Index

A

abs_path (madas.backend.backend_core.Backend property) (madas.backend.dictionary_backend.DictBackend property) add_fingerprint() (madas.data_framework.MaterialsDatabase method) add_fingerprints() (madas.data_framework.MaterialsDatabase method) add_many() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method) add_material() (madas.data_framework.MaterialsDatabase method) add_property() (madas.data_framework.MaterialsDatabase method) add_single() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method)

align() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) API (class in madas.apis.local_data_API) (class in madas.apis.NOMAD_web_API) api_call() (in module madas.apis.api_core) APIClass (class in madas.apis.api_core) APIError ASEBackend (class in madas.backend.ASE_backend)

B

Backend (class in madas.backend.backend_core) batch_iterator (madas.similarity.BatchedSimilarityMatrix property) batch_size (madas.similarity.BatchedSimilarityMatrix property) (madas.utils.BatchIterator property)

BatchedSimilarityMatrix (class in madas.similarity) batches (madas.utils.BatchIterator property) BatchIterator (class in madas.utils)

C

calculate() (madas.fingerprint.Fingerprint method) (madas.fingerprints.DOS_fingerprint.DOSFingerprint method) (madas.fingerprints.DUMMY_fingerprint.DUMMYFingerprint method) (madas.fingerprints.PROP_fingerprint.PROPFingerprint method) (madas.similarity.BatchedSimilarityMatrix method) (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method)

call_single() (madas.analysis.MetricSpaceTest method) cluster() (madas.clustering.SimilarityMatrixClusterer method) column_mids (madas.similarity.OverlapSimilarityMatrix property) copy() (madas.fingerprint.Fingerprint method) CSVPropertyReader (class in madas.apis.local_data_API)

D

data (madas.fingerprint.Fingerprint property) DatabaseEntryDoesNotExistError dataframe (madas.similarity.SimilarityMatrix property) default() (madas.utils.JSONNumpyEncoder method) deserialize() (madas.fingerprint.Fingerprint class method)

DictBackend (class in madas.backend.dictionary_backend) DOS_similarity() (in module madas.fingerprints.DOS_fingerprint) DOSFingerprint (class in madas.fingerprints.DOS_fingerprint) DUMMY_similarity() (in module madas.fingerprints.DUMMY_fingerprint) DUMMYFingerprint (class in madas.fingerprints.DUMMY_fingerprint)

F

failed_download (madas.apis.NOMAD_web_API.API property) FileReader (class in madas.apis.local_data_API) FileReaderASE (class in madas.apis.local_data_API) fill_database() (madas.data_framework.MaterialsDatabase method) Fingerprint (class in madas.fingerprint) fingerprint_file_batches() (madas.similarity.BatchedSimilarityMatrix method) fingerprints_from_batch_file() (madas.similarity.BatchedSimilarityMatrix method)

folder_path (madas.similarity.BatchedSimilarityMatrix property) fp_type (madas.fingerprint.Fingerprint property) from_json() (madas.backend.dictionary_backend.DictBackend static method) from_material() (madas.fingerprint.Fingerprint method) (madas.fingerprints.DOS_fingerprint.DOSFingerprint method) (madas.fingerprints.DUMMY_fingerprint.DUMMYFingerprint method) (madas.fingerprints.PROP_fingerprint.PROPFingerprint method) from_nomad_dos_fingerprint() (madas.fingerprints.DOS_fingerprint.DOSFingerprint class method)

