openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences Molecules API
  version: 2.0.0
  description: 'AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations.

    '
servers:
- url: /api/v2
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: Molecules are groups of atoms held together by bonds, representing entities smaller than DNA Sequences and AA Sequences. Just like other entities, they support schemas, tags, and aliases.
  name: Molecules
paths:
  /molecules:
    get:
      description: List molecules
      operationId: listMolecules
      parameters:
      - description: 'Number of results to return. Defaults to 50, maximum of 100.

          '
        in: query
        name: pageSize
        schema:
          default: 50
          maximum: 100
          minimum: 0
          nullable: false
          type: integer
      - description: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - in: query
        name: sort
        schema:
          default: modifiedAt:desc
          description: 'Method by which to order search results. Valid sorts are name, modifiedAt, and createdAt. Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

            '
          enum:
          - createdAt
          - createdAt:asc
          - createdAt:desc
          - modifiedAt
          - modifiedAt:asc
          - modifiedAt:desc
          - name
          - name:asc
          - name:desc
          nullable: false
          type: string
      - description: 'Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those created in the specified range. e.g. > 2017-04-30. Date ranges can be specified with the following nomenclature > YYYY-MM-DD AND <YYYY-MM-DD.

          '
        examples:
          and-range:
            summary: Filter for all models created within a certain range using the AND operator.
            value: '> 2022-03-01 AND < 2022-04-01'
          full-rfc-3339-format:
            summary: Filter for created models using the full RFC 3339 format
            value: '> 2020-12-31T21:07:14-05:00'
          greater-than-example:
            summary: Filter for all models created after a certain date
            value: '> 2022-03-01'
        in: query
        name: createdAt
        schema:
          type: string
      - description: 'Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30. Date ranges can be specified with the following nomenclature > YYYY-MM-DD AND <YYYY-MM-DD.

          '
        examples:
          and-range:
            summary: Filter for all models modified within a certain range using the AND operator.
            value: '> 2022-03-01 AND < 2022-04-01'
          full-rfc-3339-format:
            summary: Filter for modified models using the full RFC 3339 format
            value: '> 2020-12-31T21:07:14-05:00'
          greater-than-example:
            summary: Filter for all models modified after a certain date
            value: '> 2022-03-01'
        in: query
        name: modifiedAt
        schema:
          type: string
      - description: Name of a Molecule. Restricts results to those with the specified name, alias, or entity registry ID.
        in: query
        name: name
        schema:
          type: string
      - description: Name substring of a Molecule. Restricts results to those with names, aliases, or entity registry IDs that include the provided substring.
        in: query
        name: nameIncludes
        schema:
          type: string
      - description: ID of a folder. Restricts results to those in the folder.
        in: query
        name: folderId
        schema:
          type: string
      - description: 'Comma-separated list of entry IDs. Restricts results to Molecules mentioned in those entries.

          '
        explode: false
        in: query
        name: mentionedIn
        schema:
          items:
            type: string
          type: array
      - description: ID of a project. Restricts results to those in the project.
        in: query
        name: projectId
        schema:
          type: string
      - description: 'ID of a registry. Restricts results to those registered in this registry. Specifying "null" returns unregistered items.

          '
        in: query
        name: registryId
        schema:
          nullable: true
          type: string
      - description: 'ID of a schema. Restricts results to those of the specified schema.

          '
        in: query
        name: schemaId
        schema:
          type: string
      - description: 'Filter based on schema field value (not display value). Restricts results to those with a field whose value matches the filter. For Integer, Float, and Date type fields, supports the >= and <= operators (but not < or >). If any schemaField filters are present, the schemaId param must also be present. Note that all operators must be separated from any values by a single space.

          '
        in: query
        name: schemaFields
        schema:
          $ref: '#/components/schemas/SchemaFieldsQueryParam'
      - description: 'Archive reason. Restricts results to those with the specified archive reason. Use "NOT_ARCHIVED" to filter for unarchived Molecules. Use "ANY_ARCHIVED" to filter for archived Molecules regardless of reason. Use "ANY_ARCHIVED_OR_NOT_ARCHIVED" to return items for both archived and unarchived.

