Class: Rafflesia::Proteins

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

Instance Method Summary collapse

Constructor Details

#initialize(client) ⇒ Proteins

Returns a new instance of Proteins.



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

def initialize(client)
  @client = client
end

Instance Method Details

#aromaticStackingDetect(structure_id:, max_centroid: nil, request_options: {}) ⇒ Rafflesia::EnvelopeAromaticStackingDetectData

POST /v1/proteins/aromatic-stacking/detect

Parameters:

  • max_centroid (Float, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 18

def aromaticStackingDetect(
  structure_id:,
  max_centroid: nil,
  request_options: {}
)
  body = {
    'max_centroid' => max_centroid,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/aromatic-stacking/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeAromaticStackingDetectData.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

#cationPiDetect(structure_id:, max_angle: nil, max_distance: nil, request_options: {}) ⇒ Rafflesia::EnvelopeCationPiDetectData

POST /v1/proteins/cation-pi/detect

Parameters:

  • max_angle (Float, nil) (defaults to: nil)
  • max_distance (Float, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 45

def cationPiDetect(
  structure_id:,
  max_angle: nil,
  max_distance: nil,
  request_options: {}
)
  body = {
    'max_angle' => max_angle,
    'max_distance' => max_distance,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/cation-pi/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeCationPiDetectData.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

#complexesImport(path:, source: nil, target_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeComplexImportData

POST /v1/proteins/complexes/import

Parameters:

  • path (String)
  • source (String, nil) (defaults to: nil)
  • target_id (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 74

def complexesImport(
  path:,
  source: nil,
  target_id: nil,
  request_options: {}
)
  body = {
    'path' => path,
    'source' => source,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/complexes/import',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeComplexImportData.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

#confidenceSummary(structure_id:, chain: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeConfidenceSummaryData

POST /v1/proteins/confidence/summary

Parameters:

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

    Database name published with the relation

  • output_format (Rafflesia::Types::ConfidenceSummaryRequestOutputFormat, 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

  • structure_id (String)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 111

def confidenceSummary(
  structure_id:,
  chain: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'chain' => chain,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/confidence/summary',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeConfidenceSummaryData.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

#disulfidesDetect(structure_id:, max_distance: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDisulfideDetectData

POST /v1/proteins/disulfides/detect

Parameters:

  • max_distance (Float, nil) (defaults to: nil) —

    maximum Sγ-Sγ distance in Å treated as a bond (default 2.5)

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 155

def disulfidesDetect(
  structure_id:,
  max_distance: nil,
  request_options: {}
)
  body = {
    'max_distance' => max_distance,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/disulfides/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDisulfideDetectData.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

#dynamicsAnm(structure_id:, chain: nil, cutoff: nil, modes: nil, request_options: {}) ⇒ Rafflesia::EnvelopeAnmFluctuationsData

POST /v1/proteins/dynamics/anm

Parameters:

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

    restrict the network to a single chain id; empty uses every protein chain

  • cutoff (Float, nil) (defaults to: nil) —

    Cα–Cα contact cutoff in Å (default 13)

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

    number of slowest non-trivial modes to return (default 6)

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 183

def dynamicsAnm(
  structure_id:,
  chain: nil,
  cutoff: nil,
  modes: nil,
  request_options: {}
)
  body = {
    'chain' => chain,
    'cutoff' => cutoff,
    'modes' => modes,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/dynamics/anm',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeAnmFluctuationsData.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

#dynamicsGnm(structure_id:, chain: nil, cutoff: nil, request_options: {}) ⇒ Rafflesia::EnvelopeGnmFluctuationsData

POST /v1/proteins/dynamics/gnm

Parameters:

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

    restrict the network to a single chain id; empty uses every protein chain

  • cutoff (Float, nil) (defaults to: nil) —

    Cα–Cα contact cutoff in Å (default 7.3)

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 214

def dynamicsGnm(
  structure_id:,
  chain: nil,
  cutoff: nil,
  request_options: {}
)
  body = {
    'chain' => chain,
    'cutoff' => cutoff,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/dynamics/gnm',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeGnmFluctuationsData.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

#foldsAlign(query_id:, target_id:, backend: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldAlignData

POST /v1/proteins/folds/align

Parameters:

  • backend (String, nil) (defaults to: nil)
  • query_id (String)
  • target_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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

def foldsAlign(
  query_id:,
  target_id:,
  backend: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'query_id' => query_id,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/align',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldAlignData.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

#foldsCandidatesBuild(build_policy: nil, dataset_name: nil, dataset_version: nil, input_object_id: nil, input_path: nil, kmer_size: nil, min_shared_tokens: nil, name: nil, namespace: nil, timeout_ms: nil, version: nil, request_options: {}) ⇒ Rafflesia::EnvelopeProteinFoldCandidateBuildData

POST /v1/proteins/folds/candidates/build

Parameters:

  • build_policy (Rafflesia::Types::ProteinFoldCandidateBuildRequestBuildPolicy, nil) (defaults to: nil) —

    Immutable publish policy for an existing namespace. Defaults to if_not_exists.

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

    Optional dataset name carried into build provenance.

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

    Optional dataset version carried into build provenance.

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

    Object id containing JSON array of structure records.

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

    JSON file containing an array of structure records.

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

    Structural token k-mer size; defaults to 3.

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

    Candidate threshold on shared structural tokens; defaults to 1.

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

    Logical structure index name carried into provenance and namespace derivation.

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

    Explicit structure candidate namespace. Defaults to a deterministic namespace derived from name and version.

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

    Hard deadline for this build operation in milliseconds; defaults to the structure candidate build timeout.

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

    Immutable structure index version carried into provenance and namespace derivation.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 280

def foldsCandidatesBuild(
  build_policy: nil,
  dataset_name: nil,
  dataset_version: nil,
  input_object_id: nil,
  input_path: nil,
  kmer_size: nil,
  min_shared_tokens: nil,
  name: nil,
  namespace: nil,
  timeout_ms: nil,
  version: nil,
  request_options: {}
)
  body = {
    'build_policy' => build_policy,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'input_object_id' => input_object_id,
    'input_path' => input_path,
    'kmer_size' => kmer_size,
    'min_shared_tokens' => min_shared_tokens,
    'name' => name,
    'namespace' => namespace,
    'timeout_ms' => timeout_ms,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/candidates/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeProteinFoldCandidateBuildData.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

#foldsCandidatesSearch(namespace:, kmer_size: nil, max_hits: nil, max_object_bytes: nil, max_object_reads: nil, min_shared_tokens: nil, query_object_id: nil, query_path: nil, query_structure: nil, require_zero_materialization: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeProteinFoldCandidateSearchData

POST /v1/proteins/folds/candidates/search

Parameters:

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

    Structural token k-mer size; defaults to the build/query family default.

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

    Maximum number of hits returned; defaults to 10.

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

    Optional hard budget checked against observed object bytes.

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

    Optional hard budget checked against observed object reads.

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

    Candidate threshold on shared structural tokens; defaults to 1.

  • namespace (String) —

    Structure candidate namespace to search.

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

    Object id containing one query structure record.

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

    JSON file containing one query structure record.

  • query_structure (Rafflesia::ProteinFoldCandidateRecord, nil) (defaults to: nil) —

    Inline query structure record.

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

    Require the object-native path to materialize zero local database bytes.

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

    Hard deadline for this search in milliseconds; defaults to the structure candidate search timeout.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 333

def foldsCandidatesSearch(
  namespace:,
  kmer_size: nil,
  max_hits: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  min_shared_tokens: nil,
  query_object_id: nil,
  query_path: nil,
  query_structure: nil,
  require_zero_materialization: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'kmer_size' => kmer_size,
    'max_hits' => max_hits,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'min_shared_tokens' => min_shared_tokens,
    'namespace' => namespace,
    'query_object_id' => query_object_id,
    'query_path' => query_path,
    'query_structure' => query_structure,
    'require_zero_materialization' => require_zero_materialization,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/candidates/search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeProteinFoldCandidateSearchData.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

#foldsCollectionsBenchmark(query_ids:, exact_limit: nil, exact_verify: nil, limit: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, max_segments: nil, max_segments_per_query: nil, min_byte_reduction_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, min_routing_score_coverage: nil, min_segment_reduction_fraction: nil, nprobe: nil, recall_at: nil, ref: nil, require_adaptive_routing: nil, require_exact_verification: nil, require_routing: nil, require_zero_materialization: nil, routing_mode: nil, segment_refs: nil, store_artifact: nil, store_calibration: nil, target_score_coverage: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldCollectionBenchmarkData

POST /v1/proteins/folds/collections/benchmark

Parameters:

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

    Maximum routed candidates to verify exactly per segment; defaults to limit when exact_verify is true.

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

    Run candidate-only TM-align verification for routed collection search before measuring recall.

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

    Per-query hit limit; defaults to 100.

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

    Optional per-query cap on selected routed feature blocks across the collection.

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

    Optional per-query cap on routed collection object bytes read.

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

    Optional per-query cap on routed collection object reads.

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

    Maximum routed collection segments to search per query; defaults to a bounded planner value.

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

    Optional per-query cap on routed collection segments searched.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for object byte reduction against exhaustive collection scan.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_100.

  • min_routing_score_coverage (Float, nil) (defaults to: nil) —

    Optional pass threshold for selected routing score coverage across benchmark queries.

  • min_segment_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for routed segment fanout reduction against exhaustive collection scan.

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

    Routed object feature block count per segment; defaults to 1.

  • query_ids (Array<String>, nil) —

    Explicit query structure ids or paths to benchmark.

  • recall_at (Array<Integer>, nil) (defaults to: nil) —

    Recall cutoffs to compute against exhaustive collection scan; defaults to 1,10,100.

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

    Published fold collection ref or immutable snapshot ref.

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

    Require routed benchmark searches to use adaptive routing fanout.

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

    Require every routed collection query to report exact candidate verification.

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

    Require routed search to use the collection routing directory instead of exhaustive fanout.

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

    Require the object-native collection path to materialize zero local database bytes.

  • routing_mode (Rafflesia::Types::FoldCollectionBenchmarkRequestRoutingMode, nil) (defaults to: nil) —

    Collection fanout mode for routed benchmark searches.

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

    Explicit published fold segment refs to benchmark without resolving a collection ref.

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true.

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

    Whether to store the derived routing calibration profile in the object store; defaults to store_artifact.

  • target_score_coverage (Float, nil) (defaults to: nil) —

    Adaptive routing score-coverage target for routed benchmark searches.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 402

def foldsCollectionsBenchmark(
  query_ids:,
  exact_limit: nil,
  exact_verify: nil,
  limit: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  max_segments: nil,
  max_segments_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  min_routing_score_coverage: nil,
  min_segment_reduction_fraction: nil,
  nprobe: nil,
  recall_at: nil,
  ref: nil,
  require_adaptive_routing: nil,
  require_exact_verification: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  routing_mode: nil,
  segment_refs: nil,
  store_artifact: nil,
  store_calibration: nil,
  target_score_coverage: nil,
  request_options: {}
)
  body = {
    'exact_limit' => exact_limit,
    'exact_verify' => exact_verify,
    'limit' => limit,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'max_segments' => max_segments,
    'max_segments_per_query' => max_segments_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'min_routing_score_coverage' => min_routing_score_coverage,
    'min_segment_reduction_fraction' => min_segment_reduction_fraction,
    'nprobe' => nprobe,
    'query_ids' => query_ids,
    'recall_at' => recall_at,
    'ref' => ref,
    'require_adaptive_routing' => require_adaptive_routing,
    'require_exact_verification' => require_exact_verification,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'routing_mode' => routing_mode,
    'segment_refs' => segment_refs,
    'store_artifact' => store_artifact,
    'store_calibration' => store_calibration,
    'target_score_coverage' => target_score_coverage
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/collections/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldCollectionBenchmarkData.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

#foldsCollectionsCalibrate(query_ids:, allow_regression: nil, current_calibration_object_id: nil, exact_limit: nil, exact_verify: nil, limit: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, max_segments: nil, max_segments_per_query: nil, min_byte_reduction_fraction: nil, min_object_read_reduction_improvement: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, min_recall_at_1_improvement: nil, min_routing_score_coverage: nil, min_segment_reduction_fraction: nil, min_segment_reduction_improvement: nil, nprobe: nil, promote: nil, recall_at: nil, ref: nil, require_adaptive_routing: nil, require_exact_verification: nil, require_routing: nil, require_zero_materialization: nil, routing_mode: nil, segment_refs: nil, store_artifact: nil, store_calibration: nil, store_telemetry: nil, target_score_coverage: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldCollectionCalibrateData

POST /v1/proteins/folds/collections/calibrate

Parameters:

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

    Allow promotion even when the candidate regresses against the current calibration comparison.

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

    Explicit current calibration profile object id to compare against; defaults to the collection's current calibration.

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

    Maximum routed candidates to verify exactly per segment; defaults to limit when exact_verify is true.

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

    Run candidate-only TM-align verification before measuring recall.

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

    Per-query hit limit; defaults to 100.

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

    Optional per-query cap on selected routed feature blocks across the collection.

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

    Optional per-query cap on routed collection object bytes read.

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

    Optional per-query cap on routed collection object reads.

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

    Maximum routed collection segments to search per query; defaults to a bounded planner value.

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

    Optional per-query cap on routed collection segments searched.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for object byte reduction against exhaustive collection scan.

  • min_object_read_reduction_improvement (Float, nil) (defaults to: nil) —

    Minimum candidate planned object-read reduction improvement over the current calibration before promotion.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_100.

  • min_recall_at_1_improvement (Float, nil) (defaults to: nil) —

    Minimum candidate recall_at_1 improvement over the current calibration before promotion.

  • min_routing_score_coverage (Float, nil) (defaults to: nil) —

    Optional pass threshold for selected routing score coverage across calibration queries.

  • min_segment_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for routed segment fanout reduction against exhaustive collection scan.

