> --normalized_by_size --only_use_species <only_use_species> --prefix <prefix> --test <test_ratio> --test_ratio --use_atomic --use_atomic_descriptors --y <y> -dm -f -lc -lcp -nbs -p -t -ua -y asap-fit-kernelridge command line option --kernel <kernel> --kernel_parameter <kernel_parameter> --n_sparse <n_sparse> --sigma <sigma> --sparse_mode <sparse_mode> -k -kp -n -s asap-fit-ridge command line option --sigma <sigma> asap-gen_desc command line option --fxyz <fxyz> --fxyz_format <fxyz_format> --in <in_file> --in_file --no-periodic --nprocess <number_processes> --number_processes --periodic --prefix <prefix> --stride <stride> -f -i -np -p -s asap-gen_desc-acsf command line option --cutoff <cutoff> --element_wise --peratom --reducer_type <reducer_type> --tag <tag> --uacsf <universal_acsf> --universal_acsf --zeta <zeta> -c -e -pa -r -u -z asap-gen_desc-cm command line option --tag <tag> asap-gen_desc-soap command line option --atom-gaussian-width <atom_gaussian_width> --crossover --cutoff <cutoff> --element_wise --lmax <lmax> --nmax <nmax> --no-crossover --peratom --rbf <rbf> --reducer_type <reducer_type> --tag <tag> --universal_soap --usoap <universal_soap> --zeta <zeta> -c -e -g -l -n -pa -r -sigma -u -z asap-kde command line option --design_matrix <design_matrix> --fxyz <fxyz> --no-savetxt --no-savexyz --only_use_species <only_use_species> --prefix <prefix> --savetxt --savexyz --use_atomic --use_atomic_descriptors -dm -f -p -ua asap-kde-kde_internal command line option --dimension <dimension> -d asap-kde-kde_scipy command line option --bw_method <bw_method> --dimension <dimension> -bw -d asap-kde-kde_sklearn command line option --algorithm <algorithm> --bandwidth <bandwidth> --dimension <dimension> --kernel <kernel> --metric <metric> -bw -d asap-kde-plot_pca command line option --adjusttext --annotate <annotate> --aspect_ratio <aspect_ratio> --axes <axes> --dimension <dimension> --no-adjusttext --no-scale --peratom --prefix <prefix> --scale --style <style> -a -ar -d -p -s asap-map command line option --adjusttext --annotate <annotate> --aspect_ratio <aspect_ratio> --color <color> --color_column <color_column> --color_from_zero --color_label <color_label> --colormap <colormap> --design_matrix <design_matrix> --extra-properties <extra_properties> --fxyz <fxyz> --keepraw --no-adjusttext --no-keepraw --normalized_by_size --only_use_species <only_use_species> --output <output> --peratom --prefix <prefix> --style <style> --use_atomic --use_atomic_descriptors -a -ar -c -c0 -ccol -clab -cmap -dm -ep -f -nbs -o -p -s -ua

