ncsw_data.storage.cacs.sqlite_db

The ncsw_data.storage.cacs.sqlite_db package initialization module.

Submodules

Attributes

CaCSSQLiteDatabaseArchiveCompoundPatternStandardizationCallable

CaCSSQLiteDatabaseArchiveCompoundStandardizationCallable

CaCSSQLiteDatabaseArchiveReactionPatternStandardizationCallable

CaCSSQLiteDatabaseArchiveReactionStandardizationCallable

CaCSSQLiteDatabaseWorkbenchReactionPatternExtractionCallable

Classes

CaCSSQLiteDatabase

The computer-assisted chemical synthesis (CaCS) SQLite database class.

Package Contents

class ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabase(db_url: str = 'sqlite:///', logger: logging.Logger | None = None, **kwargs)

Bases: ncsw_data.storage.base.base.DataStorageBase

The computer-assisted chemical synthesis (CaCS) SQLite database class.

The __init__ method of the class.

Parameters:

  • db_url – The URL of the database. The value sqlite:/// indicates that the SQLite database should be created in memory.

  • logger – The logger. The value None indicates that the logger should not be utilized.

  • kwargs – The keyword arguments for the adjustment of the following underlying functions: { sqlalchemy.engine.create.create_engine }.

create_tables(**kwargs) → None

Create the tables of the database.

Parameters:

kwargs – The keyword arguments for the adjustment of the following underlying functions: { sqlalchemy.sql.schema.MetaData.create_all }.

drop_tables(**kwargs) → None

Drop the tables of the database.

Parameters:

kwargs – The keyword arguments for the adjustment of the following underlying functions: { sqlalchemy.sql.schema.MetaData.drop_all }.

execute_select_statement(select_statement_text: str) → sqlalchemy.engine.Result

Execute a select statement.

Parameters:

select_statement_text – The text of the select statement.

Returns:

The result of the select statement.

insert_archive_compounds(ac_smiles_strings: Collection[str], as_name: str, as_version: str, as_file_name: str, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Insert the archive chemical compounds into the database.

Parameters:

  • ac_smiles_strings – The SMILES strings of the archive chemical compounds.

  • as_name – The name of the archive source.

  • as_version – The version of the archive source.

  • as_file_name – The file name of the archive source.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_archive_compounds(db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveCompoundTuple]], None, None]

Select the archive chemical compounds from the database.

Parameters:

db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical compounds from the database.

select_archive_compounds_from_sources(as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveCompoundFromSourceTuple]], None, None]

Select the archive chemical compounds from sources in the database.

Parameters:

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical compounds should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical compounds from sources in the database.

insert_archive_reactions(ar_smiles_strings: Sequence[str], as_name: str, as_version: str, as_file_name: str, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Insert the archive chemical reactions into the database.

Parameters:

  • ar_smiles_strings – The SMILES strings of the archive chemical reactions.

  • as_name – The name of the archive source.

  • as_version – The version of the archive source.

  • as_file_name – The file name of the archive source.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_archive_reactions(db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveReactionTuple]], None, None]

Select the archive chemical reactions from the database.

Parameters:

db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical reactions from the database.

select_archive_reactions_from_sources(as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveReactionFromSourceTuple]], None, None]

Select the archive chemical reactions from sources in the database.

Parameters:

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical reactions should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical reactions from sources in the database.

insert_archive_compound_patterns(acp_smarts_strings: Sequence[str], as_name: str, as_version: str, as_file_name: str, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Insert the archive chemical compound patterns into the database.

Parameters:

  • acp_smarts_strings – The SMARTS strings of the archive chemical compound patterns.

  • as_name – The name of the archive source.

  • as_version – The version of the archive source.

  • as_file_name – The file name of the archive source.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_archive_compound_patterns(db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveCompoundPatternTuple]], None, None]

Select the archive chemical compound patterns from the database.

Parameters:

db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical compound patterns from the database.

select_archive_compound_patterns_from_sources(as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveCompoundPatternFromSourceTuple]], None, None]

Select the archive chemical compound patterns from sources in the database.