  • min_segment_reduction_improvement (Float, nil) (defaults to: nil) —

    Minimum candidate segment reduction improvement over the current calibration before promotion.

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

    Routed object feature block count per segment; defaults to 1.

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

    Promote the candidate calibration to the collection's mutable ref when promotion gates pass.

  • query_ids (Array<String>, nil) —

    Explicit query structure ids or paths to use as the calibration sample.

  • recall_at (Array<Integer>, nil) (defaults to: nil) —

    Recall cutoffs to compute against exhaustive collection scan; defaults to 1,10,100.

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

    Published fold collection ref or immutable snapshot ref.

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

    Require routed calibration searches to use adaptive routing fanout.

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

    Require every routed collection query to report exact candidate verification.

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

    Require routed search to use the collection routing directory instead of exhaustive fanout.

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

    Require the object-native collection path to materialize zero local database bytes.

  • routing_mode (Rafflesia::Types::FoldCollectionCalibrateRequestRoutingMode, nil) (defaults to: nil) —

    Collection fanout mode for candidate calibration searches.

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

    Explicit published fold segment refs to calibrate without resolving a collection ref.

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true.

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

    Whether to store the derived routing calibration profile in the object store; defaults to true.

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

    Whether to store per-query calibration telemetry in the object store; defaults to true.

  • target_score_coverage (Float, nil) (defaults to: nil) —

    Adaptive routing score-coverage target for candidate calibration searches.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 510

def foldsCollectionsCalibrate(
  query_ids:,
  allow_regression: nil,
  current_calibration_object_id: nil,
  exact_limit: nil,
  exact_verify: nil,
  limit: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  max_segments: nil,
  max_segments_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_object_read_reduction_improvement: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  min_recall_at_1_improvement: nil,
  min_routing_score_coverage: nil,
  min_segment_reduction_fraction: nil,
  min_segment_reduction_improvement: nil,
  nprobe: nil,
  promote: nil,
  recall_at: nil,
  ref: nil,
  require_adaptive_routing: nil,
  require_exact_verification: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  routing_mode: nil,
  segment_refs: nil,
  store_artifact: nil,
  store_calibration: nil,
  store_telemetry: nil,
  target_score_coverage: nil,
  request_options: {}
)
  body = {
    'allow_regression' => allow_regression,
    'current_calibration_object_id' => current_calibration_object_id,
    'exact_limit' => exact_limit,
    'exact_verify' => exact_verify,
    'limit' => limit,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'max_segments' => max_segments,
    'max_segments_per_query' => max_segments_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_object_read_reduction_improvement' => min_object_read_reduction_improvement,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'min_recall_at_1_improvement' => min_recall_at_1_improvement,
    'min_routing_score_coverage' => min_routing_score_coverage,
    'min_segment_reduction_fraction' => min_segment_reduction_fraction,
    'min_segment_reduction_improvement' => min_segment_reduction_improvement,
    'nprobe' => nprobe,
    'promote' => promote,
    'query_ids' => query_ids,
    'recall_at' => recall_at,
    'ref' => ref,
    'require_adaptive_routing' => require_adaptive_routing,
    'require_exact_verification' => require_exact_verification,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'routing_mode' => routing_mode,
    'segment_refs' => segment_refs,
    'store_artifact' => store_artifact,
    'store_calibration' => store_calibration,
    'store_telemetry' => store_telemetry,
    'target_score_coverage' => target_score_coverage
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/collections/calibrate',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldCollectionCalibrateData.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

#foldsCollectionsGc(candidate_refs: nil, candidate_segment_refs: nil, dry_run: nil, keep_refs: nil, keep_segment_refs: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldCollectionGcData

POST /v1/proteins/folds/collections/gc

Parameters:

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

    Published fold collection refs considered for collection; repeatable.

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

    Additional candidate published fold segment refs; repeatable.

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

    Whether to only report unused objects; defaults to true.

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

    Published fold collection refs that remain live; repeatable.

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

    Additional live published fold segment refs; repeatable.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 603

def foldsCollectionsGc(
  candidate_refs: nil,
  candidate_segment_refs: nil,
  dry_run: nil,
  keep_refs: nil,
  keep_segment_refs: nil,
  request_options: {}
)
  body = {
    'candidate_refs' => candidate_refs,
    'candidate_segment_refs' => candidate_segment_refs,
    'dry_run' => dry_run,
    'keep_refs' => keep_refs,
    'keep_segment_refs' => keep_segment_refs
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/collections/gc',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldCollectionGcData.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

#foldsCollectionsPublish(name:, segment_refs:, version:, benchmark_object_id: nil, calibration_object_id: nil, compaction_generation: nil, generation: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, max_segments_per_query: nil, min_byte_reduction_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, min_routing_score_coverage: nil, min_segment_reduction_fraction: nil, ref: nil, require_adaptive_routing: nil, require_benchmark: nil, require_calibration: nil, require_exact_verification: nil, require_routing: nil, require_zero_materialization: nil, snapshot_ref: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldCollectionPublishData

POST /v1/proteins/folds/collections/publish

Parameters:

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

    Object id produced by proteins.folds.collections.benchmark.

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

    Object id for a collection routing calibration profile produced by proteins.folds.collections.benchmark.

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

    Monotonic compaction generation represented by this snapshot.

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

    Monotonic collection generation supplied by the caller.

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

    Maximum selected routed feature blocks per benchmark query.

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

    Maximum planned routed object bytes per benchmark query.

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

    Maximum planned routed object reads per benchmark query.

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

    Maximum routed collection segments searched per benchmark query.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Publish gate threshold for planned object byte reduction.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Publish gate threshold for collection recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Publish gate threshold for collection recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Publish gate threshold for collection recall_at_100.

  • min_routing_score_coverage (Float, nil) (defaults to: nil) —

    Publish gate threshold for routed collection score coverage selected by the planner.

  • min_segment_reduction_fraction (Float, nil) (defaults to: nil) —

    Publish gate threshold for routed segment fanout reduction against exhaustive collection scan.

  • name (String) —

    Logical fold collection name.

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

    Mutable collection alias to publish atomically, for example afdb:active; defaults to snapshot_ref.

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

    Require benchmark evidence that collection search used adaptive routing fanout.

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

    Require a passing fold collection benchmark artifact before publishing.

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

    Require a benchmark-derived collection routing calibration profile before publishing.

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

    Require benchmark evidence that routed collection search exactly verified candidates.

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

    Require benchmark evidence that collection search used the routing directory instead of exhaustive fanout.

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

    Require benchmark evidence that routed collection search materialized zero local database bytes.

  • segment_refs (Array<String>, nil) —

    Published fold segment refs active in this collection snapshot.

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

    Immutable collection snapshot ref; defaults to name:version.

  • version (String) —

    Immutable collection snapshot version.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 658

def foldsCollectionsPublish(
  name:,
  segment_refs:,
  version:,
  benchmark_object_id: nil,
  calibration_object_id: nil,
  compaction_generation: nil,
  generation: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  max_segments_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  min_routing_score_coverage: nil,
  min_segment_reduction_fraction: nil,
  ref: nil,
  require_adaptive_routing: nil,
  require_benchmark: nil,
  require_calibration: nil,
  require_exact_verification: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  snapshot_ref: nil,
  request_options: {}
)
  body = {
    'benchmark_object_id' => benchmark_object_id,
    'calibration_object_id' => calibration_object_id,
    'compaction_generation' => compaction_generation,
    'generation' => generation,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'max_segments_per_query' => max_segments_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'min_routing_score_coverage' => min_routing_score_coverage,
    'min_segment_reduction_fraction' => min_segment_reduction_fraction,
    'name' => name,
    'ref' => ref,
    'require_adaptive_routing' => require_adaptive_routing,
    'require_benchmark' => require_benchmark,
    'require_calibration' => require_calibration,
    'require_exact_verification' => require_exact_verification,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'segment_refs' => segment_refs,
    'snapshot_ref' => snapshot_ref,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/collections/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldCollectionPublishData.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

#foldsCollectionsSearch(query_id:, calibration_object_id: nil, distributed: nil, dry_run: nil, exact_limit: nil, exact_verify: nil, limit: nil, max_blocks: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, max_segments: nil, max_workers: nil, nprobe: nil, ref: nil, require_complete: nil, require_routing: nil, require_zero_materialization: nil, routing_mode: nil, segment_refs: nil, store_plan: nil, target_score_coverage: nil, use_calibration: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldCollectionSearchData

POST /v1/proteins/folds/collections/search

Parameters:

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

    Explicit collection routing calibration profile object id to use for planning.

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

    Execute selected segment searches as deterministic worker tasks before merging results.

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

    Return the deterministic read plan without fetching feature blocks.

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

    Maximum routed candidates to verify exactly per segment; defaults to limit when exact_verify is true.

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

    Run candidate-only TM-align verification inside each searched segment before merging hits.

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

    Maximum merged fold feature hits to return; defaults to 50.

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

    Optional hard budget for total selected feature blocks across the collection.

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

    Optional hard budget for total local database materialization bytes.

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

    Optional hard budget for total planned collection object bytes.

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

    Optional hard budget for total planned collection object reads.

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

    Maximum routed collection segments to search; defaults to a bounded planner value when a routing directory is available.

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

    Maximum concurrent collection segment worker tasks when distributed execution is enabled.

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

    Number of adjacent feature blocks to probe per segment; defaults to 1.

  • query_id (String) —

    Stored structure id or local PDB/mmCIF path used as the query.

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

    Published fold collection ref or immutable snapshot ref.

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

    Whether distributed collection search must fail if any selected segment worker fails; defaults to true.

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

    Require collection-level routing to choose a bounded segment subset.

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

    Require the collection search path to materialize zero local database bytes.

  • routing_mode (Rafflesia::Types::FoldCollectionSearchRequestRoutingMode, nil) (defaults to: nil) —

    Collection fanout mode. auto selects adaptive fanout unless max_segments is explicitly set; fixed uses max_segments/default cap.

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

    Explicit published fold segment refs to search without resolving a collection ref.

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

    Whether to store the deterministic distributed collection search plan artifact; defaults to distributed.

  • target_score_coverage (Float, nil) (defaults to: nil) —

    Adaptive routing target for cumulative positive routing-score coverage. Defaults to a conservative planner target.

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

    Use the collection's benchmark-derived routing calibration profile to fill unset routing parameters.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 751

def foldsCollectionsSearch(
  query_id:,
  calibration_object_id: nil,
  distributed: nil,
  dry_run: nil,
  exact_limit: nil,
  exact_verify: nil,
  limit: nil,
  max_blocks: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  max_segments: nil,
  max_workers: nil,
  nprobe: nil,
  ref: nil,
  require_complete: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  routing_mode: nil,
  segment_refs: nil,
  store_plan: nil,
  target_score_coverage: nil,
  use_calibration: nil,
  request_options: {}
)
  body = {
    'calibration_object_id' => calibration_object_id,
    'distributed' => distributed,
    'dry_run' => dry_run,
    'exact_limit' => exact_limit,
    'exact_verify' => exact_verify,
    'limit' => limit,
    'max_blocks' => max_blocks,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'max_segments' => max_segments,
    'max_workers' => max_workers,
    'nprobe' => nprobe,
    'query_id' => query_id,
    'ref' => ref,
    'require_complete' => require_complete,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'routing_mode' => routing_mode,
    'segment_refs' => segment_refs,
    'store_plan' => store_plan,
    'target_score_coverage' => target_score_coverage,
    'use_calibration' => use_calibration
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/collections/search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldCollectionSearchData.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

#foldsDatasetsGc(dataset_id:, dry_run: nil, max_deletes: nil, min_age_seconds: nil, min_versions_to_keep: nil, protected_versions: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldDatasetGcData

POST /v1/proteins/folds/datasets/gc

Parameters:

  • dataset_id (String) —

    Foldsearch control-plane dataset id to collect.

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

    When true, compute and return the plan without marking or deleting storage.

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

    Maximum versions to delete in one pass; 0 means no limit.

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

    Grace period in seconds before a superseded version may be deleted.

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

    Minimum number of newest dataset versions to retain; the server floors this to current plus one predecessor.

