Index

_

__init__() (noctis.data_transformation.neo4j.neo4j_formatter.Neo4jResultFormatter method) (noctis.data_transformation.postprocessing.chemdata_generators.ChemDataGeneratorFactory method) (noctis.data_transformation.postprocessing.chemdata_generators.ChemDataGeneratorInterface method) (noctis.data_transformation.postprocessing.chemdata_generators.NetworkXGenerator method) (noctis.data_transformation.postprocessing.chemdata_generators.PandasGenerator method) (noctis.data_transformation.postprocessing.chemdata_generators.ReactionStringGenerator method) (noctis.data_transformation.postprocessing.chemdata_generators.SyngraphGenerator method) (noctis.data_transformation.preprocessing.core_graph_builder.CoreGraphBuilder method) (noctis.data_transformation.preprocessing.core_graph_builder.FormatValidator method) (noctis.data_transformation.preprocessing.core_graph_builder.UnvalidatedStringBuilder method) (noctis.data_transformation.preprocessing.core_graph_builder.ValidatedStringBuilder method) (noctis.data_transformation.preprocessing.data_preprocessing.ChemicalStringPreprocessorBase method) (noctis.data_transformation.preprocessing.data_preprocessing.CSVPreprocessor method) (noctis.data_transformation.preprocessing.data_preprocessing.DataFramePreprocessor method) (noctis.data_transformation.preprocessing.data_preprocessing.PandasRowPreprocessorBase method) (noctis.data_transformation.preprocessing.data_preprocessing.Preprocessor method) (noctis.data_transformation.preprocessing.data_preprocessing.PreprocessorConfig method) (noctis.data_transformation.preprocessing.data_preprocessing.PythonObjectPreprocessorFactory method) (noctis.data_transformation.preprocessing.data_preprocessing.PythonObjectPreprocessorInterface method) (noctis.data_transformation.preprocessing.data_preprocessing.ReactionStringsPreprocessor method) (noctis.data_transformation.preprocessing.data_preprocessing.SynGraphPreprocessor method) (noctis.data_transformation.preprocessing.graph_expander.GraphExpander method) (noctis.repository.neo4j.neo4j_queries.Neo4jQueryRegistry method) (noctis.repository.neo4j.neo4j_repository.Neo4jRepository method)

_convert_datacontainer_to_query() (in module noctis.repository.neo4j.neo4j_functions) _convert_record_to_query_neo4j() (in module noctis.repository.neo4j.neo4j_functions) _create_neo4j_import_path() (in module noctis.repository.neo4j.neo4j_functions) _create_node_queries() (in module noctis.repository.neo4j.neo4j_functions) _create_relationship_queries() (in module noctis.repository.neo4j.neo4j_functions) _delete_tmp_folder() (in module noctis.data_transformation.preprocessing.utilities) _generate_files_string() (in module noctis.repository.neo4j.neo4j_functions) _generate_nodes_files_string() (in module noctis.repository.neo4j.neo4j_functions) _generate_properties_assignment() (in module noctis.repository.neo4j.neo4j_functions) _generate_relationships_files_string() (in module noctis.repository.neo4j.neo4j_functions) _get_dict_keys_from_csv() (in module noctis.repository.neo4j.neo4j_functions) _merge_partition_files() (in module noctis.data_transformation.preprocessing.utilities) _save_dataframes_to_partition_csv() (in module noctis.data_transformation.preprocessing.utilities) _save_list_to_partition_csv() (in module noctis.data_transformation.preprocessing.utilities) _update_partition_dict_with_row() (in module noctis.data_transformation.preprocessing.utilities)

A

add_record() (noctis.data_architecture.datacontainer.DataContainer method)

B

base_nodes (noctis.data_architecture.graph_schema.GraphSchema attribute) base_relationships (noctis.data_architecture.graph_schema.GraphSchema attribute) batch_size (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute)

between_intr_in_rel (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) build_from_dict() (noctis.data_architecture.graph_schema.GraphSchema class method) (noctis.repository.neo4j.neo4j_queries.CustomQuery class method) build_from_file() (noctis.data_architecture.graph_schema.GraphSchema class method)

C

ce_label (noctis.data_architecture.datacontainer.DataContainer attribute) ChemDataGeneratorFactory (class in noctis.data_transformation.postprocessing.chemdata_generators) ChemDataGeneratorInterface (class in noctis.data_transformation.postprocessing.chemdata_generators) ChemicalStringPreprocessorBase (class in noctis.data_transformation.preprocessing.data_preprocessing)

CoreGraphBuilder (class in noctis.data_transformation.preprocessing.core_graph_builder) create_data_container() (in module noctis.data_transformation.preprocessing.utilities) create_noctis_node() (in module noctis.data_transformation.preprocessing.utilities) create_noctis_relationship() (in module noctis.data_transformation.preprocessing.utilities) CSVPreprocessor (class in noctis.data_transformation.preprocessing.data_preprocessing)