          '
        examples:
          any_archived:
            summary: Includes items archived for any reason.
            value: ANY_ARCHIVED
          any_archived_or_not_archived:
            summary: Includes both archived and unarchived items.
            value: ANY_ARCHIVED_OR_NOT_ARCHIVED
          arhived_reason:
            summary: Includes items archived for a specific reason.
            value: Retired
          not_archived:
            summary: Only include unarchived items (default).
            value: NOT_ARCHIVED
        in: query
        name: archiveReason
        schema:
          type: string
      - description: 'Comma-separated list of item IDs. Restricts results to those that mention the given items in the description.

          '
        explode: false
        in: query
        name: mentions
        schema:
          items:
            type: string
          type: array
      - description: 'Comma-separated list of ids. Matches all of the provided IDs, or returns a 400 error that includes a list of which IDs are invalid.

          '
        in: query
        name: ids
        schema:
          example: mol_yWs5X7lv,mol_RhYGVnHF
          type: string
      - description: 'Comma-separated list of entity registry IDs. Maximum of 100. Restricts results to those that match any of the specified registry IDs.

          '
        in: query
        name: entityRegistryIds.anyOf
        schema:
          example: TP001,TP002
          type: string
      - description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names, aliases, or entity registry IDs.

          '
        in: query
        name: names.anyOf
        schema:
          example: MyName1,MyName2
          type: string
      - description: Comma separated list of user or app IDs. Maximum of 100.
        in: query
        name: authorIds.anyOf
        schema:
          example: ent_a0SApq3z,ent_b4AApz9b
          type: string
      - description: mol-formatted string for a chemical substructure to search by
        in: query
        name: chemicalSubstructure.mol
        schema:
          example: "Format described at https://en.wikipedia.org/wiki/Chemical_table_file#Molfile As an example, ethanol is represented as follows: ChEBI\n  Marvin  10060515352D\n\n  3  2  0  0  0  0            999 V2000\n    4.8667   -3.3230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5812   -2.9105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.2956   -3.3230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\nM  END\n"
          type: string
      - description: SMILES string for a chemical substructure to search by
        in: query
        name: chemicalSubstructure.smiles
        schema:
          example: CCO,C(C1C(C(C(C(O1)O)O)O)O)O
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MoleculesPaginatedList'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad request
      summary: List Molecules
      tags:
      - Molecules
    post:
      description: Create a Molecule
      operationId: createMolecule
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculeCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Molecule'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '503':
          description: Deprecated, a 429 is returned for too many requests
      summary: Create a Molecule
      tags:
      - Molecules
  /molecules/{entity_registry_id}:upsert:
    patch:
      description: 'Create or update a registered Molecule.


        Schema field links can be populated using entity registry IDs or API IDs. In the `value` field of the [Field](#/components/schemas/FieldWithResolution) resource, the object `{"entityRegistryId": ENTITY_REGISTRY_ID}` may be provided instead of the API ID if desired (see example value).

        '
      operationId: upsertMolecule
      parameters:
      - in: path
        name: entity_registry_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculeUpsertRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Molecule'
          description: OK
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Molecule'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create or update a registered Molecule
      tags:
      - Molecules
  /molecules/{molecule_id}:
    get:
      description: Get a Molecule
      operationId: getMolecule
      parameters:
      - in: path
        name: molecule_id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Molecule'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get a Molecule
      tags:
      - Molecules
    patch:
      description: Update a Molecule
      operationId: updateMolecule
      parameters:
      - in: path
        name: molecule_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculeUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Molecule'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Update a Molecule
      tags:
      - Molecules
  /molecules:archive:
    post:
      description: Archive Molecules
      operationId: archiveMolecules
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculesArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MoleculesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive Molecules
      tags:
      - Molecules
  /molecules:bulk-create:
    post:
      description: Bulk Create Molecules
      operationId: bulkCreateMolecules
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculesBulkCreateRequest'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: Accepted
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Create Molecules
      tags:
      - Molecules
  /molecules:bulk-update:
    post:
      description: Bulk Update Molecules
      operationId: bulkUpdateMolecules
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculesBulkUpdateRequest'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: 'This endpoint launches a [long-running task](#/Tasks/getTask) and returns the Task ID of the launched task.