  • protected_versions (Array<Integer>, nil) (defaults to: nil) —

    Explicit dataset versions pinned by active readers or an operator; protected versions are neither marked nor deleted this pass.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 823

def foldsDatasetsGc(
  dataset_id:,
  dry_run: nil,
  max_deletes: nil,
  min_age_seconds: nil,
  min_versions_to_keep: nil,
  protected_versions: nil,
  request_options: {}
)
  body = {
    'dataset_id' => dataset_id,
    'dry_run' => dry_run,
    'max_deletes' => max_deletes,
    'min_age_seconds' => min_age_seconds,
    'min_versions_to_keep' => min_versions_to_keep,
    'protected_versions' => protected_versions
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/datasets/gc',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldDatasetGcData.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

#foldsIndexBenchmark(query_ids:, concurrency: nil, limit: nil, manifest_object_id: nil, manifest_path: nil, min_byte_reduction_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, nprobe: nil, recall_at: nil, ref: nil, store_artifact: nil, target_dir: nil, verify_index: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexBenchmarkData

POST /v1/proteins/folds/index/benchmark

Parameters:

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

    Maximum shard searches to execute concurrently

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

    Per-query hit limit; defaults to 100

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

    Object id for a Foldseek index manifest

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

    Local Foldseek index manifest path

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for materialized byte reduction

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_1

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_10

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_100

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

    Routed candidate shard cap; defaults to planner policy

  • query_ids (Array<String>, nil) —

    Explicit query structure ids or paths to benchmark

  • recall_at (Array<Integer>, nil) (defaults to: nil) —

    Recall cutoffs to compute against full scan hits; defaults to 1,10,100

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

    Published Foldseek index ref such as name:version

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true

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

    Benchmark cache root; full_scan and routed runs use separate subdirectories

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

    Verify materialized index artifacts by SHA-256

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 870

def foldsIndexBenchmark(
  query_ids:,
  concurrency: nil,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  min_byte_reduction_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  nprobe: nil,
  recall_at: nil,
  ref: nil,
  store_artifact: nil,
  target_dir: nil,
  verify_index: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'nprobe' => nprobe,
    'query_ids' => query_ids,
    'recall_at' => recall_at,
    'ref' => ref,
    'store_artifact' => store_artifact,
    'target_dir' => target_dir,
    'verify_index' => verify_index
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexBenchmarkData.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

#foldsIndexBuild(name:, version:, create_index: nil, dry_run: nil, output_dir: nil, publish: nil, routing_representatives_per_shard: nil, shard_count: nil, source_manifest_object_id: nil, store_artifacts: nil, structure_ids: nil, structure_object_ids: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexBuildData

POST /v1/proteins/folds/index/build

Parameters:

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

    Run foldseek createindex after createdb and store the generated .idx artifacts

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

    Return the deterministic plan without executing foldseek createdb

  • name (String) —

    Logical Foldseek index name, for example afdb50

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

    Directory for generated Foldseek DB files and index manifest

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

    Whether to publish the built manifest into the local Foldseek index registry

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

    Number of deterministic source representatives per non-empty shard to put in the routing segment; defaults to 1

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

    Number of deterministic Foldseek shards; defaults to 1

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

    Object id of a JSON source manifest listing structure objects

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

    Whether to store generated artifacts in the object store; defaults to true

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

    Stored structure record ids to index

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

    Structure object ids to index directly

  • version (String) —

    Immutable logical index version

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 932

def foldsIndexBuild(
  name:,
  version:,
  create_index: nil,
  dry_run: nil,
  output_dir: nil,
  publish: nil,
  routing_representatives_per_shard: nil,
  shard_count: nil,
  source_manifest_object_id: nil,
  store_artifacts: nil,
  structure_ids: nil,
  structure_object_ids: nil,
  request_options: {}
)
  body = {
    'create_index' => create_index,
    'dry_run' => dry_run,
    'name' => name,
    'output_dir' => output_dir,
    'publish' => publish,
    'routing_representatives_per_shard' => routing_representatives_per_shard,
    'shard_count' => shard_count,
    'source_manifest_object_id' => source_manifest_object_id,
    'store_artifacts' => store_artifacts,
    'structure_ids' => structure_ids,
    'structure_object_ids' => structure_object_ids,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexBuildData.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

#foldsIndexDescribe(manifest_object_id: nil, manifest_path: nil, ref: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexDescribeData

POST /v1/proteins/folds/index/describe

Parameters:

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

    Manifest object id

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

    Local manifest path

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

    Published index ref such as name:version or manifest object id

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

    Optional local cache directory to inspect

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 980

def foldsIndexDescribe(
  manifest_object_id: nil,
  manifest_path: nil,
  ref: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'ref' => ref,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/describe',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexDescribeData.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

#foldsIndexEvict(dry_run: nil, manifest_object_id: nil, manifest_path: nil, max_bytes: nil, policy: nil, ref: nil, segment_roles: nil, shards: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexEvictData

POST /v1/proteins/folds/index/evict

Parameters:

  • dry_run (Boolean, nil) (defaults to: nil)
  • manifest_object_id (String, nil) (defaults to: nil)
  • manifest_path (String, nil) (defaults to: nil)
  • max_bytes (Integer, nil) (defaults to: nil) —

    If positive, evict oldest selected cache files until selected cache bytes are less than or equal to this limit. Zero evicts every selected file.

  • policy (Rafflesia::CacheEvictionPolicy, nil) (defaults to: nil) —

    Optional cache policy for TTL and pinned-path eviction controls.

  • ref (String, nil) (defaults to: nil)
  • segment_roles (Array<String>, nil) (defaults to: nil)
  • shards (Array<String>, nil) (defaults to: nil)
  • target_dir (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1017

def foldsIndexEvict(
  dry_run: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_bytes: nil,
  policy: nil,
  ref: nil,
  segment_roles: nil,
  shards: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'dry_run' => dry_run,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_bytes' => max_bytes,
    'policy' => policy,
    'ref' => ref,
    'segment_roles' => segment_roles,
    'shards' => shards,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/evict',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexEvictData.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

#foldsIndexList(limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexListData

GET /v1/proteins/folds/index/list

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1056

def foldsIndexList(
  limit: nil,
  request_options: {}
)
  params = {
    'limit' => limit
  }.compact
  response = @client.request(
    method: :get,
    path: '/v1/proteins/folds/index/list',
    auth: true,
    params: params,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexListData.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

#foldsIndexMaterialize(manifest_object_id: nil, manifest_path: nil, ref: nil, segment_roles: nil, shards: nil, target_dir: nil, verify: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexMaterializeData

POST /v1/proteins/folds/index/materialize

Parameters:

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

    Manifest object id

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

    Local manifest path

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

    Published index ref such as name:version or manifest object id

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

    Optional Foldseek segment roles to materialize: search_index, routing_index. Empty materializes every segment.

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

    Optional shard ids to materialize; empty materializes every shard with artifacts

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

    Directory used as the local Foldseek index cache

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

    Verify materialized files by SHA-256

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1085

def foldsIndexMaterialize(
  manifest_object_id: nil,
  manifest_path: nil,
  ref: nil,
  segment_roles: nil,
  shards: nil,
  target_dir: nil,
  verify: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'ref' => ref,
    'segment_roles' => segment_roles,
    'shards' => shards,
    'target_dir' => target_dir,
    'verify' => verify
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/materialize',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexMaterializeData.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

#foldsIndexPublish(manifest_object_id: nil, manifest_path: nil, min_routing_byte_reduction_fraction: nil, min_routing_recall_at_1: nil, min_routing_recall_at_10: nil, min_routing_recall_at_100: nil, ref: nil, require_routing_benchmark: nil, routing_benchmark_object_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexPublishData

POST /v1/proteins/folds/index/publish

Parameters:

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

    Manifest object id

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

    Local manifest path

  • min_routing_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for materialized byte reduction from routed search

  • min_routing_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for routed recall_at_1

  • min_routing_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for routed recall_at_10

  • min_routing_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional publish gate threshold for routed recall_at_100

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

    Published index ref override

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

    Require a passing routing benchmark artifact before publishing a routable index

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

    Object id of a Foldseek routing benchmark artifact produced by proteins.folds.index.benchmark

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1128

def foldsIndexPublish(
  manifest_object_id: nil,
  manifest_path: nil,
  min_routing_byte_reduction_fraction: nil,
  min_routing_recall_at_1: nil,
  min_routing_recall_at_10: nil,
  min_routing_recall_at_100: nil,
  ref: nil,
  require_routing_benchmark: nil,
  routing_benchmark_object_id: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'min_routing_byte_reduction_fraction' => min_routing_byte_reduction_fraction,
    'min_routing_recall_at_1' => min_routing_recall_at_1,
    'min_routing_recall_at_10' => min_routing_recall_at_10,
    'min_routing_recall_at_100' => min_routing_recall_at_100,
    'ref' => ref,
    'require_routing_benchmark' => require_routing_benchmark,
    'routing_benchmark_object_id' => routing_benchmark_object_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexPublishData.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

#foldsIndexVerify(manifest_object_id: nil, manifest_path: nil, ref: nil, segment_roles: nil, shards: nil, target_dir: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldIndexVerifyData

POST /v1/proteins/folds/index/verify

Parameters:

  • manifest_object_id (String, nil) (defaults to: nil)
  • manifest_path (String, nil) (defaults to: nil)
  • ref (String, nil) (defaults to: nil)
  • segment_roles (Array<String>, nil) (defaults to: nil)
  • shards (Array<String>, nil) (defaults to: nil)
  • target_dir (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1172

def foldsIndexVerify(
  manifest_object_id: nil,
  manifest_path: nil,
  ref: nil,
  segment_roles: nil,
  shards: nil,
  target_dir: nil,
  request_options: {}
)
  body = {
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'ref' => ref,
    'segment_roles' => segment_roles,
    'shards' => shards,
    'target_dir' => target_dir
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/index/verify',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldIndexVerifyData.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

#foldsSearch(query_id:, concurrency: nil, database: nil, dry_run: nil, exact_rerank: nil, exact_rerank_backend: nil, exact_rerank_rank_key: nil, foldseek_alignment_type: nil, foldseek_binary_path: nil, foldseek_exhaustive_search: nil, foldseek_gpu: nil, foldseek_kmer_size: nil, foldseek_lddt_threshold: nil, foldseek_prefilter_mode: nil, foldseek_result_order: nil, foldseek_sensitivity: nil, foldseek_sort_by_structure_bits: nil, foldseek_threads: nil, foldseek_tmscore_threshold: nil, force_full_scan: nil, index_ref: nil, limit: nil, manifest_object_id: nil, manifest_path: nil, max_candidates: nil, max_exact_shards: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, nprobe: nil, object_store_root: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, profile: nil, query_mode: nil, query_structure_file_name: nil, query_structure_object_id: nil, query_structure_path: nil, relation: nil, release: nil, require_routing: nil, require_zero_materialization: nil, rerank_limit: nil, shards: nil, sort_by: nil, target_dir: nil, target_structure_objects: nil, target_structure_paths: nil, tmalign_binary_path: nil, verify_index: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSearchData

POST /v1/proteins/folds/search

Parameters:

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

    Maximum object-backed Foldseek shards to execute concurrently; defaults to 4.

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

    Database name published with the relation

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

    Return the deterministic physical plan without materializing the index or running Foldseek.

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

    When true against the current structure release, rerank returned candidates with a pairwise structure aligner.

  • exact_rerank_backend (Rafflesia::Types::FoldSearchRequestExactRerankBackend, nil) (defaults to: nil) —

    Pairwise backend used by exact_rerank. Defaults to tmalign.

  • exact_rerank_rank_key (Rafflesia::Types::FoldSearchRequestExactRerankRankKey, nil) (defaults to: nil) —

    Measurement used to order exact_rerank hits. Defaults to the backend's measured primary structural score.

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

    Optional Foldseek --alignment-type value. Numeric values are passed through to the installed binary.

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

    Optional absolute Foldseek binary path used for raw-structure token extraction.

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

    When true, pass --exhaustive-search 1 to Foldseek. Intended for calibration and diagnostics.

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

    Optional Foldseek --gpu value. Omit to use the installed binary default.

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

    Optional Foldseek k-mer size passed as -k.

  • foldseek_lddt_threshold (Float, nil) (defaults to: nil) —

    Optional Foldseek --lddt-threshold value.

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

    Optional Foldseek --prefilter-mode value. Numeric values are passed through to the installed binary.

  • foldseek_result_order (Rafflesia::Types::FoldSearchRequestFoldseekResultOrder, nil) (defaults to: nil) —

    How the adapter orders parsed Foldseek hits. Defaults to deterministic descending TM-score order; foldseek_order explicitly preserves the backend's emitted order.

  • foldseek_sensitivity (Float, nil) (defaults to: nil) —

    Optional Foldseek easy-search sensitivity passed as -s.

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

    Optional Foldseek --sort-by-structure-bits value. Omit to use the installed binary default.

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

    Optional Foldseek --threads value.

  • foldseek_tmscore_threshold (Float, nil) (defaults to: nil) —

    Optional Foldseek --tmscore-threshold value.

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

    Search every selected shard even when a routing segment is available.

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

    Published object-backed Foldseek index ref such as name:version

  • limit (Integer, nil) (defaults to: nil)
  • manifest_object_id (String, nil) (defaults to: nil) —

    Object id for a Foldseek index manifest

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

    Local Foldseek index manifest path

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

    Optional cap on ranked current-release candidates before limit.

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

    Optional hard cap on exact Foldseek shards searched after routing or explicit selection.

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

    Optional hard cap on planned local bytes materialized before exact Foldseek shard search.

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

    Optional hard cap on planned object-store bytes read for routing and search-index materialization.

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

    Optional hard cap on planned object-store reads for routing and search-index materialization.

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

    Candidate shard cap when a routing segment is available; defaults to planner policy.

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

    Optional local current-release object-store root. Defaults to the API server's release data root.

  • output_format (Rafflesia::Types::FoldSearchRequestOutputFormat, 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

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

    Include per-phase wall-clock timing (index resolve, index materialize, query resolve, shard search, normalized-output store) in the response.

  • query_id (String)
  • query_mode (Rafflesia::Types::FoldSearchRequestQueryMode, nil) (defaults to: nil) —

    Current-release query mode. Defaults to candidate_only.

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

    Stable filename used when staging query_structure_object_id for structure-token extraction.

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

    Optional raw PDB/mmCIF query object id for the current structure release. The server derives structure tokens before querying.

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

    Optional raw PDB/mmCIF query path for the current structure release. The server derives structure tokens before querying.

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Require a routing segment and routed shard selection instead of full-scan Foldseek search.

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

    Require the planned object-backed Foldseek path to materialize zero local database bytes.

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

    Maximum returned candidates to exact-rerank. Defaults to limit.

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

    Optional shard ids to search; empty searches every shard with artifacts

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

    Requested physical sort columns

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

    Directory used as the local Foldseek index cache

  • target_structure_objects (Hash{String => Rafflesia::CorpuReleaseStructureInputObject}, nil) (defaults to: nil) —

    Optional hit id to raw PDB/mmCIF object map used by exact_rerank.

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

    Optional hit id to local PDB/mmCIF path map used by exact_rerank.

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

    Optional absolute TM-align binary path used for exact_rerank.