Parameters:

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical compound patterns should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical compound patterns from sources in the database.

insert_archive_reaction_patterns(arp_smarts_strings: Sequence[str], as_name: str, as_version: str, as_file_name: str, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Insert the archive chemical reaction patterns into the database.

Parameters:

  • arp_smarts_strings – The SMARTS strings of the archive chemical reaction patterns.

  • as_name – The name of the archive source.

  • as_version – The version of the archive source.

  • as_file_name – The file name of the archive source.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_archive_reaction_patterns(db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveReactionPatternTuple]], None, None]

Select the archive chemical reaction patterns from the database.

Parameters:

db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical reaction patterns from the database.

select_archive_reaction_patterns_from_sources(as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseArchiveReactionPatternFromSourceTuple]], None, None]

Select the archive chemical reaction patterns from sources in the database.

Parameters:

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical reaction patterns should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the archive chemical reaction patterns from sources in the database.

migrate_archive_to_workbench_compounds(ac_standardization_function: ncsw_data.storage.cacs.sqlite_db.typing.CaCSSQLiteDatabaseArchiveCompoundStandardizationCallable, wcs_are_building_blocks: bool, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Migrate the chemical compounds from the archive to the workbench tables of the database.

Parameters:

  • ac_standardization_function – The standardization function of the archive chemical compounds.

  • wcs_are_building_blocks – The indicator of whether the workbench chemical compounds are building blocks.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical compounds should be retrieved.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_workbench_compounds(wcs_are_building_blocks: bool | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchCompoundTuple]], None, None]

Select the workbench chemical compounds from the database.

Parameters:

  • wcs_are_building_blocks – The indicator of whether the workbench chemical compounds are building blocks.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical compounds from the database.

select_workbench_compounds_from_sources(wcs_are_building_blocks: bool | None, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchCompoundFromSourceTuple]], None, None]

Select the workbench chemical compounds from sources in the database.

Parameters:

  • wcs_are_building_blocks – The indicator of whether the workbench chemical compounds are building blocks.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the workbench chemical compounds should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical compounds from sources in the database.

migrate_archive_to_workbench_reactions(ar_standardization_function: ncsw_data.storage.cacs.sqlite_db.typing.CaCSSQLiteDatabaseArchiveReactionStandardizationCallable, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Migrate the chemical reactions from the archive to the workbench tables of the database.

Parameters:

  • ar_standardization_function – The standardization function of the archive chemical reactions.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical reactions should be retrieved.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_workbench_reactions(wrrc_smiles_strings: Iterable[str] | None, wrsc_smiles_strings: Iterable[str] | None, wrpc_smiles_strings: Iterable[str] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchReactionTuple]], None, None]

Select the workbench chemical reactions from the database.

Parameters:

  • wrrc_smiles_strings – The SMILES strings of the workbench chemical reaction reactant compounds.

  • wrsc_smiles_strings – The SMILES strings of the workbench chemical reaction spectator compounds.

  • wrpc_smiles_strings – The SMILES strings of the workbench chemical reaction product compounds.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical reactions from the database.

select_workbench_reactions_from_sources(wrrc_smiles_strings: Iterable[str] | None, wrsc_smiles_strings: Iterable[str] | None, wrpc_smiles_strings: Iterable[str] | None, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchReactionFromSourceTuple]], None, None]

Select the workbench chemical reactions from sources of the database.

Parameters:

  • wrrc_smiles_strings – The SMILES strings of the workbench chemical reaction reactant compounds.

  • wrsc_smiles_strings – The SMILES strings of the workbench chemical reaction spectator compounds.

  • wrpc_smiles_strings – The SMILES strings of the workbench chemical reaction product compounds.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the workbench chemical reactions should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical reactions from sources of the database.

migrate_archive_to_workbench_compound_patterns(acp_standardization_function: ncsw_data.storage.cacs.sqlite_db.typing.CaCSSQLiteDatabaseArchiveCompoundPatternStandardizationCallable, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Migrate the chemical compound patterns from the archive to the workbench tables of the database.

Parameters:

  • acp_standardization_function – The standardization function of the archive chemical compound patterns.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical compound patterns should be retrieved.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_workbench_compound_patterns(db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchCompoundPatternTuple]], None, None]

Select the workbench chemical compound patterns from the database.