D

data (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) data_type (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute)

DataFramePreprocessor (class in noctis.data_transformation.preprocessing.data_preprocessing) delimiter (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) dict_to_list() (in module noctis.data_transformation.preprocessing.utilities)

E

end_at_last_intermediate (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) end_node (noctis.data_architecture.datamodel.Relationship attribute) ensure_relationship_nodes_present() (noctis.data_architecture.datamodel.GraphRecord method) ensure_unique_nodes() (noctis.data_architecture.datamodel.GraphRecord class method)

ensure_unique_relationships() (noctis.data_architecture.datamodel.GraphRecord class method) explode_smiles_like_reaction_string() (in module noctis.data_transformation.preprocessing.utilities) explode_v3000_reaction_string() (in module noctis.data_transformation.preprocessing.utilities) extra_nodes (noctis.data_architecture.graph_schema.GraphSchema attribute) extra_relationships (noctis.data_architecture.graph_schema.GraphSchema attribute)

F

field_terminator (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) file_path (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute)

folder_path (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) format_result() (in module noctis.data_transformation.neo4j.neo4j_formatter) FormatValidator (class in noctis.data_transformation.preprocessing.core_graph_builder) from_yaml() (noctis.repository.neo4j.neo4j_queries.CustomQuery class method)

G

get() (noctis.data_architecture.datamodel.Node method) (noctis.data_architecture.datamodel.Relationship method) get_all_relationships_start_end_uids() (noctis.data_architecture.datamodel.GraphRecord method) get_node_label_by_tag() (noctis.data_architecture.graph_schema.GraphSchema method) get_nodes_labels() (noctis.data_architecture.graph_schema.GraphSchema method) get_nodes_with_label() (noctis.data_architecture.datamodel.GraphRecord method) get_query() (noctis.repository.neo4j.neo4j_queries.AbstractQuery method) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships method) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints method) (noctis.repository.neo4j.neo4j_queries.CustomQuery method) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes method) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints method) (noctis.repository.neo4j.neo4j_queries.GetNode method) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates method) (noctis.repository.neo4j.neo4j_queries.GetRoutes method) (noctis.repository.neo4j.neo4j_queries.GetTree method) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv method) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv method) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv method) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints method)

get_record() (noctis.data_architecture.datacontainer.DataContainer method) get_records() (noctis.data_architecture.datacontainer.DataContainer method) get_relationship_type_by_tag() (noctis.data_architecture.graph_schema.GraphSchema method) get_relationships_types() (noctis.data_architecture.graph_schema.GraphSchema method) get_subcontainer_with_records() (noctis.data_architecture.datacontainer.DataContainer method) graph_schema (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) GraphExpander (class in noctis.data_transformation.preprocessing.graph_expander)

I

import_from_file_system (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute)

info() (noctis.data_architecture.datacontainer.DataContainer class method) input_chem_format (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) intermediates (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute)

L

limit (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute)

list_arguments() (noctis.repository.neo4j.neo4j_queries.AbstractQuery class method) list_queries() (noctis.repository.neo4j.neo4j_queries.CustomQuery class method)

M

match_property (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) max_number_reactions (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) max_reactions_between_intermediates (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) min_max_in_rel (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) min_max_n_reactions (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) module noctis.data_architecture.datacontainer noctis.data_architecture.datamodel noctis.data_architecture.graph_schema noctis.data_transformation.data_styles.dataframe_stylers noctis.data_transformation.neo4j.neo4j_formatter noctis.data_transformation.postprocessing.chemdata_generators noctis.data_transformation.preprocessing.core_graph_builder noctis.data_transformation.preprocessing.data_preprocessing noctis.data_transformation.preprocessing.graph_expander noctis.data_transformation.preprocessing.utilities noctis.repository.neo4j.neo4j_functions noctis.repository.neo4j.neo4j_queries noctis.repository.neo4j.neo4j_repository

N

Neo4jQueryRegistry (class in noctis.repository.neo4j.neo4j_queries) Neo4jRepository (class in noctis.repository.neo4j.neo4j_repository) Neo4jResultFormatter (class in noctis.data_transformation.neo4j.neo4j_formatter) NetworkXGenerator (class in noctis.data_transformation.postprocessing.chemdata_generators) noctis.data_architecture.datacontainer module noctis.data_architecture.datamodel module noctis.data_architecture.graph_schema module noctis.data_transformation.data_styles.dataframe_stylers module noctis.data_transformation.neo4j.neo4j_formatter module noctis.data_transformation.postprocessing.chemdata_generators module noctis.data_transformation.preprocessing.core_graph_builder module

noctis.data_transformation.preprocessing.data_preprocessing module noctis.data_transformation.preprocessing.graph_expander module noctis.data_transformation.preprocessing.utilities module noctis.repository.neo4j.neo4j_functions module noctis.repository.neo4j.neo4j_queries module noctis.repository.neo4j.neo4j_repository module node_label (noctis.data_architecture.datamodel.Node attribute) node_stop_property (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) nodes (noctis.data_architecture.datamodel.GraphRecord attribute) nodes_labels (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) nodes_uids (noctis.data_architecture.datamodel.GraphRecord property) NodesRelationshipsStyle (class in noctis.data_transformation.data_styles.dataframe_stylers)