asap-map-pca command line option --axes <axes> --dimension <dimension> --no-scale --scale -d asap-map-raw command line option --axes <axes> --dimension <dimension> --no-scale --scale -d asap-map-skpca command line option --axes <axes> --dimension <dimension> --kernel <kernel> --kernel_parameter <kernel_parameter> --n_sparse <n_sparse> --no-scale --scale --sparse_mode <sparse_mode> -d -k -kp -n -s asap-map-tsne command line option --axes <axes> --dimension <dimension> --early_exaggeration <early_exaggeration> --learning_rate <learning_rate> --metric <metric> --no-pca --no-scale --pca --perplexity <perplexity> --scale -d -e -l -p asap-map-umap command line option --axes <axes> --dimension <dimension> --metric <metric> --min_dist <min_dist> --n_neighbors <n_neighbors> --no-scale --scale -d -md -nn asap-select command line option --algo <algorithm> --algorithm --design_matrix <design_matrix> --fxyz <fxyz> --nkeep <nkeep> --no-savetxt --no-savexyz --prefix <prefix> --savetxt --savexyz -a -dm -f -n -p asaplib module asaplib.cli module asaplib.cli.cmd_asap module asaplib.cli.cmd_cli_options module asaplib.cli.func_asap module asaplib.cluster module asaplib.cluster.ml_cluster_base module asaplib.cluster.ml_cluster_fit module asaplib.cluster.ml_cluster_tools module asaplib.compressor module asaplib.compressor.cur module asaplib.compressor.fps module asaplib.compressor.reweight module asaplib.compressor.sparsifier module asaplib.compressor.split module asaplib.data module asaplib.data.design_matrix module asaplib.data.xyz module asaplib.descriptors module asaplib.descriptors.atomic_descriptors module asaplib.descriptors.atomic_to_global module asaplib.descriptors.global_descriptors module asaplib.fit module asaplib.fit.base module asaplib.fit.getscore module asaplib.fit.krr module asaplib.fit.ridgeregression module asaplib.fit.sparse_krr_wrapper module asaplib.hypers module asaplib.hypers.hyper_acsf module asaplib.hypers.hyper_soap module asaplib.hypers.symfun_gen module asaplib.hypers.test module asaplib.hypers.univeral_length_scales module asaplib.io module asaplib.io.cscope module asaplib.io.io_cell module asaplib.io.io_parse module asaplib.kde module asaplib.kde.density_estimation module asaplib.kde.density_estimation_internal module asaplib.kernel module asaplib.kernel.kernel_transforms module asaplib.kernel.ml_kernel_operations module asaplib.plot module asaplib.plot.plot_colors module asaplib.plot.plot_styles module asaplib.plot.plotters module asaplib.reducedim module asaplib.reducedim.dim_reducer module asaplib.reducedim.ml_kpca module asaplib.reducedim.ml_pca module asaplib.reducedim.sparse_kpca module asaplib.util module asaplib.util.util_fft module asaplib.util.util_gettcv module ASAPXYZ (class in asaplib.data.xyz) Atomic_2_Global_Average (class in asaplib.descriptors.atomic_to_global) Atomic_2_Global_Base (class in asaplib.descriptors.atomic_to_global) Atomic_2_Global_Descriptors (class in asaplib.descriptors.atomic_to_global) Atomic_2_Global_Moment_Average (class in asaplib.descriptors.atomic_to_global) Atomic_2_Global_Moment_Sum (class in asaplib.descriptors.atomic_to_global) Atomic_2_Global_Sum (class in asaplib.descriptors.atomic_to_global) Atomic_Descriptor_ACSF (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_Base (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_FCHL19 (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_LMBTR (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_LMBTR_K2 (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_LMBTR_K3 (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptor_SOAP (class in asaplib.descriptors.atomic_descriptors) Atomic_Descriptors (class in asaplib.descriptors.atomic_descriptors) atomic_to_global_desc_options() (in module asaplib.cli.cmd_cli_options)

B

bandwidth_estimate() (asaplib.kde.density_estimation_internal.KDE_internal method) bind() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptors method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Descriptors method) (asaplib.descriptors.global_descriptors.Global_Descriptors method) (asaplib.kernel.kernel_transforms.Descriptors_to_Kernels method) (asaplib.plot.plotters.Plotters method) (asaplib.reducedim.dim_reducer.Dimension_Reducers method)