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

    Require SHA-256 metadata while materializing index artifacts

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1256

def foldsSearch(
  query_id:,
  concurrency: nil,
  database: nil,
  dry_run: nil,
  exact_rerank: nil,
  exact_rerank_backend: nil,
  exact_rerank_rank_key: nil,
  foldseek_alignment_type: nil,
  foldseek_binary_path: nil,
  foldseek_exhaustive_search: nil,
  foldseek_gpu: nil,
  foldseek_kmer_size: nil,
  foldseek_lddt_threshold: nil,
  foldseek_prefilter_mode: nil,
  foldseek_result_order: nil,
  foldseek_sensitivity: nil,
  foldseek_sort_by_structure_bits: nil,
  foldseek_threads: nil,
  foldseek_tmscore_threshold: nil,
  force_full_scan: nil,
  index_ref: nil,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_candidates: nil,
  max_exact_shards: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  nprobe: nil,
  object_store_root: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  profile: nil,
  query_mode: nil,
  query_structure_file_name: nil,
  query_structure_object_id: nil,
  query_structure_path: nil,
  relation: nil,
  release: nil,
  require_routing: nil,
  require_zero_materialization: nil,
  rerank_limit: nil,
  shards: nil,
  sort_by: nil,
  target_dir: nil,
  target_structure_objects: nil,
  target_structure_paths: nil,
  tmalign_binary_path: nil,
  verify_index: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'database' => database,
    'dry_run' => dry_run,
    'exact_rerank' => exact_rerank,
    'exact_rerank_backend' => exact_rerank_backend,
    'exact_rerank_rank_key' => exact_rerank_rank_key,
    'foldseek_alignment_type' => foldseek_alignment_type,
    'foldseek_binary_path' => foldseek_binary_path,
    'foldseek_exhaustive_search' => foldseek_exhaustive_search,
    'foldseek_gpu' => foldseek_gpu,
    'foldseek_kmer_size' => foldseek_kmer_size,
    'foldseek_lddt_threshold' => foldseek_lddt_threshold,
    'foldseek_prefilter_mode' => foldseek_prefilter_mode,
    'foldseek_result_order' => foldseek_result_order,
    'foldseek_sensitivity' => foldseek_sensitivity,
    'foldseek_sort_by_structure_bits' => foldseek_sort_by_structure_bits,
    'foldseek_threads' => foldseek_threads,
    'foldseek_tmscore_threshold' => foldseek_tmscore_threshold,
    'force_full_scan' => force_full_scan,
    'index_ref' => index_ref,
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_candidates' => max_candidates,
    'max_exact_shards' => max_exact_shards,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'nprobe' => nprobe,
    'object_store_root' => object_store_root,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'profile' => profile,
    'query_id' => query_id,
    'query_mode' => query_mode,
    'query_structure_file_name' => query_structure_file_name,
    'query_structure_object_id' => query_structure_object_id,
    'query_structure_path' => query_structure_path,
    'relation' => relation,
    'release' => release,
    'require_routing' => require_routing,
    'require_zero_materialization' => require_zero_materialization,
    'rerank_limit' => rerank_limit,
    'shards' => shards,
    'sort_by' => sort_by,
    'target_dir' => target_dir,
    'target_structure_objects' => target_structure_objects,
    'target_structure_paths' => target_structure_paths,
    'tmalign_binary_path' => tmalign_binary_path,
    'verify_index' => verify_index
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSearchData.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

#foldsSearchBenchmark(query_ids:, concurrency: nil, exact_limit: nil, exact_verify: nil, index_ref: nil, limit: nil, manifest_object_id: nil, manifest_path: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_byte_reduction_fraction: nil, min_hit_overlap_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, nprobe: nil, profile: nil, recall_at: nil, require_exact_verification: nil, require_zero_materialization: nil, segment_manifest_object_id: nil, segment_manifest_path: nil, segment_ref: nil, store_artifact: nil, target_dir: nil, verify_index: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSearchBenchmarkData

POST /v1/proteins/folds/search/benchmark

Parameters:

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

    Maximum baseline Foldseek shards to search concurrently.

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

    Maximum object-native candidates to verify exactly; defaults to limit when exact_verify is true.

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

    Run candidate-only TM-align verification on object-native routed candidates before comparing to the Foldseek baseline.

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

    Published Foldseek index ref used by the materialized baseline search.

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

    Per-query hit limit; defaults to 100.

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

    Foldseek index manifest object id used by the materialized baseline search.

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

    Local Foldseek index manifest path used by the materialized baseline search.

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

    Optional per-query cap on selected object-native feature blocks.

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

    Optional per-query cap on object-native object bytes fetched.

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

    Optional per-query cap on object-native object reads.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for object-native byte reduction versus materialized baseline bytes.

  • min_hit_overlap_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for full returned-hit overlap against the materialized baseline.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_100.

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

    Object-native feature block probe count; defaults to 1.

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

    Include baseline Foldseek per-phase profile timings in nested search responses.

  • query_ids (Array<String>, nil) —

    Explicit query structure ids or paths to benchmark.

  • recall_at (Array<Integer>, nil) (defaults to: nil) —

    Recall cutoffs to compute against materialized baseline hits; defaults to 1,10,100.

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

    Require every object-native query result to report exact candidate verification.

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

    Require object-native search to materialize zero local database bytes.

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

    Object-native fold segment manifest object id.

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

    Local object-native fold segment manifest path.

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

    Published object-native fold segment ref for the object-native search path.

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

    Store the benchmark JSON artifact in object storage; defaults to true.

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

    Benchmark cache root; baseline runs materialize under a deterministic subdirectory.

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

    Verify materialized baseline Foldseek index artifacts by SHA-256.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1477

def foldsSearchBenchmark(
  query_ids:,
  concurrency: nil,
  exact_limit: nil,
  exact_verify: nil,
  index_ref: nil,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_hit_overlap_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  nprobe: nil,
  profile: nil,
  recall_at: nil,
  require_exact_verification: nil,
  require_zero_materialization: nil,
  segment_manifest_object_id: nil,
  segment_manifest_path: nil,
  segment_ref: nil,
  store_artifact: nil,
  target_dir: nil,
  verify_index: nil,
  request_options: {}
)
  body = {
    'concurrency' => concurrency,
    'exact_limit' => exact_limit,
    'exact_verify' => exact_verify,
    'index_ref' => index_ref,
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_hit_overlap_fraction' => min_hit_overlap_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'nprobe' => nprobe,
    'profile' => profile,
    'query_ids' => query_ids,
    'recall_at' => recall_at,
    'require_exact_verification' => require_exact_verification,
    'require_zero_materialization' => require_zero_materialization,
    'segment_manifest_object_id' => segment_manifest_object_id,
    'segment_manifest_path' => segment_manifest_path,
    'segment_ref' => segment_ref,
    'store_artifact' => store_artifact,
    'target_dir' => target_dir,
    'verify_index' => verify_index
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/search/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSearchBenchmarkData.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

#foldsSearchCatalog(catalog:, query_id:, store_root:, limit: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSearchData

POST /v1/proteins/folds/search-catalog

Parameters:

  • catalog (String)
  • limit (Integer, nil) (defaults to: nil)
  • query_id (String)
  • store_root (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1384

def foldsSearchCatalog(
  catalog:,
  query_id:,
  store_root:,
  limit: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'limit' => limit,
    'query_id' => query_id,
    'store_root' => store_root
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/search-catalog',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSearchData.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

#foldsSearchRouted(catalog:, query_id:, routing_db:, store_root:, limit: nil, nprobe: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSearchData

POST /v1/proteins/folds/search-routed

Parameters:

  • catalog (String)
  • limit (Integer, nil) (defaults to: nil)
  • nprobe (Integer, nil) (defaults to: nil) —

    Cap on candidate shards the router selects; omit or 0 for no cap

  • query_id (String)
  • routing_db (String)
  • store_root (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1418

def foldsSearchRouted(
  catalog:,
  query_id:,
  routing_db:,
  store_root:,
  limit: nil,
  nprobe: nil,
  request_options: {}
)
  body = {
    'catalog' => catalog,
    'limit' => limit,
    'nprobe' => nprobe,
    'query_id' => query_id,
    'routing_db' => routing_db,
    'store_root' => store_root
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/search-routed',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSearchData.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

#foldsSegmentsBenchmark(query_ids:, limit: nil, manifest_object_id: nil, manifest_path: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_byte_reduction_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, nprobe: nil, recall_at: nil, ref: nil, require_exact_verification: nil, require_zero_materialization: nil, store_artifact: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentBenchmarkData

POST /v1/proteins/folds/segments/benchmark

Parameters:

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

    Per-query hit limit; defaults to 100.

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

    Object id for an object-native fold feature segment manifest.

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

    Local path to an object-native fold feature segment manifest JSON file.

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

    Optional per-query cap on selected routed feature blocks.

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

    Optional per-query cap on routed object bytes read.

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

    Optional per-query cap on routed root plus feature block object reads.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Optional pass threshold for object byte reduction against exhaustive scan.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Optional pass threshold for recall_at_100.

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

    Routed object feature block count; defaults to 1.

  • query_ids (Array<String>, nil) —

    Explicit query structure ids or paths to benchmark.

  • recall_at (Array<Integer>, nil) (defaults to: nil) —

    Recall cutoffs to compute against exhaustive segment scan; defaults to 1,10,100.

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

    Published object-native fold segment ref such as name:version.

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

    Require every routed segment query to exactly verify candidate hits.

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

    Require the object-native path to materialize zero local database bytes.

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

    Whether to store the benchmark JSON artifact in the object store; defaults to true.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1568

def foldsSegmentsBenchmark(
  query_ids:,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  nprobe: nil,
  recall_at: nil,
  ref: nil,
  require_exact_verification: nil,
  require_zero_materialization: nil,
  store_artifact: nil,
  request_options: {}
)
  body = {
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'nprobe' => nprobe,
    'query_ids' => query_ids,
    'recall_at' => recall_at,
    'ref' => ref,
    'require_exact_verification' => require_exact_verification,
    'require_zero_materialization' => require_zero_materialization,
    'store_artifact' => store_artifact
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/benchmark',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentBenchmarkData.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

#foldsSegmentsBuild(name:, version:, block_size_bytes: nil, dataset_name: nil, dataset_version: nil, publish: nil, ref: nil, store_feature_object: nil, structure_ids: nil, structure_paths: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentBuildData

POST /v1/proteins/folds/segments/build

Parameters:

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

    Maximum bytes per immutable feature block; defaults to the search segment default.

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

    Optional dataset name carried into segment provenance.

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

    Optional dataset version carried into segment provenance.

  • name (String) —

    Logical object-native fold segment name.

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

    Publish this immutable fold segment ref into the control plane after build.

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

    Optional published ref override, for example afdb-features:2026-06-30.

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

    Whether to expose the intermediate JSONL feature object in the response.

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

    Stored structure record ids to inspect into fold feature rows.

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

    Local PDB/mmCIF paths to inspect into fold feature rows.

  • version (String) —

    Immutable segment version or source snapshot.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1632

def foldsSegmentsBuild(
  name:,
  version:,
  block_size_bytes: nil,
  dataset_name: nil,
  dataset_version: nil,
  publish: nil,
  ref: nil,
  store_feature_object: nil,
  structure_ids: nil,
  structure_paths: nil,
  request_options: {}
)
  body = {
    'block_size_bytes' => block_size_bytes,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'name' => name,
    'publish' => publish,
    'ref' => ref,
    'store_feature_object' => store_feature_object,
    'structure_ids' => structure_ids,
    'structure_paths' => structure_paths,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/build',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentBuildData.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

#foldsSegmentsCompact(name:, version:, block_size_bytes: nil, dataset_name: nil, dataset_version: nil, publish: nil, ref: nil, source_manifest_object_ids: nil, source_manifest_paths: nil, source_refs: nil, store_feature_object: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentCompactData

POST /v1/proteins/folds/segments/compact

Parameters:

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

    Maximum bytes per compacted immutable feature block.

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

    Optional dataset name carried into segment provenance.

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

    Optional dataset version carried into segment provenance.

  • name (String) —

    Logical compacted fold segment name.

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

    Publish the compacted segment ref after build.

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

    Published ref override when publish=true.

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

    Source fold segment manifest object ids to compact; repeatable.

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

    Source fold segment manifest paths to compact; repeatable.

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

    Published fold segment refs to compact; repeatable.

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

    Whether to expose the compacted intermediate JSONL feature object.

  • version (String) —

    Immutable compacted segment version.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1683

def foldsSegmentsCompact(
  name:,
  version:,
  block_size_bytes: nil,
  dataset_name: nil,
  dataset_version: nil,
  publish: nil,
  ref: nil,
  source_manifest_object_ids: nil,
  source_manifest_paths: nil,
  source_refs: nil,
  store_feature_object: nil,
  request_options: {}
)
  body = {
    'block_size_bytes' => block_size_bytes,
    'dataset_name' => dataset_name,
    'dataset_version' => dataset_version,
    'name' => name,
    'publish' => publish,
    'ref' => ref,
    'source_manifest_object_ids' => source_manifest_object_ids,
    'source_manifest_paths' => source_manifest_paths,
    'source_refs' => source_refs,
    'store_feature_object' => store_feature_object,
    'version' => version
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/compact',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentCompactData.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

#foldsSegmentsExplain(query_id:, limit: nil, manifest_object_id: nil, manifest_path: nil, max_blocks: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, nprobe: nil, ref: nil, require_zero_materialization: nil, workload_profile: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentExplainData

POST /v1/proteins/folds/segments/explain

Parameters:

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

    Maximum fold feature hits the corresponding search would return.

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

    Object id for an object-native fold feature segment manifest.

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

    Local path to an object-native fold feature segment manifest JSON file.

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

    Optional hard budget for selected feature blocks.

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

    Optional hard budget for local database materialization bytes.

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

    Optional hard budget for object bytes read.

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

    Optional hard budget for root plus selected feature block object reads.

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

    Number of adjacent feature blocks to probe from the sparse routing root.

  • query_id (String) —

    Stored structure id or local PDB/mmCIF path used as the query.

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

    Published object-native fold segment ref such as name:version, or a logical name with an active generation.

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

    Require the object-native path to materialize zero local database bytes.

