LigandReceptorYankProtocol¶
-
class
openff.evaluator.protocols.yank.
LigandReceptorYankProtocol
(protocol_id)[source]¶ A protocol for performing ligand-receptor alchemical free energy calculations using the YANK framework.
Methods
__init__
(protocol_id)Constructs a new LigandReceptorYankProtocol object.
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.
from_json
(file_path)Create this object from a JSON file.
from_schema
(schema)Initializes a protocol from it’s schema definition.
get_attributes
([attribute_type])Returns all attributes of a specific attribute_type.
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.
json
([file_path, format])Creates a JSON representation of this class.
merge
(other)Merges another Protocol with this one.
parse_json
(string_contents[, encoding])Parses a typed json string into the corresponding class structure.
replace_protocol
(old_id, new_id)Finds each input which came from a given protocol
set_uuid
(value)Prepend a unique identifier to this protocols id.
set_value
(reference_path, value)Sets the value of one of this protocols inputs.
validate
([attribute_type])Validate the values of the attributes.
Attributes
Input - Defines whether this protocols is allowed to merge with other protocols.
Input - Determines whether the ligand should be explicitly restrained to the receptor in order to stop the ligand from temporarily unbinding.
Input - The number of iterations between saving YANK checkpoint files.
Input - The list of electrostatic alchemical states that YANK should sample at when calculating the free energy of the ligand in complex with the receptor.
Input - The list of steric alchemical states that YANK should sample at when calculating the free energy of the ligand in complex with the receptor.
A list of pointers to the protocols which this protocol takes input from.
Input - The path to the force field which defines the charge method to use for the calculation.
Output - The estimated free energy difference between the two phases ofinterest.
Input - An optional list of parameters to differentiate the estimated free energy with respect to.
The unique id of this protocol.
Input - The list of electrostatic alchemical states that YANK should sample at when calculating the free energy of the solvated ligand.
Input - The residue name of the ligand.
Input - The list of steric alchemical states that YANK should sample at when calculating the free energy of the solvated ligand.
Input - The number of iterations used for equilibration before production run.
Input - The number of YANK iterations to perform.
A dictionary of the outputs of this property.
Input - The residue name of the receptor.
The inputs which must be set on this protocol.
Input - The type of ligand restraint applied, provided that apply_restraints is True The default value of this attribute is
RestraintType.Harmonic
.A serializable schema for this object.
Input - If true, YANK will only create and validate the setup files, but not actually run any simulations.
Input - The file path to the solvated complex coordinates.
Input - The parameterized solvated complex system object.
Output - The file path to the generated ligand trajectory.
Input - The file path to the solvated ligand coordinates.
Input - The parameterized solvated ligand system object.
Output - The file path to the generated ligand trajectory.
Input - The number of steps per YANK iteration to perform.
Input - The state at which to run the calculations.
Input - The length of the timestep to take.
Input - Controls whether or not to run YANK at high verbosity.
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ligand_residue_name
¶ Input - The residue name of the ligand. The default value of this attribute is not set and must be set by the user..
- Type
-
receptor_residue_name
¶ Input - The residue name of the receptor. The default value of this attribute is not set and must be set by the user..
- Type
-
solvated_ligand_coordinates
¶ Input - The file path to the solvated ligand coordinates. The default value of this attribute is not set and must be set by the user..
- Type
-
solvated_ligand_system
¶ Input - The parameterized solvated ligand system object. The default value of this attribute is not set and must be set by the user..
- Type
ParameterizedSystem
-
solvated_complex_coordinates
¶ Input - The file path to the solvated complex coordinates. The default value of this attribute is not set and must be set by the user..
- Type
-
solvated_complex_system
¶ Input - The parameterized solvated complex system object. The default value of this attribute is not set and must be set by the user..
- Type
ParameterizedSystem
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force_field_path
¶ Input - The path to the force field which defines the charge method to use for the calculation. The default value of this attribute is not set and must be set by the user..
- Type
-
apply_restraints
¶ Input - Determines whether the ligand should be explicitly restrained to the receptor in order to stop the ligand from temporarily unbinding. The default value of this attribute is
True
.- Type
-
restraint_type
¶ Input - The type of ligand restraint applied, provided that apply_restraints is True The default value of this attribute is
RestraintType.Harmonic
.