G

gen_fingerprint_batch_file_name() (madas.similarity.BatchedSimilarityMatrix method) gen_matrix_batch_file_name() (madas.similarity.BatchedSimilarityMatrix method) get_archive() (in module madas.apis.NOMAD_web_API) get_atoms() (in module madas.apis.NOMAD_web_API) get_batch_rows() (madas.utils.BatchIterator method) get_batches_for_index() (madas.utils.BatchIterator method) get_by_id() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method) get_calculation() (madas.apis.api_core.APIClass method) (madas.apis.local_data_API.API method) (madas.apis.NOMAD_web_API.API method) get_calculations_by_search() (madas.apis.api_core.APIClass method) (madas.apis.local_data_API.API method) (madas.apis.NOMAD_web_API.API method) get_cleared_matrix() (madas.similarity.SimilarityMatrix method) get_cluster_size() (madas.clustering.SimilarityMatrixClusterer method) get_cluster_sub_matrix() (madas.clustering.SimilarityMatrixClusterer method) get_column() (madas.similarity.OverlapSimilarityMatrix method) get_data_json() (madas.fingerprint.Fingerprint method) get_default_processing() (madas.apis.NOMAD_web_API.API static method) get_entries() (madas.similarity.OverlapSimilarityMatrix method) get_entry() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) get_entry_histogram() (madas.similarity.BatchedSimilarityMatrix method) get_fingerprint() (madas.data_framework.MaterialsDatabase method) get_fingerprints() (madas.data_framework.MaterialsDatabase method) get_k_most_similar() (madas.similarity.SimilarityMatrix method) get_label_dict() (madas.clustering.SimilarityMatrixClusterer method) get_length() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method)

get_many() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method) get_matching_matrices() (madas.similarity.SimilarityMatrix method) get_metadata() (madas.data_framework.MaterialsDatabase method) (madas.similarity.SimilarityMatrix method) get_mids_by_cluster_label() (madas.clustering.SimilarityMatrixClusterer method) get_mids_sorted_by_cluster_labels() (madas.clustering.SimilarityMatrixClusterer method) get_overlap_matrix() (madas.similarity.SimilarityMatrix method) get_properties() (madas.data_framework.MaterialsDatabase method) get_property() (madas.apis.api_core.APIClass method) (madas.apis.local_data_API.API method) (madas.apis.NOMAD_web_API.API method) (madas.data_framework.MaterialsDatabase method) get_property_dataframe() (madas.data_framework.MaterialsDatabase method) get_random() (madas.data_framework.MaterialsDatabase method) get_row() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) get_row_by_mid() (madas.similarity.BatchedSimilarityMatrix method) get_similarities() (madas.fingerprint.Fingerprint method) get_similarity() (madas.fingerprint.Fingerprint method) get_similarity_matrix() (madas.data_framework.MaterialsDatabase method) get_single() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method) get_sorted_similarity_matrix() (madas.clustering.SimilarityMatrixClusterer method) get_sub_matrix() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) get_symmetric_matrix() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) get_unique_entries() (madas.similarity.SimilarityMatrix method)

H

has_entry() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method)

hash_query() (madas.apis.api_core.APIClass method)

I

identity() (madas.analysis.MetricSpaceTest static method)

J

JSONNumpyEncoder (class in madas.utils)

L

labels (madas.clustering.SimilarityMatrixClusterer property) linear_batch_list() (madas.utils.BatchIterator static method) load() (madas.clustering.SimilarityMatrixClusterer static method) (madas.similarity.SimilarityMatrix static method)

log (madas.backend.backend_core.Backend property) lookup_similarity() (madas.similarity.SimilarityMatrix method)

M

madas.analysis module madas.apis.api_core module madas.apis.local_data_API module madas.apis.NOMAD_web_API module madas.backend.ASE_backend module madas.backend.backend_core module madas.backend.dictionary_backend module madas.data_framework module madas.fingerprints.DOS_fingerprint module madas.fingerprints.DUMMY_fingerprint module madas.fingerprints.PROP_fingerprint module madas.material module madas.utils module Material (class in madas.material)

MaterialsDatabase (class in madas.data_framework) matrices_for_this_task (madas.similarity.BatchedSimilarityMatrix property) matrix (madas.clustering.SimilarityMatrixClusterer property) (madas.similarity.SimilarityMatrix property) metadata (madas.backend.backend_core.Backend property) (madas.similarity.BatchedSimilarityMatrix property) metadata_filename (madas.similarity.BatchedSimilarityMatrix property) MetricSpaceTest (class in madas.analysis) mid (madas.fingerprint.Fingerprint property) mid_filename (madas.similarity.BatchedSimilarityMatrix property) mids (madas.clustering.SimilarityMatrixClusterer property) (madas.similarity.OverlapSimilarityMatrix property) (madas.similarity.SimilarityMatrix property) module madas.analysis madas.apis.api_core madas.apis.local_data_API madas.apis.NOMAD_web_API madas.backend.ASE_backend madas.backend.backend_core madas.backend.dictionary_backend madas.data_framework madas.fingerprints.DOS_fingerprint madas.fingerprints.DUMMY_fingerprint madas.fingerprints.PROP_fingerprint madas.material madas.utils most_similar_materials_filename (madas.similarity.BatchedSimilarityMatrix property)

