fairmd.lipids.core module

Core databank class and system initialization function.

Imported by fairmd.lipids.databankLibrary by default. Can be imported without additional libraries to scan Databank system file tree!

class fairmd.lipids.core.System(data: dict | Mapping)

Bases: MutableMapping, SampleComposition

Main Databank single object.

It is an extension of a dictionary with additional functionality.

property readme: dict

Get the README dictionary of the system in true dict format.

Returns:

dict-type README (dict)

property n_lipids: int

Returns total number of lipid molecules in the system.

membrane_composition(basis: Literal['molar', 'mass'] = 'molar') → dict[str, float]

Return the composition of the membrane in system.

Parameters:

which – Type of composition to return. Options are: - “molar”: compute molar fraction - “mass”: compute mass fraction

Returns:

dictionary (universal molecule name -> value)

get_hydration(basis: Literal['number', 'mass'] = 'number') → float

Get system hydration.

solution_composition(basis='molar')

Return the composition of the solution in system.

class fairmd.lipids.core.SystemsCollection(*args, **kwargs)

Bases: CollectionSingleton[System]

Immutable collection of system dicts. Can be accessed by ID using loc().

static load_from_data() → SystemsCollection

Load systems data from the designated directory.

fairmd.lipids.core.initialize_databank() → SystemsCollection

Returns Simulation collection (an alias).

Returns:

list of dictionaries that contain the content of README.yaml files for each system.

fairmd.lipids.core.print_README(system: str | Mapping) → None

Print the content of system dictionary in human readable format.

Parameters:

system – FAIRMD Lipids dictionary defining a simulation or “example”.