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.
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
If true, this protocol is allowed to merge with other identical protocols.
The backend framework to use to assign partial charges.
The file path to the coordinate file which defines the system to which the force field parameters will be assigned.
A list of pointers to the protocols which this protocol takes input from.
The file path to the force field parameters to assign to the system.
The unique id of this protocol.
A serializable schema for this object.
The composition of the system.
The file path to the system object which contains the applied parameters.
The water model to apply, if any water molecules are present.
-
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.
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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.
-
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
-
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
-
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 oneProtocolPath
.- 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
-
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
-
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.
-
property
schema
¶ A serializable schema for this object.
- Type
-
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.
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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.