C

center_square() (asaplib.reducedim.ml_kpca.KernelPCA static method) centering() (asaplib.reducedim.ml_pca.PCA method) cluster_process() (in module asaplib.cli.func_asap) ClusterBase (class in asaplib.cluster.ml_cluster_base) COLOR_PALETTE (class in asaplib.plot.plot_colors) color_setup_options() (in module asaplib.cli.cmd_cli_options) compute() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptors method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Descriptors method) (asaplib.descriptors.global_descriptors.Global_Descriptors method) (asaplib.kernel.kernel_transforms.Descriptors_to_Kernels method) compute_atomic_descriptors() (asaplib.data.xyz.ASAPXYZ method) compute_fit() (asaplib.data.design_matrix.Design_Matrix method) compute_global_descriptors() (asaplib.data.xyz.ASAPXYZ method) compute_learning_curve() (asaplib.data.design_matrix.Design_Matrix method) ConvertStrToList (class in asaplib.io.io_parse) create() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_ACSF method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_FCHL19 method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_SOAP method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Average method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Moment_Average method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Moment_Sum method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Sum method) (asaplib.descriptors.global_descriptors.Global_Descriptor_Base method) (asaplib.descriptors.global_descriptors.Global_Descriptor_CM method) (asaplib.descriptors.global_descriptors.Global_Descriptor_from_Atomic method) (asaplib.descriptors.global_descriptors.Global_Descriptor_Morgan method) (asaplib.plot.plotters.Plot_Function_Annotate method) (asaplib.plot.plotters.Plot_Function_Base method) (asaplib.plot.plotters.Plot_Function_Cluster method) (asaplib.plot.plotters.Plot_Function_Scatter method)

cur_column_select() (in module asaplib.compressor.cur) CUR_deterministic() (in module asaplib.compressor.cur) CUR_deterministic_step() (in module asaplib.compressor.cur)

D

d_reduce_options() (in module asaplib.cli.cmd_cli_options) DBCluster (class in asaplib.cluster.ml_cluster_fit) default() (asaplib.io.io_parse.NpDecoder method) (asaplib.io.io_parse.NpEncoder method) desc_options() (in module asaplib.cli.cmd_cli_options) Descriptor_By_Species() (in module asaplib.descriptors.atomic_to_global)

Descriptors_to_Kernels (class in asaplib.kernel.kernel_transforms) Design_Matrix (class in asaplib.data.design_matrix) Dimension_Reducers (class in asaplib.reducedim.dim_reducer) distorho_quick() (in module asaplib.kernel.ml_kernel_operations) dm_input_options() (in module asaplib.cli.cmd_cli_options) dump_all() (asaplib.fit.getscore.LC_SCOREBOARD method)

E

estimate_delta() (asaplib.cluster.ml_cluster_fit.old_LAIO method) evaluate_density() (asaplib.kde.density_estimation.KDE_scipy method) (asaplib.kde.density_estimation.KDE_sklearn method) (asaplib.kde.density_estimation.Kernel_Density_Base method) (asaplib.kde.density_estimation_internal.KDE_internal method)

exponential_split() (in module asaplib.compressor.split) extract_from_nested_dict() (in module asaplib.io.io_parse)

F

fast_fps() (in module asaplib.compressor.fps) fetch() (asaplib.fit.getscore.LC_SCOREBOARD method) fetch_all() (asaplib.fit.getscore.LC_SCOREBOARD method) fetch_computed_descriptors() (asaplib.data.xyz.ASAPXYZ method) fftcrosscorr() (in module asaplib.util.util_fft) fftranform() (in module asaplib.util.util_fft) figure_style_setups() (in module asaplib.cli.func_asap) file_input_format_options() (in module asaplib.cli.cmd_cli_options) file_input_options() (in module asaplib.cli.cmd_cli_options) file_output_options() (in module asaplib.cli.cmd_cli_options) find_optimal_bandwidth() (asaplib.kde.density_estimation_internal.KDE_internal method) fit() (asaplib.cluster.ml_cluster_base.ClusterBase method) (asaplib.cluster.ml_cluster_base.FitClusterBase method) (asaplib.cluster.ml_cluster_fit.DBCluster method) (asaplib.cluster.ml_cluster_fit.LAIO_DB method) (asaplib.cluster.ml_cluster_fit.old_LAIO method) (asaplib.cluster.ml_cluster_fit.sklearn_DB method) (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method) (asaplib.kde.density_estimation.KDE_scipy method) (asaplib.kde.density_estimation.KDE_sklearn method) (asaplib.kde.density_estimation.Kernel_Density_Base method) (asaplib.kde.density_estimation_internal.KDE_internal method) (asaplib.reducedim.dim_reducer.Dimension_Reducers method) (asaplib.reducedim.ml_kpca.KernelPCA method) (asaplib.reducedim.ml_pca.PCA method) (asaplib.reducedim.sparse_kpca.SPARSE_KPCA method)