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

    Optional workload profile name such as foldseek-local or foldseek-remote-object-store.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1737

def foldsSegmentsExplain(
  query_id:,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  nprobe: nil,
  ref: nil,
  require_zero_materialization: nil,
  workload_profile: nil,
  request_options: {}
)
  body = {
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks' => max_blocks,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'nprobe' => nprobe,
    'query_id' => query_id,
    'ref' => ref,
    'require_zero_materialization' => require_zero_materialization,
    'workload_profile' => workload_profile
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/explain',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentExplainData.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

#foldsSegmentsGc(candidate_manifest_object_ids: nil, candidate_manifest_paths: nil, candidate_refs: nil, dry_run: nil, keep_manifest_object_ids: nil, keep_manifest_paths: nil, keep_refs: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentGcData

POST /v1/proteins/folds/segments/gc

Parameters:

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

    Candidate fold segment manifest object ids; repeatable.

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

    Candidate fold segment manifest paths; repeatable.

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

    Published fold segment refs considered for collection; repeatable.

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

    Whether to only report unused objects; defaults to true.

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

    Live fold segment manifest object ids; repeatable.

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

    Live fold segment manifest paths; repeatable.

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

    Published fold segment refs that remain live; repeatable.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1788

def foldsSegmentsGc(
  candidate_manifest_object_ids: nil,
  candidate_manifest_paths: nil,
  candidate_refs: nil,
  dry_run: nil,
  keep_manifest_object_ids: nil,
  keep_manifest_paths: nil,
  keep_refs: nil,
  request_options: {}
)
  body = {
    'candidate_manifest_object_ids' => candidate_manifest_object_ids,
    'candidate_manifest_paths' => candidate_manifest_paths,
    'candidate_refs' => candidate_refs,
    'dry_run' => dry_run,
    'keep_manifest_object_ids' => keep_manifest_object_ids,
    'keep_manifest_paths' => keep_manifest_paths,
    'keep_refs' => keep_refs
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/gc',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentGcData.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

#foldsSegmentsGenerationsActivate(ref:, reason: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentGenerationData

POST /v1/proteins/folds/segments/generations/activate

Parameters:

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

    Optional operator-visible reason for the state transition.

  • ref (String) —

    Published immutable fold segment ref to mark active.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1824

def foldsSegmentsGenerationsActivate(
  ref:,
  reason: nil,
  request_options: {}
)
  body = {
    'reason' => reason,
    'ref' => ref
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/generations/activate',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentGenerationData.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

#foldsSegmentsGenerationsList(include_retired: nil, name: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentGenerationListData

POST /v1/proteins/folds/segments/generations/list

Parameters:

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

    Include retired generations. Defaults to true for complete lifecycle evidence.

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

    Optional logical fold segment name filter.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1850

def foldsSegmentsGenerationsList(
  include_retired: nil,
  name: nil,
  request_options: {}
)
  body = {
    'include_retired' => include_retired,
    'name' => name
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/generations/list',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentGenerationListData.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

#foldsSegmentsGenerationsRollback(name: nil, reason: nil, to_ref: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentGenerationData

POST /v1/proteins/folds/segments/generations/rollback

Parameters:

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

    Logical fold segment name to roll back when to_ref is not provided.

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

    Optional operator-visible reason for the rollback.

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

    Published immutable ref to mark active. When empty, the most recently retired generation for name is selected.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1877

def foldsSegmentsGenerationsRollback(
  name: nil,
  reason: nil,
  to_ref: nil,
  request_options: {}
)
  body = {
    'name' => name,
    'reason' => reason,
    'to_ref' => to_ref
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/generations/rollback',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentGenerationData.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

#foldsSegmentsPublish(activate: nil, benchmark_object_id: nil, manifest_object_id: nil, manifest_path: nil, max_blocks_per_query: nil, max_object_bytes_per_query: nil, max_object_reads_per_query: nil, min_byte_reduction_fraction: nil, min_hit_overlap_fraction: nil, min_recall_at_1: nil, min_recall_at_10: nil, min_recall_at_100: nil, policy: nil, ref: nil, require_benchmark: nil, require_exact_verification: nil, require_search_benchmark: nil, require_zero_materialization: nil, search_benchmark_object_id: nil, workload_profile: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentPublishData

POST /v1/proteins/folds/segments/publish

Parameters:

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

    Mark this published generation active for its logical name after publish.

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

    Object id produced by proteins.folds.segments.benchmark.

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

    Object id for an object-native fold feature segment manifest.

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

    Local path to an object-native fold feature segment manifest JSON file.

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

    Maximum routed feature blocks selected per benchmark query.

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

    Maximum planned routed object bytes per benchmark query.

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

    Maximum planned routed object reads per benchmark query.

  • min_byte_reduction_fraction (Float, nil) (defaults to: nil) —

    Publish gate threshold for planned object byte reduction.

  • min_hit_overlap_fraction (Float, nil) (defaults to: nil) —

    Publish gate threshold for Foldseek-vs-object-native hit overlap.

  • min_recall_at_1 (Float, nil) (defaults to: nil) —

    Publish gate threshold for recall_at_1.

  • min_recall_at_10 (Float, nil) (defaults to: nil) —

    Publish gate threshold for recall_at_10.

  • min_recall_at_100 (Float, nil) (defaults to: nil) —

    Publish gate threshold for recall_at_100.

  • policy (Rafflesia::ServerlessPublishPolicy, nil) (defaults to: nil) —

    Optional normalized publish policy; top-level gate fields remain supported.

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

    Published fold segment ref override; defaults to manifest name:version.

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

    Require a passing fold segment benchmark artifact before publishing.

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

    Require search benchmark evidence that object-native candidates were exactly verified.

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

    Require a passing materialized-Foldseek-vs-object-native benchmark artifact before publishing.

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

    Require benchmark evidence that routed search materialized zero local database bytes.

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

    Object id produced by proteins.folds.search.benchmark.

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

    Optional workload profile name used to fill unset policy gates.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 1923

def foldsSegmentsPublish(
  activate: nil,
  benchmark_object_id: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks_per_query: nil,
  max_object_bytes_per_query: nil,
  max_object_reads_per_query: nil,
  min_byte_reduction_fraction: nil,
  min_hit_overlap_fraction: nil,
  min_recall_at_1: nil,
  min_recall_at_10: nil,
  min_recall_at_100: nil,
  policy: nil,
  ref: nil,
  require_benchmark: nil,
  require_exact_verification: nil,
  require_search_benchmark: nil,
  require_zero_materialization: nil,
  search_benchmark_object_id: nil,
  workload_profile: nil,
  request_options: {}
)
  body = {
    'activate' => activate,
    'benchmark_object_id' => benchmark_object_id,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks_per_query' => max_blocks_per_query,
    'max_object_bytes_per_query' => max_object_bytes_per_query,
    'max_object_reads_per_query' => max_object_reads_per_query,
    'min_byte_reduction_fraction' => min_byte_reduction_fraction,
    'min_hit_overlap_fraction' => min_hit_overlap_fraction,
    'min_recall_at_1' => min_recall_at_1,
    'min_recall_at_10' => min_recall_at_10,
    'min_recall_at_100' => min_recall_at_100,
    'policy' => policy,
    'ref' => ref,
    'require_benchmark' => require_benchmark,
    'require_exact_verification' => require_exact_verification,
    'require_search_benchmark' => require_search_benchmark,
    'require_zero_materialization' => require_zero_materialization,
    'search_benchmark_object_id' => search_benchmark_object_id,
    'workload_profile' => workload_profile
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/publish',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentPublishData.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

#foldsSegmentsSearch(query_id:, database: nil, dry_run: nil, exact_limit: nil, exact_verify: nil, limit: nil, manifest_object_id: nil, manifest_path: nil, max_blocks: nil, max_materialized_bytes: nil, max_object_bytes: nil, max_object_reads: nil, nprobe: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, ref: nil, relation: nil, release: nil, require_zero_materialization: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeFoldSegmentSearchData

POST /v1/proteins/folds/segments/search

Parameters:

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

    Database name published with the relation

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

    Return the deterministic read plan without fetching feature blocks.

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

    Maximum routed candidates to verify exactly; defaults to limit when exact_verify is true.

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

    Run candidate-only TM-align verification over the routed feature hits before returning them.

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

    Maximum fold feature hits to return; defaults to 50.

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

    Object id for an object-native fold feature segment manifest.

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

    Local path to an object-native fold feature segment manifest JSON file.

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

    Optional hard budget for selected feature blocks.

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

    Optional hard budget for local database materialization bytes.

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

    Optional hard budget for object bytes read.

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

    Optional hard budget for root plus selected feature block object reads.

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

    Number of adjacent feature blocks to probe from the sparse routing root; defaults to 1.

  • output_format (Rafflesia::Types::FoldSegmentSearchRequestOutputFormat, 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

  • query_id (String) —

    Stored structure id or local PDB/mmCIF path used as the query.

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

    Published object-native fold segment ref such as name:version.

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

    Requested logical relation name

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

    Immutable database release published with the relation

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

    Require the object-native path to materialize zero local database bytes.

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

    Requested physical sort columns

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2005

def foldsSegmentsSearch(
  query_id:,
  database: nil,
  dry_run: nil,
  exact_limit: nil,
  exact_verify: nil,
  limit: nil,
  manifest_object_id: nil,
  manifest_path: nil,
  max_blocks: nil,
  max_materialized_bytes: nil,
  max_object_bytes: nil,
  max_object_reads: nil,
  nprobe: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  ref: nil,
  relation: nil,
  release: nil,
  require_zero_materialization: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'dry_run' => dry_run,
    'exact_limit' => exact_limit,
    'exact_verify' => exact_verify,
    'limit' => limit,
    'manifest_object_id' => manifest_object_id,
    'manifest_path' => manifest_path,
    'max_blocks' => max_blocks,
    'max_materialized_bytes' => max_materialized_bytes,
    'max_object_bytes' => max_object_bytes,
    'max_object_reads' => max_object_reads,
    'nprobe' => nprobe,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query_id' => query_id,
    'ref' => ref,
    'relation' => relation,
    'release' => release,
    'require_zero_materialization' => require_zero_materialization,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/folds/segments/search',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeFoldSegmentSearchData.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

#helicesHydrophobicMoment(structure_id:, angle_degrees: nil, chain: nil, min_length: nil, request_options: {}) ⇒ Rafflesia::EnvelopeHelixHydrophobicMomentData

POST /v1/proteins/helices/hydrophobic-moment

Parameters:

  • angle_degrees (Float, nil) (defaults to: nil) —

    per-residue angle in degrees (default 100, the ideal alpha-helix)

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

    restrict to a single chain id

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

    skip helices shorter than this many residues (default 7)

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2073

def helicesHydrophobicMoment(
  structure_id:,
  angle_degrees: nil,
  chain: nil,
  min_length: nil,
  request_options: {}
)
  body = {
    'angle_degrees' => angle_degrees,
    'chain' => chain,
    'min_length' => min_length,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/helices/hydrophobic-moment',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeHelixHydrophobicMomentData.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

#interfacesBurial(structure_id:, min_delta_sasa: nil, partners: nil, request_options: {}) ⇒ Rafflesia::EnvelopeInterfaceBurialData

POST /v1/proteins/interfaces/burial

Parameters:

  • min_delta_sasa (Float, nil) (defaults to: nil)
  • partners (String, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2104

def interfacesBurial(
  structure_id:,
  min_delta_sasa: nil,
  partners: nil,
  request_options: {}
)
  body = {
    'min_delta_sasa' => min_delta_sasa,
    'partners' => partners,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/interfaces/burial',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeInterfaceBurialData.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

#interfacesDetect(structure_id:, database: nil, include_pairs: nil, include_residue_contacts: nil, include_same_chain: nil, include_waters: nil, max_interfaces: nil, max_pairs: nil, method_: nil, min_sequence_separation: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius: nil, relation: nil, release: nil, residues: nil, residues_require_both: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeInterfaceDetectData

POST /v1/proteins/interfaces/detect

Parameters:

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

    Database name published with the relation

  • include_pairs (Boolean, nil) (defaults to: nil)
  • include_residue_contacts (Boolean, nil) (defaults to: nil) —

    Include a per-residue contact rollup (residue_contacts_a/b) built from the full contact set before any max_pairs cap.

  • include_same_chain (Boolean, nil) (defaults to: nil)
  • include_waters (Boolean, nil) (defaults to: nil) —

    Include water (HOH/WAT/DOD) residues; by default solvent is excluded so an interface reflects polymer-polymer contacts.

  • max_interfaces (Integer, nil) (defaults to: nil)
  • max_pairs (Integer, nil) (defaults to: nil)
  • method (String, nil)
  • min_sequence_separation (Integer, nil) (defaults to: nil) —

    For same-chain contacts, drop pairs whose residues are fewer than N positions apart (|pos_a - pos_b| < N). Removes trivial sequence-adjacent contacts. Cross-chain contacts are unaffected.

  • output_format (Rafflesia::Types::InterfaceDetectRequestOutputFormat, 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 (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

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

    Restrict contacts to those where at least one partner is a named residue. Each entry is CHAIN/POSITION (e.g. A/57) or a bare POSITION (e.g. 57, any chain); comma-separated lists are also accepted. Scopes every derived field (residue lists, counts, rollups, distances), not just contact_pairs.

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

    With residues set, keep a contact only when BOTH partners are named (instead of the default: either partner). Use to measure geometry among a specific residue set (e.g. a catalytic triad's internal H-bonds) rather than everything those residues touch.

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

    Requested physical sort columns

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2150

def interfacesDetect(
  structure_id:,
  database: nil,
  include_pairs: nil,
  include_residue_contacts: nil,
  include_same_chain: nil,
  include_waters: nil,
  max_interfaces: nil,
  max_pairs: nil,
  method_: nil,
  min_sequence_separation: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius: nil,
  relation: nil,
  release: nil,
  residues: nil,
  residues_require_both: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'include_pairs' => include_pairs,
    'include_residue_contacts' => include_residue_contacts,
    'include_same_chain' => include_same_chain,
    'include_waters' => include_waters,
    'max_interfaces' => max_interfaces,
    'max_pairs' => max_pairs,
    'method' => method_,
    'min_sequence_separation' => min_sequence_separation,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius' => radius,
    'relation' => relation,
    'release' => release,
    'residues' => residues,
    'residues_require_both' => residues_require_both,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/interfaces/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeInterfaceDetectData.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

#interfacesFeatures(structure_id:, chain_a: nil, chain_b: nil, compute_buried_surface_area: nil, compute_pae: nil, compute_plddt: nil, compute_region_ids: nil, include_pairs: nil, include_residue_contacts: nil, include_same_chain: nil, interface_id: nil, max_interfaces: nil, max_pairs: nil, method_: nil, radius: nil, request_options: {}) ⇒ Rafflesia::EnvelopeInterfaceFeaturesData

POST /v1/proteins/interfaces/features

Parameters:

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

    If set with chain_b, restrict to this chain pair (order-insensitive).

