cgexplore.utilities.AtomliteDatabase¶

class cgexplore.utilities.AtomliteDatabase(db_file)[source]¶

Bases: object

Holds an atomlite database with some useful methods.

Methods

`add_entries`	Add molecules to database as entry.
`add_molecule`	Add molecule to database as entry.
`add_properties`	Add properties to an entry by key.
`get_database`	Access the atomlite Database object.
`get_entries`	Get all entries.
`get_entry`	Get specific entry.
`get_entry_list`	Get all entries.
`get_molecule`	Get a molecule.
`get_num_entries`	Get the number of molecular entries in the database.
`get_num_property_entries`	Get the number of property entries in the database.
`get_property`	Get the properties of an entry.
`get_property_df`	Get a DataFrame of the properties in the database.
`get_property_entries`	Get all property entries.
`get_property_entry`	Get specific entry.
`has_molecule`	Check if database has a molecule by key.
`keep_if`	Filter database entries by properties.
`remove_entry`	Remove an entry by key.
`remove_property`	Add properties to an entry by key.
`set_property`	Add properties to an entry by key.

Parameters:: db_file (Path)

add_entries(entries)[source]¶

Add molecules to database as entry.

Parameters:: entries (Sequence[Entry])
Return type:: None

add_molecule(molecule, key)[source]¶

Add molecule to database as entry.

Parameters:

molecule (Molecule)
key (str)

Return type:

None

add_properties(key, property_dict)[source]¶

Add properties to an entry by key.

Parameters:

key (str)
property_dict (dict[str, bool | float | str | None | list[Json] | dict[str, Json]])

Return type:

None

get_database()[source]¶

Access the atomlite Database object.

Return type:: Database

get_entries()[source]¶

Get all entries.

Return type:: Iterator[Entry]

get_entry(key)[source]¶

Get specific entry.

Parameters:: key (str)
Return type:: Entry

get_entry_list()[source]¶

Get all entries.

Return type:: list[Entry]

get_molecule(key)[source]¶

Get a molecule.

Parameters:: key (str)
Return type:: Molecule

get_num_entries()[source]¶

Get the number of molecular entries in the database.

Return type:: int

get_num_property_entries()[source]¶

Get the number of property entries in the database.

Return type:: int

get_property(key, property_key, property_type)[source]¶

Get the properties of an entry.

Parameters:

key (str)
property_key (str)
property_type (type)

Return type:

get_property_df(properties, allow_missing=False)[source]¶

Get a DataFrame of the properties in the database.

Parameters:

properties (Sequence[str]) – The paths of the properties to retrieve. Valid paths are described in the atomlite docs.
allow_missing (bool) – If True, rows with some missing properties will be included in the DataFrame and hold null values.

Returns:

A DataFrame of the property entries in the database.

Return type:

DataFrame

get_property_entries()[source]¶

Get all property entries.

Return type:: Iterator[PropertyEntry]

get_property_entry(key)[source]¶

Get specific entry.

Parameters:: key (str)
Return type:: PropertyEntry

has_molecule(key)[source]¶

Check if database has a molecule by key.

Parameters:: key (str)
Return type:: bool

keep_if(column, value)[source]¶

Filter database entries by properties.

Parameters:

column (str)
value (str | float)

Return type:

Iterator[Entry]

remove_entry(key)[source]¶

Remove an entry by key.

Parameters:: key (str)
Return type:: None

remove_property(key, property_path)[source]¶

Add properties to an entry by key.

Parameters:

key (str)
property_path (str)

Return type:

None

set_property(key, property_path, value)[source]¶

Add properties to an entry by key.

Parameters:

key (str)
property_path (str)
value (float | str | bool | None)

Return type:

None