N

n_entries (madas.utils.BatchIterator property) n_tasks (madas.similarity.BatchedSimilarityMatrix property)

name (madas.fingerprint.Fingerprint property) nclusters (madas.clustering.SimilarityMatrixClusterer property)

O

OverlapSimilarityMatrix (class in madas.similarity)

P

pass_on_exceptions (madas.fingerprint.Fingerprint property) plot() (madas.fingerprints.DOS_fingerprint.DOSFingerprint method) (madas.similarity.SimilarityMatrix method) plot_batch_rows() (madas.utils.BatchIterator method) plot_batches() (madas.utils.BatchIterator method)

print_dict_tree() (in module madas.utils) print_key_paths() (in module madas.utils) processing (madas.apis.NOMAD_web_API.API property) PROP_similarity() (in module madas.fingerprints.PROP_fingerprint) PROPFingerprint (class in madas.fingerprints.PROP_fingerprint)

R

read() (madas.apis.local_data_API.CSVPropertyReader method) (madas.apis.local_data_API.FileReaderASE method) report_error() (in module madas.utils)

resolve_nested_dict() (in module madas.utils) retry() (madas.apis.NOMAD_web_API.API method) rmsle() (in module madas.utils) row_mids (madas.similarity.OverlapSimilarityMatrix property)

S

safe_log() (in module madas.utils) save() (madas.clustering.SimilarityMatrixClusterer method) (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) save_metadata() (madas.similarity.BatchedSimilarityMatrix method) seed_random_number_generators() (in module madas.utils) serialize() (madas.fingerprint.Fingerprint method) set_clusterer_params() (madas.clustering.SimilarityMatrixClusterer method) set_data() (madas.fingerprint.Fingerprint method) set_dataframe() (madas.similarity.SimilarityMatrix method) set_file_path() (madas.apis.local_data_API.FileReader method) set_import_function() (madas.fingerprint.Fingerprint method) set_logger() (madas.apis.api_core.APIClass method) (madas.backend.backend_core.Backend method) set_matrix() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method)

set_metadata() (madas.similarity.SimilarityMatrix method) set_mid() (madas.fingerprint.Fingerprint method) set_mids() (madas.similarity.OverlapSimilarityMatrix method) (madas.similarity.SimilarityMatrix method) set_name() (madas.data_framework.MaterialsDatabase method) set_pass_on_exceptions() (madas.fingerprint.Fingerprint method) set_processing() (madas.apis.NOMAD_web_API.API method) set_similarity_function() (madas.fingerprint.Fingerprint method) SimilarityMatrix (class in madas.similarity) SimilarityMatrixClusterer (class in madas.clustering) size (madas.similarity.BatchedSimilarityMatrix property) specify() (madas.fingerprint.Fingerprint method) StrideSpectrumComparison (class in madas.analysis) symmetric (madas.similarity.BatchedSimilarityMatrix property) symmetry() (madas.analysis.MetricSpaceTest static method)

T

task_id (madas.similarity.BatchedSimilarityMatrix property) to_json() (madas.backend.dictionary_backend.DictBackend method)

train_test_split() (madas.similarity.SimilarityMatrix method) transpose() (madas.similarity.OverlapSimilarityMatrix method) triangle_inequality() (madas.analysis.MetricSpaceTest static method)

U

unique_labels (madas.clustering.SimilarityMatrixClusterer property) uniqueness() (madas.analysis.MetricSpaceTest static method) update_derived_properties() (madas.data_framework.MaterialsDatabase method) update_entries() (madas.data_framework.MaterialsDatabase method) update_entry() (madas.data_framework.MaterialsDatabase method) update_many() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method)

update_metadata() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method) update_single() (madas.backend.ASE_backend.ASEBackend method) (madas.backend.backend_core.Backend method) (madas.backend.dictionary_backend.DictBackend method)

W

write_most_similar_materials_file() (madas.similarity.BatchedSimilarityMatrix method)