Parameters:

db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical compound patterns from the database.

select_workbench_compound_patterns_from_sources(as_names_versions_and_file_names: Sequence[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchCompoundPatternFromSourceTuple]], None, None]

Select the workbench chemical compound patterns from sources in the database.

Parameters:

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the workbench chemical compound patterns should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical compound patterns from sources in the database.

migrate_archive_to_workbench_reaction_patterns(arp_standardization_function: ncsw_data.storage.cacs.sqlite_db.typing.CaCSSQLiteDatabaseArchiveReactionPatternStandardizationCallable, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Migrate the chemical reaction patterns from the archive to the workbench tables of the database.

Parameters:

  • arp_standardization_function – The standardization function of the archive chemical reaction patterns.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the archive chemical reaction patterns should be retrieved.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_workbench_reaction_patterns(wrrcp_smarts_strings: Iterable[str] | None, wrscp_smarts_strings: Iterable[str] | None, wrpcp_smarts_strings: Iterable[str] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchReactionPatternTuple]], None, None]

Select the workbench chemical reaction patterns from the database.

Parameters:

  • wrrcp_smarts_strings – The SMARTS strings of the workbench chemical reaction reactant compound patterns.

  • wrscp_smarts_strings – The SMARTS strings of the workbench chemical reaction spectator compound patterns.

  • wrpcp_smarts_strings – The SMARTS strings of the workbench chemical reaction product compound patterns.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical reaction patterns from the database.

select_workbench_reaction_patterns_from_sources(wrrcp_smarts_strings: Iterable[str] | None, wrscp_smarts_strings: Iterable[str] | None, wrpcp_smarts_strings: Iterable[str] | None, as_names_versions_and_file_names: Iterable[Tuple[str, str, str]] | None, db_chunk_limit: int = 10000) → Generator[Sequence[sqlalchemy.engine.Row[CaCSSQLiteDatabaseWorkbenchReactionPatternFromSourceTuple]], None, None]

Select the workbench chemical reaction patterns from sources in the database.

Parameters:

  • wrrcp_smarts_strings – The SMARTS strings of the workbench chemical reaction reactant compound patterns.

  • wrscp_smarts_strings – The SMARTS strings of the workbench chemical reaction spectator compound patterns.

  • wrpcp_smarts_strings – The SMARTS strings of the workbench chemical reaction product compound patterns.

  • as_names_versions_and_file_names – The names, versions, and file names of the archive sources from which the workbench chemical reaction patterns should be retrieved.

  • db_chunk_limit – The chunk limit of the database.

Returns:

The generator of the workbench chemical reaction patterns from sources in the database.

extract_workbench_reaction_transformation_patterns(wrp_extraction_function: ncsw_data.storage.cacs.sqlite_db.typing.CaCSSQLiteDatabaseWorkbenchReactionPatternExtractionCallable, db_user: str = 'user', db_chunk_limit: int = 10000) → None

Extract the workbench chemical reaction transformation patterns of the database.

Parameters:

  • wrp_extraction_function – The extraction function of the workbench chemical reaction patterns.

  • db_user – The user of the database.

  • db_chunk_limit – The chunk limit of the database.

select_reversed_synthesis_routes(wc_smiles: str, reversed_sr_maximum_depth: int = 10) → Sequence[sqlalchemy.engine.Row[Tuple[int, int, str, bool, bool, int | None, int | None, str | None]]]

Select the reversed chemical synthesis routes from the database.

Parameters:

  • wc_smiles – The SMILES string of the workbench chemical compound.

  • reversed_sr_maximum_depth – The maximum depth of the reversed chemical synthesis routes.

Returns:

The reversed chemical synthesis routes from the database.

ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabaseArchiveCompoundPatternStandardizationCallable
ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabaseArchiveCompoundStandardizationCallable
ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabaseArchiveReactionPatternStandardizationCallable
ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabaseArchiveReactionStandardizationCallable
ncsw_data.storage.cacs.sqlite_db.CaCSSQLiteDatabaseWorkbenchReactionPatternExtractionCallable