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

    If set with chain_a, restrict to this chain pair (order-insensitive).

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

    Compute buried surface area (deterministic Shrake–Rupley SASA: ΔSASA over the two participant chains, in Angstrom^2).

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

    Compute mean PAE over contact pairs (requires a PAE matrix).

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

    Compute mean pLDDT over participant residues.

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

    Attach interface region ids when available.

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

    Include contact residue pairs per interface.

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

    Include a per-residue contact rollup (residue_contacts_a/b) built from the full contact set before any max_pairs cap. When compute_plddt is set, each rollup entry also carries residue_plddt.

  • include_same_chain (Boolean, nil) (defaults to: nil)
  • interface_id (String, nil) (defaults to: nil) —

    If set, compute features only for this interface.

  • max_interfaces (Integer, nil) (defaults to: nil)
  • max_pairs (Integer, nil) (defaults to: nil)
  • method (String, nil) —

    Interface method: atom_min_distance or representative_residue_distance.

  • radius (Float, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2225

def interfacesFeatures(
  structure_id:,
  chain_a: nil,
  chain_b: nil,
  compute_buried_surface_area: nil,
  compute_pae: nil,
  compute_plddt: nil,
  compute_region_ids: nil,
  include_pairs: nil,
  include_residue_contacts: nil,
  include_same_chain: nil,
  interface_id: nil,
  max_interfaces: nil,
  max_pairs: nil,
  method_: nil,
  radius: nil,
  request_options: {}
)
  body = {
    'chain_a' => chain_a,
    'chain_b' => chain_b,
    'compute_buried_surface_area' => compute_buried_surface_area,
    'compute_pae' => compute_pae,
    'compute_plddt' => compute_plddt,
    'compute_region_ids' => compute_region_ids,
    'include_pairs' => include_pairs,
    'include_residue_contacts' => include_residue_contacts,
    'include_same_chain' => include_same_chain,
    'interface_id' => interface_id,
    'max_interfaces' => max_interfaces,
    'max_pairs' => max_pairs,
    'method' => method_,
    'radius' => radius,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/interfaces/features',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeInterfaceFeaturesData.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

#ligandsNeighbors(structure_id:, database: nil, include_waters: nil, ligands: nil, max_neighbors: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeLigandNeighborsData

POST /v1/proteins/ligands/neighbors

Parameters:

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

    Database name published with the relation

  • include_waters (Boolean, nil) (defaults to: nil)
  • ligands (Array<String>, nil) (defaults to: nil) —

    Restrict measurement to the named ligand(s); each selector matches a residue name (e.g. MOV), a full ligand_id, or CHAIN:POSITION

  • max_neighbors (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::LigandNeighborsRequestOutputFormat, 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 (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

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

    Requested physical sort columns

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2288

def ligandsNeighbors(
  structure_id:,
  database: nil,
  include_waters: nil,
  ligands: nil,
  max_neighbors: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'include_waters' => include_waters,
    'ligands' => ligands,
    'max_neighbors' => max_neighbors,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius' => radius,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/ligands/neighbors',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeLigandNeighborsData.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

#metalsDetect(structure_id:, max_distance: nil, request_options: {}) ⇒ Rafflesia::EnvelopeMetalDetectData

POST /v1/proteins/metals/detect

Parameters:

  • max_distance (Float, nil) (defaults to: nil) —

    metal-donor first-shell distance cutoff in Ã… (default 2.8)

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2336

def metalsDetect(
  structure_id:,
  max_distance: nil,
  request_options: {}
)
  body = {
    'max_distance' => max_distance,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/metals/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeMetalDetectData.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

#peptideBondsOmega(structure_id:, cis_cutoff: nil, include_all_bonds: nil, request_options: {}) ⇒ Rafflesia::EnvelopePeptideBondOmegaData

POST /v1/proteins/peptide-bonds/omega

Parameters:

  • cis_cutoff (Float, nil) (defaults to: nil)
  • include_all_bonds (Boolean, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2363

def peptideBondsOmega(
  structure_id:,
  cis_cutoff: nil,
  include_all_bonds: nil,
  request_options: {}
)
  body = {
    'cis_cutoff' => cis_cutoff,
    'include_all_bonds' => include_all_bonds,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/peptide-bonds/omega',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopePeptideBondOmegaData.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

#pocketsDetect(structure_id:, backend: nil, cache_mode: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopePocketDetectData

POST /v1/proteins/pockets/detect

Parameters:

  • backend (Rafflesia::Types::PocketDetectRequestBackend, nil) (defaults to: nil)
  • cache_mode (Rafflesia::Types::PocketDetectRequestCacheMode, nil) (defaults to: nil) —

    Pocket cache mode. use reuses matching cached pockets, refresh recomputes and stores, off recomputes without storing.

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

    Database name published with the relation

  • output_format (Rafflesia::Types::PocketDetectRequestOutputFormat, 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2400

def pocketsDetect(
  structure_id:,
  backend: nil,
  cache_mode: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'backend' => backend,
    'cache_mode' => cache_mode,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/pockets/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopePocketDetectData.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

#pocketsFeatures(pocket_id:, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopePocketFeaturesData

POST /v1/proteins/pockets/features

Parameters:

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

    Database name published with the relation

  • output_format (Rafflesia::Types::PocketFeaturesRequestOutputFormat, 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

  • pocket_id (String)
  • 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2451

def pocketsFeatures(
  pocket_id:,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'pocket_id' => pocket_id,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/pockets/features',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopePocketFeaturesData.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

#pocketsLigandDistances(structure_id:, database: nil, distance_threshold_angstrom: nil, include_waters: nil, ligand_grouping: nil, ligands: nil, max_pairs: nil, output_format: nil, output_relation: nil, partition_by: nil, pockets: nil, prediction_format: nil, prediction_method: nil, prediction_path: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, top_extra: nil, top_n_reference: nil, request_options: {}) ⇒ Rafflesia::EnvelopePocketLigandDistancesData

POST /v1/proteins/pockets/ligand-distances

Parameters:

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

    Database name published with the relation

  • distance_threshold_angstrom (Float, nil) (defaults to: nil)
  • include_waters (Boolean, nil) (defaults to: nil)
  • ligand_grouping (Rafflesia::Types::PocketLigandDistancesRequestLigandGrouping, nil) (defaults to: nil) —

    Optional grouping for denominator-sensitive measurements. residue_name groups selected ligand instances by residue name within the structure.

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

    Restrict measurement to the named ligand(s); each selector matches a residue name, ligand_id, or CHAIN:POSITION.

  • max_pairs (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::PocketLigandDistancesRequestOutputFormat, 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

  • pockets (Array<Rafflesia::Pocket>, nil) (defaults to: nil) —

    Optional inline pocket candidates; used when prediction_path is empty.

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

    Prediction file format. p2rank_csv reads P2Rank *_predictions.csv files.

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

    Method label attached to parsed pocket candidates, for example p2rank.

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

    Local path to pocket candidate predictions, for example a P2Rank *_predictions.csv file.

  • 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

  • structure_id (String)
  • top_extra (Integer, nil) (defaults to: nil)
  • top_n_reference (Rafflesia::Types::PocketLigandDistancesRequestTopNReference, nil) (defaults to: nil) —

    Determines n for Top-n measurements. ligand_instance uses selected ligand instance count; ligand_group uses ligand_grouping group count.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2509

def pocketsLigandDistances(
  structure_id:,
  database: nil,
  distance_threshold_angstrom: nil,
  include_waters: nil,
  ligand_grouping: nil,
  ligands: nil,
  max_pairs: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  pockets: nil,
  prediction_format: nil,
  prediction_method: nil,
  prediction_path: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  top_extra: nil,
  top_n_reference: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'distance_threshold_angstrom' => distance_threshold_angstrom,
    'include_waters' => include_waters,
    'ligand_grouping' => ligand_grouping,
    'ligands' => ligands,
    'max_pairs' => max_pairs,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'pockets' => pockets,
    'prediction_format' => prediction_format,
    'prediction_method' => prediction_method,
    'prediction_path' => prediction_path,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'top_extra' => top_extra,
    'top_n_reference' => top_n_reference
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/pockets/ligand-distances',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopePocketLigandDistancesData.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

#regionsSplit(structure_id:, chain: nil, database: nil, include_low_confidence: nil, method_: nil, min_length: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, threshold: nil, request_options: {}) ⇒ Rafflesia::EnvelopeRegionSplitData

POST /v1/proteins/regions/split

Parameters:

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

    Database name published with the relation

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

    Also emit the complementary below-threshold segments (type low_confidence_segment) so the split is a full partition of the chain; ignored for the pae method.

  • method (Rafflesia::Types::RegionSplitRequestMethod, nil)
  • min_length (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::RegionSplitRequestOutputFormat, 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

  • structure_id (String)
  • threshold (Float, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2583

def regionsSplit(
  structure_id:,
  chain: nil,
  database: nil,
  include_low_confidence: nil,
  method_: nil,
  min_length: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  threshold: nil,
  request_options: {}
)
  body = {
    'chain' => chain,
    'database' => database,
    'include_low_confidence' => include_low_confidence,
    'method' => method_,
    'min_length' => min_length,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'threshold' => threshold
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/regions/split',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeRegionSplitData.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

#residuesFeatures(structure_id:, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeResidueFeaturesData

POST /v1/proteins/residues/features

Parameters:

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

    Database name published with the relation

  • output_format (Rafflesia::Types::ResidueFeaturesRequestOutputFormat, 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 (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

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

    Requested physical sort columns

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2641

def residuesFeatures(
  structure_id:,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius' => radius,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/residues/features',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeResidueFeaturesData.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

#residuesRotamers(structure_id:, request_options: {}) ⇒ Rafflesia::EnvelopeResidueRotamersData

POST /v1/proteins/residues/rotamers

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2682

def residuesRotamers(
  structure_id:,
  request_options: {}
)
  body = {
    'structure_id' => structure_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/proteins/residues/rotamers',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeResidueRotamersData.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

#secondaryStructureAssign(structure_id:, chain: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeSecondaryStructureData

POST /v1/proteins/secondary-structure/assign

Parameters:

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

    restrict assignment to a single chain id

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

    Database name published with the relation

  • output_format (Rafflesia::Types::SecondaryStructureRequestOutputFormat, 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2714

def secondaryStructureAssign(
  structure_id:,
  chain: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'chain' => chain,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/secondary-structure/assign',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeSecondaryStructureData.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

#structureAlign(query_id:, target_id:, allow_network: nil, multimer_mode: nil, terminus_mode: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureAlignData

POST /v1/proteins/structure/align

Parameters:

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

    Fetch either structure from its source (PDB/AlphaFold) when it is not already cached, mirroring proteins structures fetch --allow-network.

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

    Optional US-align -mm multimer alignment mode; omitted leaves the US-align default.

  • query_id (String) —

    Query structure id, chain-scoped id (:CHAIN:), or local path (normalized as Structure_1).

  • target_id (String) —

    Target structure id, chain-scoped id (:CHAIN:), or local path (normalized as Structure_2).

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

    Optional US-align -ter chain/terminus handling mode; omitted leaves the US-align default.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2759

def structureAlign(
  query_id:,
  target_id:,
  allow_network: nil,
  multimer_mode: nil,
  terminus_mode: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'multimer_mode' => multimer_mode,
    'query_id' => query_id,
    'target_id' => target_id,
    'terminus_mode' => terminus_mode
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structure/align',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureAlignData.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

#structureAlignMatrix(structure_ids:, allow_network: nil, database: nil, multimer_mode: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, terminus_mode: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureAlignMatrixData

POST /v1/proteins/structure/align-matrix

Parameters:

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

    Fetch any structure from its source (PDB/AlphaFold) when it is not already cached.

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

    Database name published with the relation

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

    Optional US-align -mm multimer alignment mode; omitted leaves the US-align default.

  • output_format (Rafflesia::Types::StructureAlignMatrixRequestOutputFormat, 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

  • structure_ids (Array<String>, nil) —

    Structure ids to align all-vs-all (unordered pairs); 2-32 entries.

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

    Optional US-align -ter chain/terminus handling mode; omitted leaves the US-align default.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2801

def structureAlignMatrix(
  structure_ids:,
  allow_network: nil,
  database: nil,
  multimer_mode: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  terminus_mode: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'database' => database,
    'multimer_mode' => multimer_mode,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_ids' => structure_ids,
    'terminus_mode' => terminus_mode
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structure/align-matrix',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureAlignMatrixData.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

#structuresAxisProfile(structure_id:, axis_direction: nil, axis_point: nil, bins: nil, chain_ids: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, radius_percentiles: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureAxisProfileData

POST /v1/proteins/structures/axis-profile

Parameters:

  • axis_direction (Array<Float>, nil) (defaults to: nil) —

    Axis direction vector [x,y,z]; defaults to [0,0,1]. Normalized internally.

  • axis_point (Array<Float>, nil) (defaults to: nil) —

    Point on the axis [x,y,z] in angstrom; defaults to the (filtered) atom centroid.

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

    Number of axial bins for the radial profile; defaults to 24.

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

    Restrict measurement to these chain ids; empty means all chains.