fit_evaluate_density() (asaplib.kde.density_estimation.Kernel_Density_Base method) fit_predict() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRRSparse method) fit_predict_error() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRRSparse method) fit_setup_options() (in module asaplib.cli.cmd_cli_options) fit_transform() (asaplib.reducedim.dim_reducer.Dimension_Reducers method) (asaplib.reducedim.ml_kpca.KernelPCA method) (asaplib.reducedim.ml_pca.PCA method) (asaplib.reducedim.sparse_kpca.SPARSE_KPCA method) fit_vectors() (asaplib.reducedim.ml_kpca.KernelPCA method) FitClusterBase (class in asaplib.cluster.ml_cluster_base) fps() (in module asaplib.compressor.fps)

G

gen_default_acsf_hyperparameters() (in module asaplib.hypers.hyper_acsf) gen_default_soap_hyperparameters() (in module asaplib.hypers.hyper_soap) genh2abc() (in module asaplib.io.io_cell) get_acronym() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptors method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base method) (asaplib.descriptors.global_descriptors.Global_Descriptor_Base method) (asaplib.kde.density_estimation.Kernel_Density_Base method) (asaplib.kernel.kernel_transforms.Descriptors_to_Kernels method) (asaplib.kernel.kernel_transforms.Kernel_Function_Base method) (asaplib.plot.plotters.Plot_Function_Base method) (asaplib.plot.plotters.Plotters method) get_assignation() (asaplib.cluster.ml_cluster_fit.LAIO_DB method) get_atomic_descriptors() (asaplib.data.xyz.ASAPXYZ method) get_atomic_property() (asaplib.data.xyz.ASAPXYZ method) get_cluster_labels() (asaplib.cluster.ml_cluster_base.ClusterBase method) (asaplib.cluster.ml_cluster_fit.DBCluster method) get_cluster_properties() (in module asaplib.cluster.ml_cluster_tools) get_cluster_size() (in module asaplib.cluster.ml_cluster_tools) get_cluster_weighted_avg_properties() (in module asaplib.cluster.ml_cluster_tools) get_dc() (asaplib.cluster.ml_cluster_fit.LAIO_DB method) get_decision_graph() (asaplib.cluster.ml_cluster_fit.LAIO_DB method) get_descriptors() (asaplib.data.xyz.ASAPXYZ method) get_global_species() (asaplib.data.xyz.ASAPXYZ method) get_mae() (in module asaplib.fit.getscore) get_n_cluster() (asaplib.cluster.ml_cluster_fit.DBCluster method) get_n_noise() (asaplib.cluster.ml_cluster_fit.DBCluster method) get_n_splits() (asaplib.compressor.split.LCSplit method) get_name() (asaplib.cluster.ml_cluster_base.ClusterBase method) (asaplib.fit.base.RegressorBase method)

get_natom_list() (asaplib.data.xyz.ASAPXYZ method) get_natom_list_by_species() (asaplib.data.xyz.ASAPXYZ method) get_num_frames() (asaplib.data.xyz.ASAPXYZ method) get_params() (asaplib.cluster.ml_cluster_base.ClusterBase method) (asaplib.compressor.split.KFold method) (asaplib.compressor.split.LCSplit method) (asaplib.compressor.split.ShuffleSplit method) (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method) get_property() (asaplib.data.xyz.ASAPXYZ method) get_r2() (in module asaplib.fit.getscore) get_rmse() (in module asaplib.fit.getscore) get_score() (in module asaplib.fit.getscore) get_sparsified_matrix() (asaplib.data.design_matrix.Design_Matrix method) get_spearman() (in module asaplib.fit.getscore) get_sup() (in module asaplib.fit.getscore) get_total_natoms() (asaplib.data.xyz.ASAPXYZ method) get_train_test_error() (asaplib.fit.base.RegressorBase method) get_xyz() (asaplib.data.xyz.ASAPXYZ method) getcomplextxv() (in module asaplib.util.util_gettcv) getfftxv() (in module asaplib.util.util_gettcv) gettxv() (in module asaplib.util.util_gettcv) Global_Descriptor_Base (class in asaplib.descriptors.global_descriptors) Global_Descriptor_CM (class in asaplib.descriptors.global_descriptors) Global_Descriptor_from_Atomic (class in asaplib.descriptors.global_descriptors) Global_Descriptor_Morgan (class in asaplib.descriptors.global_descriptors) Global_Descriptors (class in asaplib.descriptors.global_descriptors)

