Class: Rafflesia::Simulations

Inherits:
Object
  • Object
show all
Defined in:
lib/rafflesia/simulations.rb

Instance Method Summary collapse

Constructor Details

#initialize(client) ⇒ Simulations

Returns a new instance of Simulations.



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# File 'lib/rafflesia/simulations.rb', line 9

def initialize(client)
  @client = client
end

Instance Method Details

#contactsNativeFraction(backend: nil, database: nil, end_frame: nil, min_seq_sep: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius_angstrom: nil, reference_frame: nil, reference_structure_format: nil, reference_structure_object_id: nil, reference_structure_path: nil, relation: nil, release: nil, selection: nil, soft_cutoff_factor: nil, sort_by: nil, start_frame: nil, stride: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationNativeContactFractionTableData

POST /v1/simulations/contacts/native-fraction

Parameters:

  • backend (String, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • end_frame (Integer, nil) (defaults to: nil)
  • min_seq_sep (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SimulationNativeContactFractionTableRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • radius_angstrom (Float, nil) (defaults to: nil)
  • reference_frame (Integer, nil) (defaults to: nil)
  • reference_structure_format (String, nil) (defaults to: nil)
  • reference_structure_object_id (String, nil) (defaults to: nil)
  • reference_structure_path (String, nil) (defaults to: nil)
  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • selection (String, nil) (defaults to: nil)
  • soft_cutoff_factor (Float, nil) (defaults to: nil)
  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • start_frame (Integer, nil) (defaults to: nil)
  • stride (Integer, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 44

def contactsNativeFraction(
  backend: nil,
  database: nil,
  end_frame: nil,
  min_seq_sep: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius_angstrom: nil,
  reference_frame: nil,
  reference_structure_format: nil,
  reference_structure_object_id: nil,
  reference_structure_path: nil,
  relation: nil,
  release: nil,
  selection: nil,
  soft_cutoff_factor: nil,
  sort_by: nil,
  start_frame: nil,
  stride: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'database' => database,
    'end_frame' => end_frame,
    'min_seq_sep' => min_seq_sep,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius_angstrom' => radius_angstrom,
    'reference_frame' => reference_frame,
    'reference_structure_format' => reference_structure_format,
    'reference_structure_object_id' => reference_structure_object_id,
    'reference_structure_path' => reference_structure_path,
    'relation' => relation,
    'release' => release,
    'selection' => selection,
    'soft_cutoff_factor' => soft_cutoff_factor,
    'sort_by' => sort_by,
    'start_frame' => start_frame,
    'stride' => stride,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/contacts/native-fraction',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationNativeContactFractionTableData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#contactsRelation(backend: nil, database: nil, end_frame: nil, max_pairs: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius_angstrom: nil, relation: nil, release: nil, selection_a: nil, selection_b: nil, sort_by: nil, start_frame: nil, stride: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationContactsTableData

POST /v1/simulations/contacts/relation

Parameters:

  • backend (String, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • end_frame (Integer, nil) (defaults to: nil)
  • max_pairs (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SimulationContactsTableRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • radius_angstrom (Float, nil) (defaults to: nil)
  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • selection_a (String, nil) (defaults to: nil)
  • selection_b (String, nil) (defaults to: nil)
  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • start_frame (Integer, nil) (defaults to: nil)
  • stride (Integer, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 144

def contactsRelation(
  backend: nil,
  database: nil,
  end_frame: nil,
  max_pairs: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius_angstrom: nil,
  relation: nil,
  release: nil,
  selection_a: nil,
  selection_b: nil,
  sort_by: nil,
  start_frame: nil,
  stride: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'database' => database,
    'end_frame' => end_frame,
    'max_pairs' => max_pairs,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius_angstrom' => radius_angstrom,
    'relation' => relation,
    'release' => release,
    'selection_a' => selection_a,
    'selection_b' => selection_b,
    'sort_by' => sort_by,
    'start_frame' => start_frame,
    'stride' => stride,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/contacts/relation',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationContactsTableData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsCheckInputs(script_object_id:, max_bytes: nil, root_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsCheckInputsData

POST /v1/simulations/gromacs/check-inputs

Parameters:

  • max_bytes (Integer, nil) (defaults to: nil)
  • root_object_ids (Array<String>, nil) (defaults to: nil) —

    Objects containing material inventories, for example GitHub contents JSON arrays. Repeat roots to cover multiple directories.

