SolvateExistingStructure

class openff.evaluator.protocols.coordinates.SolvateExistingStructure(protocol_id)[source]

Solvates a set of 3D coordinates with a specified solvent using the PACKMOL package.

__init__(protocol_id)

Methods

`__init__`(protocol_id)
`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)	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

`allow_merging`	Input - Defines whether this protocols is allowed to merge with other protocols.
`assigned_residue_names`	Output - The residue names which were assigned to each of the components.
`box_aspect_ratio`	Input - The aspect ratio of the simulation box.
`center_solute_in_box`	Input - If True, the solute to solvate will be centered in the simulation box.
`coordinate_file_path`	Output - The file path to the created PDB coordinate file.
`count_exact_amount`	Input - Whether components present in an exact amount (i.e.
`dependencies`	A list of pointers to the protocols which this protocol takes input from.
`id`	The unique id of this protocol.
`mass_density`	Input - The target density of the created system.
`max_molecules`	Input - The maximum number of molecules to be added to the system.
`output_number_of_molecules`	Output - The number of molecules in the created system.
`output_substance`	Output - The substance which was built by packmol.
`outputs`	A dictionary of the outputs of this property.
`required_inputs`	The inputs which must be set on this protocol.
`retain_packmol_files`	Input - If True, packmol will not delete all of the temporary files it creates while building the coordinates.
`schema`	A serializable schema for this object.
`solute_coordinate_file`	Input - A file path to the solute to solvate.
`substance`	Input - The composition of the system to build.
`tolerance`	Input - The packmol distance tolerance in units compatible with angstroms.
`verbose_packmol`	Input - If True, packmol will print verbose information to the logger The default value of this attribute is `False`.

solute_coordinate_file

Input - A file path to the solute to solvate. The default value of this attribute is not set and must be set by the user..

Type: str

center_solute_in_box

Input - If True, the solute to solvate will be centered in the simulation box. The default value of this attribute is True.

Type: bool

allow_merging

Input - Defines whether this protocols is allowed to merge with other protocols. The default value of this attribute is True.

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

assigned_residue_names

Output - The residue names which were assigned to each of the components. Each key corresponds to a component identifier. The default value of this attribute is not set and must be set by the user..

Type: dict

box_aspect_ratio

Input - The aspect ratio of the simulation box. The default value of this attribute is [1.0, 1.0, 1.0].

Type: list

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

bool

coordinate_file_path

Output - The file path to the created PDB coordinate file. The default value of this attribute is not set and must be set by the user..

Type: str

count_exact_amount

Input - Whether components present in an exact amount (i.e. defined with an ExactAmount) should be considered when apply the maximum number of molecules constraint. This may be set false, for example, when building a separate solvated protein (n = 1) and solvated protein + ligand complex (n = 2) system but wish for both systems to have the same number of solvent molecules. The default value of this attribute is True.

Type: bool

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.

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: object

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 (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

id

The unique id of this protocol. The default value of this attribute is not set and must be set by the user..

Type: str

json(file_path=None, format=False)

Creates a JSON representation of this class.

Parameters

file_path (str, optional) – The (optional) file path to save the JSON file to.
format (bool) – Whether to format the JSON or not.

Returns

The JSON representation of this class.

Return type

str

mass_density

Input - The target density of the created system. The default value of this attribute is 0.95 gram / milliliter.

Type: Quantity

max_molecules

Input - The maximum number of molecules to be added to the system. The default value of this attribute is 1000.

Type: int

merge(other)

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

Parameters: other (Protocol) – 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]

output_number_of_molecules

Output - The number of molecules in the created system. This may be less than maximum requested due to rounding of mole fractions The default value of this attribute is not set and must be set by the user..

Type: int

output_substance

Output - The substance which was built by packmol. This may differ from the input substance for system containing two or more components due to rounding of mole fractions. The mole fractions provided by this output should always be used when weighting values by a mole fraction. The default value of this attribute is not set and must be set by the user..

Type: Substance

property outputs

A dictionary of the outputs of this property.

Type: dict of ProtocolPath and Any

classmethod parse_json(string_contents)

Parses a typed json string into the corresponding class structure.

Parameters: string_contents (str or bytes) – The typed json string.
Returns: The parsed class.
Return type: Any

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 required_inputs

The inputs which must be set on this protocol.

Type: list of ProtocolPath

retain_packmol_files

Input - If True, packmol will not delete all of the temporary files it creates while building the coordinates. The default value of this attribute is False.

Type: bool

property schema

A serializable schema for this object.

Type: ProtocolSchema

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.

substance

Input - The composition of the system to build. The default value of this attribute is not set and must be set by the user..

Type: Substance

tolerance

Input - The packmol distance tolerance in units compatible with angstroms. The default value of this attribute is 2.0 angstrom.

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 –

verbose_packmol

Input - If True, packmol will print verbose information to the logger The default value of this attribute is False.

Type: bool