H

h2abc() (in module asaplib.io.io_cell)

h2abc_deg() (in module asaplib.io.io_cell)

I

ifftranform() (in module asaplib.util.util_fft) irfftranform() (in module asaplib.util.util_fft)

is_atomic() (asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base method) (asaplib.descriptors.global_descriptors.Global_Descriptor_Base method)

K

KDE_internal (class in asaplib.kde.density_estimation_internal) kde_process() (in module asaplib.cli.func_asap) KDE_scipy (class in asaplib.kde.density_estimation) KDE_sklearn (class in asaplib.kde.density_estimation) Kernel_Density_Base (class in asaplib.kde.density_estimation) Kernel_Function_Base (class in asaplib.kernel.kernel_transforms) Kernel_Function_Cosine (class in asaplib.kernel.kernel_transforms) Kernel_Function_Linear (class in asaplib.kernel.kernel_transforms) Kernel_Function_Polynomial (class in asaplib.kernel.kernel_transforms) kernel_options() (in module asaplib.cli.cmd_cli_options)

kernel_random_split() (in module asaplib.compressor.split) KernelPCA (class in asaplib.reducedim.ml_kpca) kerneltodis() (in module asaplib.kernel.ml_kernel_operations) kerneltodis_linear() (in module asaplib.kernel.ml_kernel_operations) kerneltorho() (in module asaplib.kernel.ml_kernel_operations) KFold (class in asaplib.compressor.split) km_input_options() (in module asaplib.cli.cmd_cli_options) KRR (class in asaplib.fit.krr) KRRFastCV (class in asaplib.fit.krr) KRRSparse (class in asaplib.fit.krr)

L

LAIO_DB (class in asaplib.cluster.ml_cluster_fit) LC_SCOREBOARD (class in asaplib.fit.getscore) LCSplit (class in asaplib.compressor.split) list2str() (in module asaplib.io.io_parse) load_asapxyz() (in module asaplib.cli.func_asap) load_in_file() (in module asaplib.cli.func_asap) load_properties() (asaplib.data.xyz.ASAPXYZ method)

loads() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method) log_likelihood_test_set() (asaplib.kde.density_estimation_internal.KDE_internal method)