  • script_object_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 215

def gromacsCheckInputs(
  script_object_id:,
  max_bytes: nil,
  root_object_ids: nil,
  request_options: {}
)
  body = {
    'max_bytes' => max_bytes,
    'root_object_ids' => root_object_ids,
    'script_object_id' => script_object_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/check-inputs',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsCheckInputsData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsInspectMdp(mdp_object_id:, max_bytes: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsInspectMdpData

POST /v1/simulations/gromacs/inspect-mdp

Parameters:

  • max_bytes (Integer, nil) (defaults to: nil)
  • mdp_object_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 243

def gromacsInspectMdp(
  mdp_object_id:,
  max_bytes: nil,
  request_options: {}
)
  body = {
    'max_bytes' => max_bytes,
    'mdp_object_id' => mdp_object_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/inspect-mdp',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsInspectMdpData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsInspectScript(script_object_id:, max_bytes: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsInspectScriptData

POST /v1/simulations/gromacs/inspect-script

Parameters:

  • max_bytes (Integer, nil) (defaults to: nil)
  • script_object_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 269

def gromacsInspectScript(
  script_object_id:,
  max_bytes: nil,
  request_options: {}
)
  body = {
    'max_bytes' => max_bytes,
    'script_object_id' => script_object_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/inspect-script',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsInspectScriptData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsMaterializeInputs(output_dir:, allow_network: nil, input_object_ids: nil, max_bytes: nil, max_download_bytes: nil, preflight_object_id: nil, root_object_ids: nil, script_object_id: nil, stage_index: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsMaterializeInputsData

POST /v1/simulations/gromacs/materialize-inputs

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil) —

    Allow resolved inventory download_url values to be fetched into the object store when no object id is available.

  • input_object_ids (Hash{String => String}, nil) (defaults to: nil) —

    Optional explicit mapping from requested input path to object id, used for planned outputs from earlier stages or inventories without object ids.

  • max_bytes (Integer, nil) (defaults to: nil)
  • max_download_bytes (Integer, nil) (defaults to: nil) —

    Maximum bytes for each network materialization. Defaults to the server object download limit.

  • output_dir (String) —

    Local server directory where object-backed inputs are materialized.

  • preflight_object_id (String, nil) (defaults to: nil) —

    Optional object id containing a SimulationGromacsPreflightData document or response envelope. When set, script_object_id/root_object_ids are not required.

  • root_object_ids (Array<String>, nil) (defaults to: nil) —

    Objects containing material inventories used to build a preflight plan and resolve inputs.

  • script_object_id (String, nil) (defaults to: nil) —

    Script object id used to build a preflight plan when preflight_object_id is omitted.

  • stage_index (Integer, nil) (defaults to: nil) —

    Optional one-based preflight stage index. When omitted, materializes external required script inputs.

  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 302

def gromacsMaterializeInputs(
  output_dir:,
  allow_network: nil,
  input_object_ids: nil,
  max_bytes: nil,
  max_download_bytes: nil,
  preflight_object_id: nil,
  root_object_ids: nil,
  script_object_id: nil,
  stage_index: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'input_object_ids' => input_object_ids,
    'max_bytes' => max_bytes,
    'max_download_bytes' => max_download_bytes,
    'output_dir' => output_dir,
    'preflight_object_id' => preflight_object_id,
    'root_object_ids' => root_object_ids,
    'script_object_id' => script_object_id,
    'stage_index' => stage_index
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/materialize-inputs',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsMaterializeInputsData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsPreflight(script_object_id:, engine: nil, max_bytes: nil, root_object_ids: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsPreflightData

POST /v1/simulations/gromacs/preflight

Parameters:

  • engine (Rafflesia::Types::SimulationGromacsPreflightRequestEngine, nil) (defaults to: nil) —

    Simulation engine to preflight. Defaults to gromacs.

  • max_bytes (Integer, nil) (defaults to: nil)
  • root_object_ids (Array<String>, nil) (defaults to: nil) —

    Objects containing material inventories, for example GitHub contents JSON arrays. Repeat roots to cover multiple directories.

  • script_object_id (String)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 345

def gromacsPreflight(
  script_object_id:,
  engine: nil,
  max_bytes: nil,
  root_object_ids: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'engine' => engine,
    'max_bytes' => max_bytes,
    'root_object_ids' => root_object_ids,
    'script_object_id' => script_object_id,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/preflight',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsPreflightData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#gromacsRunStage(output_dir:, stage_index:, gromacs_binary_path: nil, input_object_ids: nil, max_bytes: nil, max_log_bytes: nil, preflight_object_id: nil, root_object_ids: nil, script_object_id: nil, stdin: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationGromacsRunStageData

POST /v1/simulations/gromacs/run-stage

Parameters:

  • gromacs_binary_path (String, nil) (defaults to: nil) —

    Optional explicit Gromacs executable. Defaults to RAFFLESIA_GROMACS_BINARY or PATH.

  • input_object_ids (Hash{String => String}, nil) (defaults to: nil) —

    Optional explicit mapping from requested stage input path to object id, used for planned outputs from earlier stages or inventories without object ids.