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

    Database name published with the relation

  • output_format (Rafflesia::Types::StructureAxisProfileRequestOutputFormat, 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_percentiles (Array<Float>, nil) (defaults to: nil) —

    Per-bin radius percentiles to report, in [0,100]; defaults to 5,10.

  • 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2859

def structuresAxisProfile(
  structure_id:,
  axis_direction: nil,
  axis_point: nil,
  bins: nil,
  chain_ids: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  radius_percentiles: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'axis_direction' => axis_direction,
    'axis_point' => axis_point,
    'bins' => bins,
    'chain_ids' => chain_ids,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'radius_percentiles' => radius_percentiles,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/axis-profile',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureAxisProfileData.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

#structuresChains(structure_id:, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureChainsData

POST /v1/proteins/structures/chains

Parameters:

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

    Database name published with the relation

  • output_format (Rafflesia::Types::StructureChainsRequestOutputFormat, 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2916

def structuresChains(
  structure_id:,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/chains',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureChainsData.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

#structuresExtractChain(chain_id:, structure_id:, request_options: {}) ⇒ Rafflesia::EnvelopeStructureChainExtractData

POST /v1/proteins/structures/extract-chain

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2956

def structuresExtractChain(
  chain_id:,
  structure_id:,
  request_options: {}
)
  body = {
    'chain_id' => chain_id,
    'structure_id' => structure_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/extract-chain',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureChainExtractData.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

#structuresFetch(target_id:, allow_network: nil, source: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureData

POST /v1/proteins/structures/fetch

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil)
  • source (Rafflesia::Types::StructureFetchRequestSource, nil) (defaults to: nil)
  • target_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 2983

def structuresFetch(
  target_id:,
  allow_network: nil,
  source: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'source' => source,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/fetch',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureData.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

#structuresImport(path:, source: nil, target_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureData

POST /v1/proteins/structures/import

Parameters:

  • path (String)
  • source (String, nil) (defaults to: nil)
  • target_id (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3012

def structuresImport(
  path:,
  source: nil,
  target_id: nil,
  request_options: {}
)
  body = {
    'path' => path,
    'source' => source,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/import',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureData.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

#structuresInspect(structure_id:, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureInspectData

POST /v1/proteins/structures/inspect

Parameters:

  • structure_id (String)
  • timeout_ms (Integer, nil) (defaults to: nil) —

    Maximum time to spend reading and parsing the structure before returning a partial inspect response. Zero uses the server default.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3040

def structuresInspect(
  structure_id:,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'structure_id' => structure_id,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureInspectData.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

#structuresMetadata(structure_id:, request_options: {}) ⇒ Rafflesia::EnvelopeStructureMetadataData

POST /v1/proteins/structures/metadata

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3065

def structuresMetadata(
  structure_id:,
  request_options: {}
)
  body = {
    'structure_id' => structure_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/metadata',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureMetadataData.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

#structuresPredict(entities:, affinity_binder_id: nil, constraints: nil, idempotency_key: nil, max_retries: nil, max_template_date: nil, metadata: nil, model: nil, model_type: nil, msa_inputs: nil, msa_mode: nil, msa_server_url: nil, num_diffusion_samples: nil, num_loops: nil, num_models: nil, num_recycles: nil, num_sampling_steps: nil, num_seeds: nil, pair_mode: nil, predict_affinity: nil, random_seed: nil, relax_top_n: nil, templates: nil, timeout_ms: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructurePredictionSubmitData

POST /v1/proteins/structures/predict

Parameters:

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

    Ligand entity id used by an affinity-capable backend.

  • constraints (Object, nil) (defaults to: nil) —

    Backend-native constraint object; unsupported mappings fail explicitly.

  • entities (Array<Rafflesia::StructurePredictionEntity>, nil)
  • idempotency_key (String, nil) (defaults to: nil)
  • max_retries (Integer, nil) (defaults to: nil)
  • max_template_date (String, nil) (defaults to: nil) —

    Template cutoff in YYYY-MM-DD format.

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

    Inference backend: esmfold2-fast, esmfold2, protenix-v2, boltz-2, alphafold2, rf3, or chai-1.

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

    AlphaFold2 model type; auto chooses monomer or multimer.

  • msa_inputs (Array<Rafflesia::StructurePredictionMsaInput>, nil) (defaults to: nil) —

    Per-protein Rafflesia alignment object references.

  • msa_mode (Rafflesia::Types::StructurePredictionRequestMsaMode, nil) (defaults to: nil)
  • msa_server_url (String, nil) (defaults to: nil) —

    HTTPS ColabFold-compatible MSA service URL for explicit mmseqs2 modes.

  • num_diffusion_samples (Integer, nil) (defaults to: nil)
  • num_loops (Integer, nil) (defaults to: nil)
  • num_models (Integer, nil) (defaults to: nil)
  • num_recycles (Integer, nil) (defaults to: nil)
  • num_sampling_steps (Integer, nil) (defaults to: nil)
  • num_seeds (Integer, nil) (defaults to: nil)
  • pair_mode (Rafflesia::Types::StructurePredictionRequestPairMode, nil) (defaults to: nil)
  • predict_affinity (Boolean, nil) (defaults to: nil)
  • random_seed (Integer, nil) (defaults to: nil)
  • relax_top_n (Integer, nil) (defaults to: nil)
  • templates (Boolean, nil) (defaults to: nil)
  • timeout_ms (Integer, nil) (defaults to: nil) —

    Durable worker deadline in milliseconds.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3111

def structuresPredict(
  entities:,
  affinity_binder_id: nil,
  constraints: nil,
  idempotency_key: nil,
  max_retries: nil,
  max_template_date: nil,
  metadata: nil,
  model: nil,
  model_type: nil,
  msa_inputs: nil,
  msa_mode: nil,
  msa_server_url: nil,
  num_diffusion_samples: nil,
  num_loops: nil,
  num_models: nil,
  num_recycles: nil,
  num_sampling_steps: nil,
  num_seeds: nil,
  pair_mode: nil,
  predict_affinity: nil,
  random_seed: nil,
  relax_top_n: nil,
  templates: nil,
  timeout_ms: nil,
  request_options: {}
)
  body = {
    'affinity_binder_id' => affinity_binder_id,
    'constraints' => constraints,
    'entities' => entities,
    'idempotency_key' => idempotency_key,
    'max_retries' => max_retries,
    'max_template_date' => max_template_date,
    'metadata' => metadata,
    'model' => model,
    'model_type' => model_type,
    'msa_inputs' => msa_inputs,
    'msa_mode' => msa_mode,
    'msa_server_url' => msa_server_url,
    'num_diffusion_samples' => num_diffusion_samples,
    'num_loops' => num_loops,
    'num_models' => num_models,
    'num_recycles' => num_recycles,
    'num_sampling_steps' => num_sampling_steps,
    'num_seeds' => num_seeds,
    'pair_mode' => pair_mode,
    'predict_affinity' => predict_affinity,
    'random_seed' => random_seed,
    'relax_top_n' => relax_top_n,
    'templates' => templates,
    'timeout_ms' => timeout_ms
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/predict',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructurePredictionSubmitData.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

#structuresPredictionCapabilities(request_options: {}) ⇒ Rafflesia::EnvelopeStructurePredictionCapabilitiesData

GET /v1/proteins/structures/prediction-capabilities

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3179

def structuresPredictionCapabilities(request_options: {})
  response = @client.request(
    method: :get,
    path: '/v1/proteins/structures/prediction-capabilities',
    auth: true,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructurePredictionCapabilitiesData.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

#structuresPrepare(structure_id:, encoding: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructurePrepareData

POST /v1/proteins/structures/prepare

Parameters:

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

    Prepared artifact encoding: gzip or none. Defaults to gzip.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3196

def structuresPrepare(
  structure_id:,
  encoding: nil,
  request_options: {}
)
  body = {
    'encoding' => encoding,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/prepare',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructurePrepareData.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

#structuresPreparedInspect(structure_id:, encoding: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructurePreparedInspectData

POST /v1/proteins/structures/prepared/inspect

Parameters:

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

    Prepared artifact encoding to inspect: gzip or none. Defaults to gzip.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3222

def structuresPreparedInspect(
  structure_id:,
  encoding: nil,
  request_options: {}
)
  body = {
    'encoding' => encoding,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/prepared/inspect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructurePreparedInspectData.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

#structuresPrincipalAxes(structure_id:, chain_ids: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructurePrincipalAxesData

POST /v1/proteins/structures/principal-axes

Parameters:

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

    Restrict to these chain ids; empty means all chains.

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

    Database name published with the relation

  • output_format (Rafflesia::Types::StructurePrincipalAxesRequestOutputFormat, 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3256

def structuresPrincipalAxes(
  structure_id:,
  chain_ids: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'chain_ids' => chain_ids,
    'database' => database,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/principal-axes',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructurePrincipalAxesData.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

#structuresStatus(structure_id:, request_options: {}) ⇒ Rafflesia::EnvelopeStructureStatusData

POST /v1/proteins/structures/status

Parameters:

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3297

def structuresStatus(
  structure_id:,
  request_options: {}
)
  body = {
    'structure_id' => structure_id
  }
  response = @client.request(
    method: :post,
    path: '/v1/proteins/structures/status',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureStatusData.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

#turnsDetect(structure_id:, max_ca_distance: nil, request_options: {}) ⇒ Rafflesia::EnvelopeBetaTurnDetectData

POST /v1/proteins/turns/detect

Parameters:

  • max_ca_distance (Float, nil) (defaults to: nil)
  • structure_id (String)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3321

def turnsDetect(
  structure_id:,
  max_ca_distance: nil,
  request_options: {}
)
  body = {
    'max_ca_distance' => max_ca_distance,
    'structure_id' => structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/turns/detect',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeBetaTurnDetectData.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

#validationAlphafoldChain(chain_id:, structure_id:, allow_network: nil, method_: nil, uniprot_id: nil, request_options: {}) ⇒ Rafflesia::EnvelopeAlphaFoldChainCompareData

POST /v1/proteins/validation/alphafold-chain

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil)
  • chain_id (String)
  • method (String, nil)
  • structure_id (String)
  • uniprot_id (String, nil) (defaults to: nil)
  • request_options (Hash) (defaults to: {}) —

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3350

def validationAlphafoldChain(
  chain_id:,
  structure_id:,
  allow_network: nil,
  method_: nil,
  uniprot_id: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'chain_id' => chain_id,
    'method' => method_,
    'structure_id' => structure_id,
    'uniprot_id' => uniprot_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/alphafold-chain',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeAlphaFoldChainCompareData.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

#validationAlphafoldChainComparisonsExport(structure_id:, allow_network: nil, backend: nil, chain_ids: nil, database: nil, foldseek_binary_path: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, tmalign_binary_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeTableExportData

POST /v1/proteins/validation/alphafold-chain-comparisons/export

Parameters:

  • allow_network (Boolean, nil) (defaults to: nil)
  • backend (String, nil) (defaults to: nil)
  • chain_ids (Array<String>, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

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

    Optional absolute foldseek binary path used by the server for this export.

  • output_format (Rafflesia::Types::AlphaFoldChainComparisonsExportRequestOutputFormat, 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

  • structure_id (String)
  • tmalign_binary_path (String, nil) (defaults to: nil) —

    Optional absolute TM-align binary path used by the server for this export.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3394

def validationAlphafoldChainComparisonsExport(
  structure_id:,
  allow_network: nil,
  backend: nil,
  chain_ids: nil,
  database: nil,
  foldseek_binary_path: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  tmalign_binary_path: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'backend' => backend,
    'chain_ids' => chain_ids,
    'database' => database,
    'foldseek_binary_path' => foldseek_binary_path,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'tmalign_binary_path' => tmalign_binary_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/alphafold-chain-comparisons/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeTableExportData.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

#validationDockq(query_structure_id:, target_structure_id:, dockq_binary_path: nil, model_chain_mapping: nil, native_chain_mapping: nil, request_options: {}) ⇒ Rafflesia::EnvelopeDockQData

POST /v1/proteins/validation/dockq

Parameters:

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

    Optional absolute DockQ binary path used by the server for this measurement.

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

    Optional DockQ model chain mapping string; passed through only when a DockQ backend is integrated.

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

    Optional DockQ native chain mapping string; passed through only when a DockQ backend is integrated.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3447

def validationDockq(
  query_structure_id:,
  target_structure_id:,
  dockq_binary_path: nil,
  model_chain_mapping: nil,
  native_chain_mapping: nil,
  request_options: {}
)
  body = {
    'dockq_binary_path' => dockq_binary_path,
    'model_chain_mapping' => model_chain_mapping,
    'native_chain_mapping' => native_chain_mapping,
    'query_structure_id' => query_structure_id,
    'target_structure_id' => target_structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/dockq',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeDockQData.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

#validationDockqExport(database: nil, dockq_binary_path: nil, max_comparisons: nil, model_chain_mapping: nil, native_chain_mapping: nil, output_format: nil, output_relation: nil, pairs: nil, pairs_path: nil, pairs_table_object_id: nil, pairs_table_path: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeTableExportData

POST /v1/proteins/validation/dockq/export

Parameters:

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

    Database name published with the relation

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

    Optional absolute DockQ binary path used by the server for this export.

  • max_comparisons (Integer, nil) (defaults to: nil)
  • model_chain_mapping (String, nil) (defaults to: nil) —

    Optional DockQ model chain mapping string.

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

    Optional DockQ native chain mapping string.

  • output_format (Rafflesia::Types::DockQMeasurementsExportRequestOutputFormat, 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

  • pairs (Array<Rafflesia::StructureComparisonPair>, nil) (defaults to: nil)
  • pairs_path (String, nil) (defaults to: nil) —

    Local CSV/TSV file containing measurement pairs. Columns: query_structure_id,target_structure_id, optional comparison_id,sample_id.

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

    Content-addressed archive_member_pairs parquet object id.

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

    Local archive_member_pairs parquet table path containing query_structure_id,target_structure_id columns.