O

output_chem_format (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute)

P

PandasExportStyle (class in noctis.data_transformation.data_styles.dataframe_stylers) PandasGenerator (class in noctis.data_transformation.postprocessing.chemdata_generators) PandasRowPreprocessorBase (class in noctis.data_transformation.preprocessing.data_preprocessing) parameters_embedded (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute)

prefix (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) Preprocessor (class in noctis.data_transformation.preprocessing.data_preprocessing) PreprocessorConfig (class in noctis.data_transformation.preprocessing.data_preprocessing) properties (noctis.data_architecture.datamodel.Node attribute) (noctis.data_architecture.datamodel.Relationship attribute) PythonObjectPreprocessorFactory (class in noctis.data_transformation.preprocessing.data_preprocessing) PythonObjectPreprocessorInterface (class in noctis.data_transformation.preprocessing.data_preprocessing)

Q

query (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute) query_args_optional (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute) query_args_required (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute)

query_name (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute) query_type (noctis.repository.neo4j.neo4j_queries.AbstractQuery attribute) (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute) (noctis.repository.neo4j.neo4j_queries.CreateUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.CustomQuery attribute) (noctis.repository.neo4j.neo4j_queries.DeleteAllNodes attribute) (noctis.repository.neo4j.neo4j_queries.DropUniquenessConstraints attribute) (noctis.repository.neo4j.neo4j_queries.GetGDBSchema attribute) (noctis.repository.neo4j.neo4j_queries.GetNode attribute) (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute) (noctis.repository.neo4j.neo4j_queries.GetTree attribute) (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadNodesFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.LoadRelationshipsFromCsv attribute) (noctis.repository.neo4j.neo4j_queries.ShowUniquenessConstraints attribute)

R

ReactionStringGenerator (class in noctis.data_transformation.postprocessing.chemdata_generators) ReactionStringsPreprocessor (class in noctis.data_transformation.preprocessing.data_preprocessing) records (noctis.data_architecture.datacontainer.DataContainer attribute) relationship_type (noctis.data_architecture.datamodel.Relationship attribute)

relationships (noctis.data_architecture.datamodel.GraphRecord attribute) relationships_nodes_uids (noctis.data_architecture.datamodel.GraphRecord property) relationships_types (noctis.repository.neo4j.neo4j_queries.ImportDbFromCsv attribute) root_match_value (noctis.repository.neo4j.neo4j_queries.GetRoutes attribute)

S

save_to_file() (noctis.data_architecture.graph_schema.GraphSchema method) set_ce_label() (noctis.data_architecture.datacontainer.DataContainer method) start_end_uids (noctis.data_architecture.datamodel.Relationship property)

start_match_value (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) start_node (noctis.data_architecture.datamodel.Relationship attribute) SyngraphGenerator (class in noctis.data_transformation.postprocessing.chemdata_generators) SynGraphPreprocessor (class in noctis.data_transformation.preprocessing.data_preprocessing)

T

total_in_rel (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute)

total_n_reactions (noctis.repository.neo4j.neo4j_queries.GetPathsThroughIntermediates attribute) transform_to() (noctis.data_architecture.datacontainer.DataContainer method)

U

uid (noctis.data_architecture.datamodel.Node attribute)

UnvalidatedStringBuilder (class in noctis.data_transformation.preprocessing.core_graph_builder)

V

validate_base_nodes() (noctis.data_architecture.graph_schema.GraphSchema class method) validate_base_relationships() (noctis.data_architecture.graph_schema.GraphSchema class method) validate_extra_relationships() (noctis.data_architecture.graph_schema.GraphSchema class method) validate_query_kwargs() (noctis.repository.neo4j.neo4j_queries.AbstractQuery class method) (noctis.repository.neo4j.neo4j_queries.CustomQuery method)

validate_query_structure() (noctis.repository.neo4j.neo4j_queries.CustomQuery class method) ValidatedStringBuilder (class in noctis.data_transformation.preprocessing.core_graph_builder) validation (noctis.repository.neo4j.neo4j_queries.AddNodesAndRelationships attribute)