-
ligand_electrostatic_lambdas
¶ Input - The list of electrostatic alchemical states that YANK should sample at when calculating the free energy of the solvated ligand. 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 attribute is optional.
- Type
-
ligand_steric_lambdas
¶ Input - The list of steric alchemical states that YANK should sample at when calculating the free energy of the solvated ligand. 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 attribute is optional.
- Type
-
complex_electrostatic_lambdas
¶ Input - The list of electrostatic alchemical states that YANK should sample at when calculating the free energy of the ligand in complex with the receptor. 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 attribute is optional.
- Type
-
complex_steric_lambdas
¶ Input - The list of steric alchemical states that YANK should sample at when calculating the free energy of the ligand in complex with the receptor. 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 attribute is optional.
- Type
-
solvated_ligand_trajectory_path
¶ Output - The file path to the generated ligand trajectory. The default value of this attribute is not set and must be set by the user..
- Type
-
solvated_complex_trajectory_path
¶ Output - The file path to the generated ligand trajectory. The default value of this attribute is not set and must be set by the user..
- Type
-
allow_merging
¶ 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 (
Protocol
) – 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
¶ Input - The number of iterations between saving YANK checkpoint files. When two protocols are merged, the largest value of this attribute from either protocol is retained. The default value of this attribute is
1
.- Type
-
property
dependencies
¶ A list of pointers to the protocols which this protocol takes input from.
- Type
list of ProtocolPath
-
execute
(directory='', available_resources=None)¶ Execute the protocol.
- Parameters
directory (str) – The directory to store output data in.
available_resources (ComputeResources) – The resources available to execute on. If None, the protocol will be executed on a single CPU.
-
free_energy_difference
¶ Output - The estimated free energy difference between the two phases ofinterest. The default value of this attribute is not set and must be set by the user..
- Type
-
classmethod
from_json
(file_path)¶ Create this object from a JSON file.
- Parameters
file_path (str) – The path to load the JSON from.
- Returns
The parsed class.
- Return type
cls
-
classmethod
from_schema
(schema)¶ Initializes a protocol from it’s schema definition.
- Parameters
schema (ProtocolSchema) – The schema to initialize the protocol using.
- Returns
The initialized protocol.
- Return type
cls
-
classmethod
get_attributes
(attribute_type=None)¶ Returns all attributes of a specific attribute_type.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to search for.
- Returns
The names of the attributes of the specified type.
- Return type
list of str
-
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 (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
-
gradient_parameters
¶ Input - An optional list of parameters to differentiate the estimated free energy with respect to.
- Type
-
id
¶ The unique id of this protocol. The default value of this attribute is not set and must be set by the user..
- Type
-
json
(file_path=None, format=False)¶ Creates a JSON representation of this class.
-
merge
(other)¶ Merges another Protocol with this one. The id of this protocol will remain unchanged.
-
number_of_equilibration_iterations
¶ 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
¶ Input - The number of YANK iterations to perform. The default value of this attribute is
5000
.- Type
-
property
outputs
¶ A dictionary of the outputs of this property.
- Type
dict of ProtocolPath and Any
-
classmethod
parse_json
(string_contents, encoding='utf8')¶ Parses a typed json string into the corresponding class structure.
-
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
required_inputs
¶ The inputs which must be set on this protocol.
- Type
list of ProtocolPath
-
property
schema
¶ A serializable schema for this object.
- Type
-
set_uuid
(value)¶ Prepend a unique identifier to this protocols id. If the id already has a prepended uuid, it will be overwritten by this value.
- Parameters
value (str) – The uuid to prepend.
-
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
¶ 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
¶ Input - The number of steps per YANK iteration to perform. The default value of this attribute is
500
.- Type
-
thermodynamic_state
¶ 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
¶ Input - The length of the timestep to take. When two protocols are merged, the largest value of this attribute from either protocol is retained. The default value of this attribute is
2 fs
.- Type
Quantity
-
validate
(attribute_type=None)¶ Validate the values of the attributes. If attribute_type is set, only attributes of that type will be validated.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to validate.
- Raises
ValueError or AssertionError –
-