M

main() (in module asaplib.hypers.symfun_gen) (in module asaplib.hypers.test) map_io_options() (in module asaplib.cli.cmd_cli_options) map_plot() (in module asaplib.cli.func_asap) map_process() (in module asaplib.cli.func_asap) map_save() (in module asaplib.cli.func_asap) map_setup_options() (in module asaplib.cli.cmd_cli_options) module asaplib asaplib.cli asaplib.cli.cmd_asap asaplib.cli.cmd_cli_options asaplib.cli.func_asap asaplib.cluster asaplib.cluster.ml_cluster_base asaplib.cluster.ml_cluster_fit asaplib.cluster.ml_cluster_tools asaplib.compressor asaplib.compressor.cur asaplib.compressor.fps asaplib.compressor.reweight asaplib.compressor.sparsifier asaplib.compressor.split asaplib.data asaplib.data.design_matrix asaplib.data.xyz asaplib.descriptors asaplib.descriptors.atomic_descriptors asaplib.descriptors.atomic_to_global asaplib.descriptors.global_descriptors asaplib.fit asaplib.fit.base asaplib.fit.getscore asaplib.fit.krr asaplib.fit.ridgeregression asaplib.fit.sparse_krr_wrapper asaplib.hypers asaplib.hypers.hyper_acsf asaplib.hypers.hyper_soap asaplib.hypers.symfun_gen asaplib.hypers.test asaplib.hypers.univeral_length_scales asaplib.io asaplib.io.cscope asaplib.io.io_cell asaplib.io.io_parse asaplib.kde asaplib.kde.density_estimation asaplib.kde.density_estimation_internal asaplib.kernel asaplib.kernel.kernel_transforms asaplib.kernel.ml_kernel_operations asaplib.plot asaplib.plot.plot_colors asaplib.plot.plot_styles asaplib.plot.plotters asaplib.reducedim asaplib.reducedim.dim_reducer asaplib.reducedim.ml_kpca asaplib.reducedim.ml_pca asaplib.reducedim.sparse_kpca asaplib.util asaplib.util.util_fft asaplib.util.util_gettcv

most_frequent() (in module asaplib.cluster.ml_cluster_tools)

N

normalizekernel() (in module asaplib.kernel.ml_kernel_operations)

NpDecoder (class in asaplib.io.io_parse) NpEncoder (class in asaplib.io.io_parse)

O

old_LAIO (class in asaplib.cluster.ml_cluster_fit) output_cluster() (in module asaplib.cluster.ml_cluster_tools)

output_cluster_sort() (in module asaplib.cluster.ml_cluster_tools) output_desc() (in module asaplib.cli.func_asap) output_setup_options() (in module asaplib.cli.cmd_cli_options)

P

pack() (asaplib.cluster.ml_cluster_fit.DBCluster method) (asaplib.cluster.ml_cluster_fit.LAIO_DB method) (asaplib.cluster.ml_cluster_fit.old_LAIO method) (asaplib.cluster.ml_cluster_fit.sklearn_DB method) (asaplib.descriptors.atomic_descriptors.Atomic_Descriptors method) (asaplib.descriptors.atomic_to_global.Atomic_2_Global_Descriptors method) (asaplib.descriptors.global_descriptors.Global_Descriptor_from_Atomic method) (asaplib.descriptors.global_descriptors.Global_Descriptors method) (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method) (asaplib.kernel.kernel_transforms.Descriptors_to_Kernels method) (asaplib.plot.plotters.Plotters method) (asaplib.reducedim.dim_reducer.Dimension_Reducers method) para_options() (in module asaplib.cli.cmd_cli_options) pbcdist() (in module asaplib.io.io_cell) PCA (class in asaplib.reducedim.ml_pca)

plot() (asaplib.plot.plotters.Plotters method) plot_cluster_w_label() (in module asaplib.plot.plot_styles) plot_cluster_w_size() (in module asaplib.plot.plot_styles) plot_density_map() (in module asaplib.plot.plot_styles) Plot_Function_Annotate (class in asaplib.plot.plotters) Plot_Function_Base (class in asaplib.plot.plotters) Plot_Function_Cluster (class in asaplib.plot.plotters) Plot_Function_Scatter (class in asaplib.plot.plotters) plot_learning_curve() (asaplib.fit.getscore.LC_SCOREBOARD method) plot_outlier_scatter() (in module asaplib.plot.plot_styles) plot_scatter_w_label() (in module asaplib.plot.plot_styles) Plotters (class in asaplib.plot.plotters) predict() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method) predict_error() (asaplib.fit.base.RegressorBase method) predict_uncertainty() (asaplib.fit.krr.KRR method) PythonLiteralOption (class in asaplib.io.io_parse)

