BuildTLeapSystem

class propertyestimator.protocols.forcefield.BuildTLeapSystem(protocol_id)[source]

Parametrise a set of molecules with an Amber based force field. using the tleap package.

Notes

  • This protocol is currently a work in progress and as such has limited functionality compared to the more established BuildSmirnoffSystem protocol.

  • This protocol requires the optional ambertools ==19.0 dependency to be installed.

__init__(protocol_id)[source]

Constructs a new BuildTLeapSystem object.

Methods

__init__(protocol_id)

Constructs a new BuildTLeapSystem object.

apply_replicator(replicator, template_values)

Applies a ProtocolReplicator to this protocol.

can_merge(other)

Determines whether this protocol can be merged with another.

execute(directory, available_resources)

Execute the protocol.

get_attribute_type(reference_path)

Returns the type of one of the protocol input/output attributes.

get_value(reference_path)

Returns the value of one of this protocols inputs / outputs.

get_value_references(input_path)

Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.

merge(other)

Merges another BaseProtocol with this one.

replace_protocol(old_id, new_id)

Finds each input which came from a given protocol

set_uuid(value)

Store the uuid of the calculation this protocol belongs to

set_value(reference_path, value)

Sets the value of one of this protocols inputs.

Attributes

allow_merging

If true, this protocol is allowed to merge with other identical protocols.

charge_backend

The backend framework to use to assign partial charges.

coordinate_file_path

The file path to the coordinate file which defines the system to which the force field parameters will be assigned.

dependencies

A list of pointers to the protocols which this protocol takes input from.

force_field_path

The file path to the force field parameters to assign to the system.

id

The unique id of this protocol.

schema

A serializable schema for this object.

substance

The composition of the system.

system_path

The file path to the system object which contains the applied parameters.

water_model

The water model to apply, if any water molecules are present.

class ChargeBackend[source]

The framework to use to assign partial charges.

charge_backend

The backend framework to use to assign partial charges.

force_field_path

The file path to the force field parameters to assign to the system. This path must point to a json serialized TLeapForceFieldSource object.

execute(directory, available_resources)[source]

Execute the protocol.

Protocols may be chained together by passing the output of previous protocols as input to the current one.

Parameters
  • directory (str) – The directory to store output data in.

  • available_resources (ComputeResources) – The resources available to execute on.

Returns

The output of the execution.

Return type

Dict[str, Any]

class WaterModel

An enum which describes which water model is being used, so that correct charges can be applied.

Warning

This is only a temporary addition until full water model support is introduced.

allow_merging

If true, this protocol is allowed to merge with other identical protocols.

Type

bool

apply_replicator(replicator, template_values, template_index=-1, template_value=None, update_input_references=False)

Applies a ProtocolReplicator to this protocol. This method should clone any protocols whose id contains the id of the replicator (in the format $(replicator.id)).

Parameters
  • replicator (ProtocolReplicator) – The replicator to apply.

  • template_values (list of Any) –

    A list of the values which will be inserted into the newly replicated protocols.

    This parameter is mutually exclusive with template_index and template_value

  • template_index (int, optional) –

    A specific value which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

    This parameter is mutually exclusive with template_values and must be set along with a template_value.

  • template_value (Any, optional) –

    A specific index which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

    This parameter is mutually exclusive with template_values and must be set along with a template_index.

  • update_input_references (bool) –

    If true, any protocols which take their input from a protocol which was flagged for replication will be updated to take input from the actually replicated protocol. This should only be set to true if this protocol is not nested within a workflow or a protocol group.

    This option cannot be used when a specific template_index or template_value is providied.

Returns

A dictionary of references to all of the protocols which have been replicated, with keys of original protocol ids. Each value is comprised of a list of the replicated protocol ids, and their index into the template_values array.

Return type

dict of ProtocolPath and list of tuple of ProtocolPath and int

can_merge(other)

Determines whether this protocol can be merged with another.

Parameters

other (BaseProtocol) – The protocol to compare against.

Returns

True if the two protocols are safe to merge.

Return type

bool

coordinate_file_path

The file path to the coordinate file which defines the system to which the force field parameters will be assigned.

property dependencies

A list of pointers to the protocols which this protocol takes input from.

Type

list of ProtocolPath

get_attribute_type(reference_path)

Returns the type of one of the protocol input/output attributes.

Parameters

reference_path (ProtocolPath) – The path pointing to the value whose type to return.

Returns

The type of the attribute.

Return type

type

get_value(reference_path)

Returns the value of one of this protocols inputs / outputs.

Parameters

reference_path (ProtocolPath) – The path pointing to the value to return.

Returns

The value of the input / output

Return type

Any

get_value_references(input_path)

Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.

Notes

Currently this method only functions correctly for an input value which is either currently a ProtocolPath, or a list / dict which contains at least one ProtocolPath.

Parameters

input_path (propertyestimator.workflow.utils.ProtocolPath) – The input value to check.

Returns

A dictionary of the protocol paths that the input targeted by input_path depends upon.

Return type

dict of ProtocolPath and ProtocolPath

property id

The unique id of this protocol.

Type

str

merge(other)

Merges another BaseProtocol with this one. The id of this protocol will remain unchanged.

It is assumed that can_merge has already returned that these protocols are compatible to be merged together.

Parameters

other (BaseProtocol) – The protocol to merge into this one.

Returns

A map between any original protocol ids and their new merged values.

Return type

Dict[str, str]

replace_protocol(old_id, new_id)
Finds each input which came from a given protocol

and redirects it to instead take input from a new one.

Notes

This method is mainly intended to be used only when merging multiple protocols into one.

Parameters
  • old_id (str) – The id of the old input protocol.

  • new_id (str) – The id of the new input protocol.

property schema

A serializable schema for this object.

Type

ProtocolSchema

set_uuid(value)

Store the uuid of the calculation this protocol belongs to

Parameters

value (str) – The uuid of the parent calculation.

set_value(reference_path, value)

Sets the value of one of this protocols inputs.

Parameters
  • reference_path (ProtocolPath) – The path pointing to the value to return.

  • value (Any) – The value to set.

substance

The composition of the system.

system_path

The file path to the system object which contains the applied parameters.

water_model

The water model to apply, if any water molecules are present.

Warning

This is only a temporary addition until full water model support is introduced.