# ConcatenateTrajectories

class `openff.evaluator.protocols.reweighting.``ConcatenateTrajectories`(protocol_id)

  A protocol which concatenates multiple trajectories into a single one.

  `__init__`(protocol_id)

    Initialize self. See help(type(self)) for accurate signature.

  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.
  `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

  `allow_merging` | Input - Defines whether this protocols is allowed to merge with other protocols.
  `dependencies` | A list of pointers to the protocols which this protocol takes input from.
  `id` | The unique id of this protocol.
  `input_coordinate_paths` | Input - A list of paths to the starting PDB coordinates for each of the trajectories.
  `input_trajectory_paths` | Input - A list of paths to the trajectories to concatenate.
  `output_coordinate_path` | Output - The path the PDB coordinate file which contains the topology of the concatenated trajectory.
  `output_trajectory_path` | Output - The path to the concatenated trajectory.
  `outputs` | A dictionary of the outputs of this property.
  `required_inputs` | The inputs which must be set on this protocol.
  `schema` | A serializable schema for this object.

  `input_coordinate_paths`

    Input - A list of paths to the starting PDB coordinates for each of the trajectories. The default value of this attribute is not set and must be set by the user..

    Type

      list

  `input_trajectory_paths`

    Input - A list of paths to the trajectories to concatenate. The default value of this attribute is not set and must be set by the user..

    Type

      list

  `output_coordinate_path`

    Output - The path the PDB coordinate file which contains the topology of the concatenated trajectory. The default value of this attribute is not set and must be set by the user..

    Type

      str

  `output_trajectory_path`

    Output - The path to the concatenated trajectory. The default value of this attribute is not set and must be set by the user..

    Type

      str

  `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

  `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

  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

  `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]

  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.

    Parameters

      - string_contents (str or bytes) – The typed json string.

      - encoding (str) – The encoding of the string_contents.

    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

  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.

  `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 –