Calculation Layers

A CalculationLayer is an implementation of one calculation approach for estimating a set of physical properties, such as via molecular simulation or evaluating some QSAR like model.

The framework stacks multiple layers together when estimating a data set of properties.


A schematic of the layer system. A set of properties to estimate are fed into the first layer. Those which can be calculated are returned back. Those that can’t are passed to the next layer until no layer are left.

Each layer will in turn attempt to evaluate the properties being estimated using the specific approach the layer represents, such as by running a set of simulations. If the layer is unable to estimate a given property, for example if a layer does not yet support a given property, or if the layer has insufficient data to reprocesses, the property will be passed to the next layer for it to try and evaluate.

In practice, this allows the framework to attempt to estimate a data set using the most rapid calculation layer first, before moving to successively slower yet more robust layers, and thus enabling as efficient as possible property estimation.

Defining a Calculation Layer

A calculation layer is defined by two objects - a CalculationLayer object which implements the main layer logic, and a CalculationLayerSchema which defines those settings and options exposed required by the layer.

One CalculationLayerSchema will be provided to the for each type of property that the layer is being asked to estimate. The base CalculationLayerSchema currently only exposes options for optionally defining either the relative or absolute uncertainty that the layer should attempt to estimate the associated property type to within, however custom schemas can be defined per layer.

The structure of a CalculationLayer is relatively simple and permissive:

class MyCalculationLayer(CalculationLayer):

    def required_schema_type(cls):
        return CalculationLayerSchema

    def _schedule_calculation(

The first thing to note is the calculation_layer() decorator which is being applied to the class. This registers the calculation layer with the frameworks plug-in system, allowing it to be used in future calculations.

The only other requirements is that the class implement a required_schema_type class method, which returns the type of CalculationLayerSchema that is associated with this layer, and a _schedule_calculation(). The _schedule_calculation() is responsible for performing the actual property calculations.

The form of the _schedule_calculation() function is very flexible:

def _schedule_calculation(

    futures = []

    for queued_property in batch.queued_properties:

                cls.process_property, queued_property, cls.__name__

    return futures

It takes as arguments:

  • a CalculationBackend which is used to asynchronously distribute any calculations across the available compute resources.

  • a StorageBackend which may be used to store / cache any data generated by the calculations.

  • the path to the directory within which all of the calculation working files should be stored.

  • the Batch of properties which this layer should attempt to estimate. This object includes the properties to estimate, as well as the CalculationLayerSchema for each property type.

and must return a list of Future objects (which either must be or implement the same API as the asyncio Future object). The easiest way to generate the futures is to perform any calculations using the calculation_backend which will automatically return the results of any functions as such.

The future objects returned by _schedule_calculation() must return a CalculationLayerResult object, which includes

  • the estimated property if the calculation was successful (or UNDEFINED otherwise).

  • a list of any exceptions (of type EvaluatorException) which were raised during the calculation.

  • a list of any data to be stored by the storage backend.

As a minimal example of a method which returns one such object:

def process_property(cls, physical_property, **_):
    """Return a result as if the property had been successfully estimated.

    # TODO: Do some calculations

    # Set the property provenance
    physical_property.source = CalculationSource(fidelity=cls.__name__)

    # Return the results object.
    results = CalculationLayerResult()
    results.physical_property = physical_property
    return results

Default Schemas

Default schemas for each pair of a calculation layer and a type of physical property may be registered using the register_calculation_schema() function:

# Register the default schema to use for density measurements being estimated
# by the direct simulation calculation layer.

where the schema object should either be an instance of a CalculationLayerSchema, or a function with no required arguments which returns a CalculationLayerSchema.

A list of the registered schemas is provided by the registered_calculation_schemas module attribute.