  • 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

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3493

def validationDockqExport(
  database: nil,
  dockq_binary_path: nil,
  max_comparisons: nil,
  model_chain_mapping: nil,
  native_chain_mapping: nil,
  output_format: nil,
  output_relation: nil,
  pairs: nil,
  pairs_path: nil,
  pairs_table_object_id: nil,
  pairs_table_path: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'dockq_binary_path' => dockq_binary_path,
    'max_comparisons' => max_comparisons,
    'model_chain_mapping' => model_chain_mapping,
    'native_chain_mapping' => native_chain_mapping,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'pairs' => pairs,
    'pairs_path' => pairs_path,
    'pairs_table_object_id' => pairs_table_object_id,
    'pairs_table_path' => pairs_table_path,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/dockq/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeTableExportData.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

#validationLddt(query_structure_id:, target_structure_id:, cutoff_angstrom: nil, thresholds: nil, request_options: {}) ⇒ Rafflesia::EnvelopeLocalDistanceDifferenceData

POST /v1/proteins/validation/lddt

Parameters:

  • cutoff_angstrom (Float, nil) (defaults to: nil)
  • query_structure_id (String)
  • target_structure_id (String)
  • thresholds (Array<Float>, nil) (defaults to: nil) —

    Distance-difference thresholds in angstroms; defaults to 0.5,1,2,4.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3549

def validationLddt(
  query_structure_id:,
  target_structure_id:,
  cutoff_angstrom: nil,
  thresholds: nil,
  request_options: {}
)
  body = {
    'cutoff_angstrom' => cutoff_angstrom,
    'query_structure_id' => query_structure_id,
    'target_structure_id' => target_structure_id,
    'thresholds' => thresholds
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/lddt',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeLocalDistanceDifferenceData.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

#validationLddtExport(cutoff_angstrom: nil, database: nil, max_comparisons: nil, output_format: nil, output_relation: nil, pairs: nil, pairs_path: nil, pairs_table_object_id: nil, pairs_table_path: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, thresholds: nil, request_options: {}) ⇒ Rafflesia::EnvelopeTableExportData

POST /v1/proteins/validation/lddt/export

Parameters:

  • cutoff_angstrom (Float, nil) (defaults to: nil)
  • database (String, nil) (defaults to: nil) —

    Database name published with the relation

  • max_comparisons (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::LocalDistanceDifferenceExportRequestOutputFormat, 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

  • pairs (Array<Rafflesia::StructureComparisonPair>, nil) (defaults to: nil)
  • pairs_path (String, nil) (defaults to: nil) —

    Local CSV/TSV file containing measurement pairs. Columns: query_structure_id,target_structure_id, optional comparison_id,sample_id.

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

    Content-addressed archive_member_pairs parquet object id.

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

    Local archive_member_pairs parquet table path containing query_structure_id,target_structure_id columns.

  • 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

  • thresholds (Array<Float>, nil) (defaults to: nil) —

    Distance-difference thresholds in angstroms; defaults to 0.5,1,2,4.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3592

def validationLddtExport(
  cutoff_angstrom: nil,
  database: nil,
  max_comparisons: nil,
  output_format: nil,
  output_relation: nil,
  pairs: nil,
  pairs_path: nil,
  pairs_table_object_id: nil,
  pairs_table_path: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  thresholds: nil,
  request_options: {}
)
  body = {
    'cutoff_angstrom' => cutoff_angstrom,
    'database' => database,
    'max_comparisons' => max_comparisons,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'pairs' => pairs,
    'pairs_path' => pairs_path,
    'pairs_table_object_id' => pairs_table_object_id,
    'pairs_table_path' => pairs_table_path,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'thresholds' => thresholds
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/lddt/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeTableExportData.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

#validationLigandCompare(query_structure_id:, target_structure_id:, include_waters: nil, query_ligands: nil, radius: nil, target_ligands: nil, request_options: {}) ⇒ Rafflesia::EnvelopeLigandCompareData

POST /v1/proteins/validation/ligand-compare

Parameters:

  • include_waters (Boolean, nil) (defaults to: nil)
  • query_ligands (Array<String>, nil) (defaults to: nil) —

    Restrict query measurement to ligand selectors; each selector matches residue name, ligand_id, or CHAIN:POSITION.

  • query_structure_id (String)
  • radius (Float, nil) (defaults to: nil)
  • target_ligands (Array<String>, nil) (defaults to: nil) —

    Restrict target measurement to ligand selectors; each selector matches residue name, ligand_id, or CHAIN:POSITION.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3648

def validationLigandCompare(
  query_structure_id:,
  target_structure_id:,
  include_waters: nil,
  query_ligands: nil,
  radius: nil,
  target_ligands: nil,
  request_options: {}
)
  body = {
    'include_waters' => include_waters,
    'query_ligands' => query_ligands,
    'query_structure_id' => query_structure_id,
    'radius' => radius,
    'target_ligands' => target_ligands,
    'target_structure_id' => target_structure_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/ligand-compare',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeLigandCompareData.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

#validationLigandCompareExport(database: nil, include_waters: nil, max_comparisons: nil, output_format: nil, output_relation: nil, pairs: nil, pairs_path: nil, pairs_table_object_id: nil, pairs_table_path: nil, partition_by: nil, preview_limit: nil, query_ligands: nil, radius: nil, relation: nil, release: nil, sort_by: nil, target_ligands: nil, request_options: {}) ⇒ Rafflesia::EnvelopeTableExportData

POST /v1/proteins/validation/ligand-compare/export

Parameters:

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

    Database name published with the relation

  • include_waters (Boolean, nil) (defaults to: nil)
  • max_comparisons (Integer, nil) (defaults to: nil)
  • output_format (Rafflesia::Types::LigandComparisonsExportRequestOutputFormat, 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

  • pairs (Array<Rafflesia::StructureComparisonPair>, nil) (defaults to: nil)
  • pairs_path (String, nil) (defaults to: nil) —

    Local CSV/TSV file containing comparison pairs. Columns: query_structure_id,target_structure_id, optional comparison_id,sample_id.

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

    Content-addressed archive_member_pairs parquet object id.

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

    Local archive_member_pairs parquet table path containing query_structure_id,target_structure_id columns.

  • 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

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

    Restrict query measurement to ligand selectors; each selector matches residue name, ligand_id, or CHAIN:POSITION.

  • radius (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

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

    Requested physical sort columns

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

    Restrict target measurement to ligand selectors; each selector matches residue name, ligand_id, or CHAIN:POSITION.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3697

def validationLigandCompareExport(
  database: nil,
  include_waters: nil,
  max_comparisons: nil,
  output_format: nil,
  output_relation: nil,
  pairs: nil,
  pairs_path: nil,
  pairs_table_object_id: nil,
  pairs_table_path: nil,
  partition_by: nil,
  preview_limit: nil,
  query_ligands: nil,
  radius: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  target_ligands: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'include_waters' => include_waters,
    'max_comparisons' => max_comparisons,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'pairs' => pairs,
    'pairs_path' => pairs_path,
    'pairs_table_object_id' => pairs_table_object_id,
    'pairs_table_path' => pairs_table_path,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'query_ligands' => query_ligands,
    'radius' => radius,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'target_ligands' => target_ligands
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/ligand-compare/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeTableExportData.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

#validationStructureCompare(query_structure_id:, target_structure_id:, foldseek_binary_path: nil, method_: nil, tmalign_binary_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeStructureCompareData

POST /v1/proteins/validation/structure-compare

Parameters:

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

    Optional absolute foldseek binary path used by the server for this comparison.

  • method (String, nil)
  • query_structure_id (String)
  • target_structure_id (String)
  • tmalign_binary_path (String, nil) (defaults to: nil) —

    Optional absolute TM-align binary path used by the server for this comparison.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3756

def validationStructureCompare(
  query_structure_id:,
  target_structure_id:,
  foldseek_binary_path: nil,
  method_: nil,
  tmalign_binary_path: nil,
  request_options: {}
)
  body = {
    'foldseek_binary_path' => foldseek_binary_path,
    'method' => method_,
    'query_structure_id' => query_structure_id,
    'target_structure_id' => target_structure_id,
    'tmalign_binary_path' => tmalign_binary_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/structure-compare',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeStructureCompareData.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

#validationStructureComparisonsExport(database: nil, foldseek_binary_path: nil, max_comparisons: nil, method_: nil, output_format: nil, output_relation: nil, pairs: nil, pairs_path: nil, pairs_table_object_id: nil, pairs_table_path: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, tmalign_binary_path: nil, request_options: {}) ⇒ Rafflesia::EnvelopeTableExportData

POST /v1/proteins/validation/structure-comparisons/export

Parameters:

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

    Database name published with the relation

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

    Optional absolute foldseek binary path used by the server for this export.

  • max_comparisons (Integer, nil) (defaults to: nil)
  • method (String, nil)
  • output_format (Rafflesia::Types::StructureComparisonsExportRequestOutputFormat, 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

  • pairs (Array<Rafflesia::StructureComparisonPair>, nil) (defaults to: nil)
  • pairs_path (String, nil) (defaults to: nil) —

    Local CSV/TSV/JSON file containing comparison pairs. CSV/TSV columns: query_structure_id,target_structure_id, optional comparison_id,sample_id,method.

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

    Content-addressed archive_member_pairs parquet object id.

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

    Local archive_member_pairs parquet table path containing query_structure_id,target_structure_id columns.

  • 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

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

    Optional absolute TM-align binary path used by the server for this export.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3802

def validationStructureComparisonsExport(
  database: nil,
  foldseek_binary_path: nil,
  max_comparisons: nil,
  method_: nil,
  output_format: nil,
  output_relation: nil,
  pairs: nil,
  pairs_path: nil,
  pairs_table_object_id: nil,
  pairs_table_path: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  tmalign_binary_path: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'foldseek_binary_path' => foldseek_binary_path,
    'max_comparisons' => max_comparisons,
    'method' => method_,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'pairs' => pairs,
    'pairs_path' => pairs_path,
    'pairs_table_object_id' => pairs_table_object_id,
    'pairs_table_path' => pairs_table_path,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'tmalign_binary_path' => tmalign_binary_path
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/validation/structure-comparisons/export',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeTableExportData.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

#variantsFeatures(features:, structure_id:, variants:, database: nil, output_format: nil, output_relation: nil, partition_by: nil, pockets: nil, preview_limit: nil, radius: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantFeaturesData

POST /v1/proteins/variants/features

Parameters:

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

    Database name published with the relation

  • features (Array<String>, nil) —

    Requested feature codes: plddt, burial, pocket_distance, interface_distance.

  • output_format (Rafflesia::Types::VariantFeaturesRequestOutputFormat, 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

  • pockets (Array<Rafflesia::Pocket>, nil) (defaults to: nil) —

    Optional caller-provided pockets used for pocket_distance; a warning is emitted when pocket_distance is requested and none are available.

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

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

  • radius (Float, nil) (defaults to: nil) —

    Neighbor radius in Angstroms for burial (default 8).

  • 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

  • structure_id (String) —

    Structure identifier providing residue coordinates.

  • variants (Array<Rafflesia::MappedVariant>, nil) —

    Mapped variants, typically from /v1/proteins/variants/map output.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3867

def variantsFeatures(
  features:,
  structure_id:,
  variants:,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  pockets: nil,
  preview_limit: nil,
  radius: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'database' => database,
    'features' => features,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'pockets' => pockets,
    'preview_limit' => preview_limit,
    'radius' => radius,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'variants' => variants
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/variants/features',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantFeaturesData.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

#variantsMap(mutations:, structure_id:, target_id:, allow_network: nil, chain: nil, database: nil, output_format: nil, output_relation: nil, partition_by: nil, preview_limit: nil, relation: nil, release: nil, sort_by: nil, request_options: {}) ⇒ Rafflesia::EnvelopeVariantMapData

POST /v1/proteins/variants/map

Parameters:

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

    Allow network fetch of the target sequence when not cached.

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

    Structure chain id to map onto. When omitted and the target sequence is available, the chain whose residues best match the target sequence is selected automatically; otherwise the first chain is used.

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

    Database name published with the relation

  • mutations (Array<String>, nil) —

    Mutation strings in parse format.

  • output_format (Rafflesia::Types::VariantMapRequestOutputFormat, 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

  • structure_id (String) —

    Structure identifier to map onto.

  • target_id (String) —

    Target identifier, e.g. uniprot:P38398.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3926

def variantsMap(
  mutations:,
  structure_id:,
  target_id:,
  allow_network: nil,
  chain: nil,
  database: nil,
  output_format: nil,
  output_relation: nil,
  partition_by: nil,
  preview_limit: nil,
  relation: nil,
  release: nil,
  sort_by: nil,
  request_options: {}
)
  body = {
    'allow_network' => allow_network,
    'chain' => chain,
    'database' => database,
    'mutations' => mutations,
    'output_format' => output_format,
    'output_relation' => output_relation,
    'partition_by' => partition_by,
    'preview_limit' => preview_limit,
    'relation' => relation,
    'release' => release,
    'sort_by' => sort_by,
    'structure_id' => structure_id,
    'target_id' => target_id
  }.compact
  response = @client.request(
    method: :post,
    path: '/v1/proteins/variants/map',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantMapData.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

#variantsParse(mutations:, request_options: {}) ⇒ Rafflesia::EnvelopeVariantParseData

POST /v1/proteins/variants/parse

Parameters:

  • mutations (Array<String>, nil) —

    Mutation strings in the form WILDTYPE_AA + POSITION (1-based) + MUTANT_AA, e.g. M1775R or Y1853X. X (or *) as the mutant denotes a stop/nonsense change.

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

    (see Rafflesia::Types::RequestOptions)

Returns:



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# File 'lib/rafflesia/proteins.rb', line 3973

def variantsParse(
  mutations:,
  request_options: {}
)
  body = {
    'mutations' => mutations
  }
  response = @client.request(
    method: :post,
    path: '/v1/proteins/variants/parse',
    auth: true,
    body: body,
    request_options: request_options
  )
  result = Rafflesia::EnvelopeVariantParseData.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