  • max_bytes (Integer, nil) (defaults to: nil)
  • max_log_bytes (Integer, nil) (defaults to: nil)
  • output_dir (String) —

    Local server directory where the bounded stage working directory and output files are written.

  • preflight_object_id (String, nil) (defaults to: nil) —

    Optional object id containing a SimulationGromacsPreflightData document or response envelope. When set, script_object_id/root_object_ids are not required.

  • root_object_ids (Array<String>, nil) (defaults to: nil) —

    Objects containing material inventories used to build a preflight plan and materialize stage inputs.

  • script_object_id (String, nil) (defaults to: nil) —

    Script object id used to build a preflight plan when preflight_object_id is omitted.

  • stage_index (Integer) —

    One-based preflight stage index to execute.

  • stdin (String, nil) (defaults to: nil) —

    Optional stdin supplied to the stage command, for example make_ndx selections.

  • timeout_ms (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 386

def gromacsRunStage(
  output_dir:,
  stage_index:,
  gromacs_binary_path: nil,
  input_object_ids: nil,
  max_bytes: nil,
  max_log_bytes: nil,
  preflight_object_id: nil,
  root_object_ids: nil,
  script_object_id: nil,
  stdin: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'gromacs_binary_path' => gromacs_binary_path,
    'input_object_ids' => input_object_ids,
    'max_bytes' => max_bytes,
    'max_log_bytes' => max_log_bytes,
    'output_dir' => output_dir,
    'preflight_object_id' => preflight_object_id,
    'root_object_ids' => root_object_ids,
    'script_object_id' => script_object_id,
    'stage_index' => stage_index,
    'stdin' => stdin,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/gromacs/run-stage',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationGromacsRunStageData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#runtimeBootstrap(install:, force_recreate: nil, output_dir: nil, packages: nil, python_path: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationRuntimeBootstrapData

POST /v1/simulations/runtime/bootstrap

Parameters:

  • force_recreate (Boolean, nil) (defaults to: nil) —

    Remove and recreate the output_dir before bootstrapping.

  • install (Boolean) —

    Install requested packages into the virtual environment after creation.

  • output_dir (String, nil) (defaults to: nil) —

    Local directory for the simulation Python virtual environment. Defaults to .evidence/simulations/mdanalysis-venv when called from the repo.

  • packages (Array<String>, nil) (defaults to: nil) —

    Python packages to install when install is true. Defaults to MDAnalysis.

  • python_path (String, nil) (defaults to: nil) —

    Python executable used to create the virtual environment. Defaults to python3 on PATH.

  • timeout_ms (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 434

def runtimeBootstrap(
  install:,
  force_recreate: nil,
  output_dir: nil,
  packages: nil,
  python_path: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'force_recreate' => force_recreate,
    'install' => install,
    'output_dir' => output_dir,
    'packages' => packages,
    'python_path' => python_path,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/runtime/bootstrap',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationRuntimeBootstrapData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#runtimeInspect(engine: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationRuntimeInspectData

POST /v1/simulations/runtime/inspect

Parameters:

  • engine (Rafflesia::Types::SimulationRuntimeInspectRequestEngine, nil) (defaults to: nil) —

    Runtime engine to inspect. Defaults to all available simulation runtimes.

  • timeout_ms (Integer, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 468

def runtimeInspect(
  engine: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'engine' => engine,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/runtime/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationRuntimeInspectData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#trajectoriesFramesRelation(backend: nil, database: nil, end_frame: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, start_frame: nil, stride: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationTrajectoryFramesTableData

POST /v1/simulations/trajectories/frames/relation

Parameters:

  • backend (String, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • end_frame (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SimulationTrajectoryFramesTableRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • start_frame (Integer, nil) (defaults to: nil)
  • stride (Integer, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 512

def trajectoriesFramesRelation(
  backend: nil,
  database: nil,
  end_frame: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  start_frame: nil,
  stride: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'database' => database,
    'end_frame' => end_frame,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'start_frame' => start_frame,
    'stride' => stride,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/trajectories/frames/relation',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationTrajectoryFramesTableData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#trajectoriesGeometryRelation(backend: nil, database: nil, end_frame: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, selection: nil, sort_by: nil, start_frame: nil, stride: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationTrajectoryGeometryTableData

POST /v1/simulations/trajectories/geometry/relation

Parameters:

  • backend (String, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • end_frame (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SimulationTrajectoryGeometryTableRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • selection (String, nil) (defaults to: nil)
  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • start_frame (Integer, nil) (defaults to: nil)
  • stride (Integer, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 593

def trajectoriesGeometryRelation(
  backend: nil,
  database: nil,
  end_frame: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  selection: nil,
  sort_by: nil,
  start_frame: nil,
  stride: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'database' => database,
    'end_frame' => end_frame,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'selection' => selection,
    'sort_by' => sort_by,
    'start_frame' => start_frame,
    'stride' => stride,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/trajectories/geometry/relation',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationTrajectoryGeometryTableData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#trajectoriesImport(backend: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationTrajectoryImportData

