SolvationYankProtocol¶
-
class
propertyestimator.protocols.yank.
SolvationYankProtocol
(protocol_id)[source]¶ A protocol for performing solvation alchemical free energy calculations using the YANK framework.
This protocol can be used for box solvation free energies (setting the solvent_1 input to the solvent of interest and setting solvent_2 as an empty Substance) or transfer free energies (setting both the solvent_1 and solvent_2 inputs to different solvents).
Methods
__init__
(protocol_id)Initialize self.
apply_replicator
(replicator, template_values)Applies a ProtocolReplicator to this protocol.
can_merge
(other[, path_replacements])Determines whether this protocol can be merged with another.
execute
(directory, available_resources)Execute the protocol.
get_class_attribute
(reference_path)Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).
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
Protocol Input - Defines whether this protocols is allowed to merge with other protocols.
Protocol Input - The number of iterations between saving YANK checkpoint files.
A list of pointers to the protocols which this protocol takes input from.
Protocol Input - The list of electrostatic alchemical states that YANK should sample at.
Protocol Input - The list of electrostatic alchemical states that YANK should sample at.
Protocol Output - The estimated free energy value and its uncertainty returned by YANK.
The unique id of this protocol.
Protocol Input - The number of iterations used for equilibration before production run.
Protocol Input - The number of YANK iterations to perform.
A serializable schema for this object.
Protocol Input - If true, YANK will only create and validate the setup files, but not actually run any simulations.
Protocol Input - The substance describing the composition of the solute.
Protocol Input - The substance describing the composition of the first solvent.
Protocol Input - The file path to the coordinates of the solute embedded in the first solvent.
Protocol Input - The file path to the system object of the solute embedded in the first solvent.
Protocol Output - The file path to the trajectory of the solute in the first solvent.
Protocol Input - The substance describing the composition of the second solvent.
Protocol Input - The file path to the coordinates of the solute embedded in the second solvent.
Protocol Input - The file path to the system object of the solute embedded in the second solvent.
Protocol Output - The file path to the trajectory of the solute in the second solvent.
Protocol Input - The number of steps per YANK iteration to perform.
Protocol Input - The list of steric alchemical states that YANK should sample at.
Protocol Input - The list of steric alchemical states that YANK should sample at.
Protocol Input - The state at which to run the calculations.
Protocol Input - The length of the timestep to take.
Protocol Input - Controls whether or not to run YANK at high verbosity.
-
solute
¶ Protocol Input - The substance describing the composition of the solute. This should include the solute molecule as well as any counter ions. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_1
¶ Protocol Input - The substance describing the composition of the first solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_2
¶ Protocol Input - The substance describing the composition of the second solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_1_coordinates
¶ Protocol Input - The file path to the coordinates of the solute embedded in the first solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_1_system
¶ Protocol Input - The file path to the system object of the solute embedded in the first solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_2_coordinates
¶ Protocol Input - The file path to the coordinates of the solute embedded in the second solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
solvent_2_system
¶ Protocol Input - The file path to the system object of the solute embedded in the second solvent. The default value of this attribute is not set and must be set by the user..
- Type
-
electrostatic_lambdas_1
¶ Protocol Input - The list of electrostatic alchemical states that YANK should sample at. These values will be passed to the YANK lambda_electrostatics option. If no option is set, YANK will use trailblaze algorithm to determine this option automatically. The default value of this attribute is not set. This input is optional.
- Type
-
steric_lambdas_1
¶ Protocol Input - The list of steric alchemical states that YANK should sample at. These values will be passed to the YANK lambda_sterics option. If no option is set, YANK will use trailblaze algorithm to determine this option automatically. The default value of this attribute is not set. This input is optional.
- Type
-
electrostatic_lambdas_2
¶ Protocol Input - The list of electrostatic alchemical states that YANK should sample at. These values will be passed to the YANK lambda_electrostatics option. If no option is set, YANK will use trailblaze algorithm to determine this option automatically. The default value of this attribute is not set. This input is optional.
- Type
-
steric_lambdas_2
¶ Protocol Input - The list of steric alchemical states that YANK should sample at. These values will be passed to the YANK lambda_sterics option. If no option is set, YANK will use trailblaze algorithm to determine this option automatically. The default value of this attribute is not set. This input is optional.
- Type
-
solvent_1_trajectory_path
¶ Protocol Output - The file path to the trajectory of the solute in the first solvent.
- Type
-
solvent_2_trajectory_path
¶ Protocol Output - The file path to the trajectory of the solute in the second solvent.
- Type
-
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]
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allow_merging
¶ Protocol Input - Defines whether this protocols is allowed to merge with other protocols. The default value of this attribute is
True
.- Type
-
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, path_replacements=None)¶ Determines whether this protocol can be merged with another.
- Parameters
other (
BaseProtocol
) – The protocol to compare against.path_replacements (list of tuple of str, optional) – Replacements to make in any value reference protocol paths before comparing for equality.
- Returns
True if the two protocols are safe to merge.
- Return type
-
checkpoint_interval
¶ Protocol Input - The number of iterations between saving YANK checkpoint files. The default value of this attribute is
50
. When two protocols are merged, the largest value of this attribute from either protocol is retained.- Type
-
property
dependencies
¶ A list of pointers to the protocols which this protocol takes input from.
- Type
list of ProtocolPath
-
estimated_free_energy
¶ Protocol Output - The estimated free energy value and its uncertainty returned by YANK.
- Type
EstimatedQuantity
-
get_class_attribute
(reference_path)¶ Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).
- Parameters
reference_path (ProtocolPath) – The path pointing to the attribute to return.
- Returns
The class 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
-
number_of_equilibration_iterations
¶ Protocol Input - The number of iterations used for equilibration before production run. Only post-equilibration iterations are written to file. The default value of this attribute is
1
.- Type
-
number_of_iterations
¶ Protocol Input - The number of YANK iterations to perform. The default value of this attribute is
5000
.- 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.
-
setup_only
¶ Protocol Input - If true, YANK will only create and validate the setup files, but not actually run any simulations. This argument is mainly only to be used for testing purposes. The default value of this attribute is
False
.- Type
-
steps_per_iteration
¶ Protocol Input - The number of steps per YANK iteration to perform. The default value of this attribute is
500
.- Type
-
thermodynamic_state
¶ Protocol Input - The state at which to run the calculations. The default value of this attribute is not set and must be set by the user..
- Type
-
timestep
¶ Protocol Input - The length of the timestep to take. The default value of this attribute is
2 femtosecond
. When two protocols are merged, the largest value of this attribute from either protocol is retained.- Type
Quantity
-