R

random_split() (in module asaplib.compressor.split) randomString() (in module asaplib.io.io_parse) read_xyz_n_dm() (in module asaplib.cli.func_asap) RegressorBase (class in asaplib.fit.base) remove_atomic_descriptors() (asaplib.data.xyz.ASAPXYZ method) remove_descriptors() (asaplib.data.xyz.ASAPXYZ method)

reweight() (in module asaplib.compressor.reweight) rfftcrosscorr() (in module asaplib.util.util_fft) rfftranform() (in module asaplib.util.util_fft) RidgeRegression (class in asaplib.fit.ridgeregression) round_float() (in module asaplib.kde.density_estimation_internal) round_sigfigs() (in module asaplib.hypers.univeral_length_scales)

S

save_descriptor_acronym_state() (asaplib.data.xyz.ASAPXYZ method) save_state() (asaplib.cluster.ml_cluster_fit.DBCluster method) (asaplib.data.design_matrix.Design_Matrix method) (asaplib.data.xyz.ASAPXYZ method) scalecenter_matrix() (asaplib.reducedim.ml_pca.PCA method) set_atomic_descriptors() (asaplib.data.xyz.ASAPXYZ method) set_color_function() (in module asaplib.plot.plot_colors) set_descriptors() (asaplib.data.xyz.ASAPXYZ method) set_nice_font() (in module asaplib.plot.plot_styles) set_params() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method)

set_reducer() (in module asaplib.cli.func_asap) ShuffleSplit (class in asaplib.compressor.split) sklearn_DB (class in asaplib.cluster.ml_cluster_fit) smooth() (in module asaplib.util.util_fft) SPARSE_KPCA (class in asaplib.reducedim.sparse_kpca) SPARSE_KRR_Wrapper (class in asaplib.fit.sparse_krr_wrapper) sparsification_options() (in module asaplib.cli.cmd_cli_options) Sparsifier (class in asaplib.compressor.sparsifier) sparsify() (asaplib.compressor.sparsifier.Sparsifier method) (asaplib.data.design_matrix.Design_Matrix method) split() (asaplib.compressor.split.LCSplit method) standardize() (asaplib.data.xyz.ASAPXYZ method) state_input_options() (in module asaplib.cli.cmd_cli_options) str2bool() (in module asaplib.io.io_parse) symmetrise() (asaplib.data.xyz.ASAPXYZ method) system_pair_bond_lengths() (in module asaplib.hypers.univeral_length_scales)

T

transform() (asaplib.kernel.kernel_transforms.Kernel_Function_Base method) (asaplib.kernel.kernel_transforms.Kernel_Function_Cosine method) (asaplib.kernel.kernel_transforms.Kernel_Function_Linear method) (asaplib.kernel.kernel_transforms.Kernel_Function_Polynomial method) (asaplib.reducedim.dim_reducer.Dimension_Reducers method) (asaplib.reducedim.ml_kpca.KernelPCA method) (asaplib.reducedim.ml_pca.PCA method) (asaplib.reducedim.sparse_kpca.SPARSE_KPCA method)

transform_vectors() (asaplib.reducedim.ml_kpca.KernelPCA method) type_cast_value() (asaplib.io.io_parse.ConvertStrToList method) (asaplib.io.io_parse.PythonLiteralOption method)

U

universal_acsf_hyper() (in module asaplib.hypers.hyper_acsf) universal_soap_hyper() (in module asaplib.hypers.hyper_soap) unpack() (asaplib.fit.base.RegressorBase method) (asaplib.fit.krr.KRR method) (asaplib.fit.krr.KRRFastCV method) (asaplib.fit.krr.KRRSparse method) (asaplib.fit.ridgeregression.RidgeRegression method) (asaplib.fit.sparse_krr_wrapper.SPARSE_KRR_Wrapper method)

W

write() (asaplib.data.xyz.ASAPXYZ method) write_atomic_descriptor_matrix() (asaplib.data.xyz.ASAPXYZ method) write_chemiscope() (asaplib.data.xyz.ASAPXYZ method)

write_chemiscope_input() (in module asaplib.io.cscope) write_computed_descriptors() (asaplib.data.xyz.ASAPXYZ method) write_descriptor_matrix() (asaplib.data.xyz.ASAPXYZ method)