POST /v1/simulations/trajectories/import

Parameters:

  • backend (String, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 663

def trajectoriesImport(
  backend: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/trajectories/import',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationTrajectoryImportData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#trajectoriesInspect(backend: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationTrajectoryInspectData

POST /v1/simulations/trajectories/inspect

Parameters:

  • backend (String, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 708

def trajectoriesInspect(
  backend: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/trajectories/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationTrajectoryInspectData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end

#trajectoriesRmsdRelation(backend: nil, database: nil, end_frame: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, reference_frame: nil, reference_structure_format: nil, reference_structure_object_id: nil, reference_structure_path: nil, relation: nil, release: nil, selection: nil, sort_by: nil, start_frame: nil, stride: nil, superpose: nil, timeout_ms: nil, topology_format: nil, topology_object_id: nil, topology_path: nil, trajectory_format: nil, trajectory_manifest_object_id: nil, trajectory_object_id: nil, trajectory_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSimulationTrajectoryRmsdTableData

POST /v1/simulations/trajectories/rmsd/relation

Parameters:

  • backend (String, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • end_frame (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::SimulationTrajectoryRmsdTableRequestOutputFormat, nil) (defaults to: nil) —

    Requested durable relation format; parquet is the initial physical format

  • output_relation (String, nil) (defaults to: nil) —

    Local output path or alias for a durable relation artifact

  • partition_by (Array<String>, nil) (defaults to: nil) —

    Requested physical partition columns

  • preview_limit (Integer, nil) (defaults to: nil) —

    When output_relation is requested, include at most this many rows as a non-pageable preview

  • reference_frame (Integer, nil) (defaults to: nil)
  • reference_structure_format (String, nil) (defaults to: nil)
  • reference_structure_object_id (String, nil) (defaults to: nil)
  • reference_structure_path (String, nil) (defaults to: nil)
  • relation (String, nil) (defaults to: nil) —

    Requested logical relation name

  • release (String, nil) (defaults to: nil) —

    Immutable database release published with the relation

  • selection (String, nil) (defaults to: nil)
  • sort_by (Array<String>, nil) (defaults to: nil) —

    Requested physical sort columns

  • start_frame (Integer, nil) (defaults to: nil)
  • stride (Integer, nil) (defaults to: nil)
  • superpose (Boolean, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil)
  • topology_format (String, nil) (defaults to: nil)
  • topology_object_id (String, nil) (defaults to: nil)
  • topology_path (String, nil) (defaults to: nil)
  • trajectory_format (String, nil) (defaults to: nil)
  • trajectory_manifest_object_id (String, nil) (defaults to: nil)
  • trajectory_object_id (String, nil) (defaults to: nil)
  • trajectory_path (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/simulations.rb', line 772

def trajectoriesRmsdRelation(
  backend: nil,
  database: nil,
  end_frame: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  reference_frame: nil,
  reference_structure_format: nil,
  reference_structure_object_id: nil,
  reference_structure_path: nil,
  relation: nil,
  release: nil,
  selection: nil,
  sort_by: nil,
  start_frame: nil,
  stride: nil,
  superpose: nil,
  timeout_ms: nil,
  topology_format: nil,
  topology_object_id: nil,
  topology_path: nil,
  trajectory_format: nil,
  trajectory_manifest_object_id: nil,
  trajectory_object_id: nil,
  trajectory_path: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'database' => database,
    'end_frame' => end_frame,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'reference_frame' => reference_frame,
    'reference_structure_format' => reference_structure_format,
    'reference_structure_object_id' => reference_structure_object_id,
    'reference_structure_path' => reference_structure_path,
    'relation' => relation,
    'release' => release,
    'selection' => selection,
    'sort_by' => sort_by,
    'start_frame' => start_frame,
    'stride' => stride,
    'superpose' => superpose,
    'timeout_ms' => timeout_ms,
    'topology_format' => topology_format,
    'topology_object_id' => topology_object_id,
    'topology_path' => topology_path,
    'trajectory_format' => trajectory_format,
    'trajectory_manifest_object_id' => trajectory_manifest_object_id,
    'trajectory_object_id' => trajectory_object_id,
    'trajectory_path' => trajectory_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/simulations/trajectories/rmsd/relation',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSimulationTrajectoryRmsdTableData.new(response.body)
  result.last_response = Rafflesia::Types::ApiResponse.new(http_status: response.code.to_i, http_headers: response.each_header.to_h, request_id: response["x-request-id"])
  result
end