            When successful, the task returns a full list of [Molecule](#/Molecules/getMolecule) resources that were updated.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Update Molecules
      tags:
      - Molecules
  /molecules:bulk-upsert:
    post:
      description: 'All entities and their schemas must be within the same registry.


        This operation performs the following actions:

        1. Any existing objects are looked up in Benchling by the provided entity registry ID.

        2. Then, all objects are either created or updated accordingly, temporarily skipping any schema field links between objects.

        3. Schema field links can be populated using entity registry IDs or API IDs. In the `value` field of the [Field](#/components/schemas/FieldWithResolution) resource, the object `{"entityRegistryId": ENTITY_REGISTRY_ID}` may be provided instead of the API ID if desired (see example value). You may link to objects being created in the same operation.

        4. Entities are registered, using the provided name and entity registry ID.


        If any action fails, the whole operation is canceled and no objects are created or updated.

        '
      operationId: bulkUpsertMolecules
      parameters:
      - description: 'Comma-separated list of fields to return. Modifies the output shape. To return all keys at a given level, enumerate them or use the wildcard, ''*''. For more information, [click here](https://docs.benchling.com/docs/getting-started-1#returning-query-parameter).

          '
        in: query
        name: returning
        schema:
          example: molecules.id,molecules.creator.handle
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculesBulkUpsertRequest'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: 'This endpoint launches a [long-running task](#/Tasks/getTask) and returns the Task ID of the launched task.

            When successful, the task returns the resources of the objects that were upserted.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk upsert Molecules
      tags:
      - Molecules
  /molecules:unarchive:
    post:
      description: Unarchive Molecules
      operationId: unarchiveMolecules
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MoleculesUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MoleculesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive Molecules
      tags:
      - Molecules
components:
  schemas:
    Molecule:
      additionalProperties: false
      properties:
        aliases:
          description: Array of aliases.
          items:
            type: string
          type: array
        apiURL:
          description: The canonical url of the Molecule in the API.
          format: uri
          readOnly: true
          type: string
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        authors:
          items:
            $ref: '#/components/schemas/UserSummary'
          type: array
        canonicalizedSmiles:
          description: The canonicalized chemical structure in SMILES format.
          example: Nc1nc(=O)n([H])cc1C1CC1
          type: string
        createdAt:
          description: DateTime the Molecule was created.
          format: date-time
          readOnly: true
          type: string
        creator:
          $ref: '#/components/schemas/UserSummary'
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: Custom fields set on the Molecule.
        entityRegistryId:
          description: Registry ID of the Molecule if registered.
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
        folderId:
          description: ID of the folder that contains the Molecule.
          nullable: true
          type: string
        id:
          description: ID of the Molecule.
          example: mol_bhuDUw9D
          type: string
        modifiedAt:
          description: DateTime the Molecule was last modified.
          format: date-time
          readOnly: true
          type: string
        name:
          description: Name of the Molecule.
          type: string
        originalSmiles:
          description: The original chemical structure supplied by the user in SMILES format. Null if the user did not originally supply SMILES.
          example: Nc1nc(=O)n([H])cc1C1CC1
          nullable: true
          type: string
        registrationOrigin:
          allOf:
          - $ref: '#/components/schemas/RegistrationOrigin'
          nullable: true
          readOnly: true
        registryId:
          description: Registry the Molecule is registered in.
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          nullable: true
        webURL:
          description: URL of the Molecule.
          example: https://benchling.com/benchling/f/lib_R8KcsjhW-molecules/mol_xCUXNVyG-molecule1/edit
          format: uri
          readOnly: true
          type: string
      type: object
    MoleculeBaseRequestForCreate:
      allOf:
      - $ref: '#/components/schemas/MoleculeBaseRequest'
      - required:
        - name
        - chemicalStructure
    MoleculeUpdate:
      additionalProperties: false
      allOf:
      - properties:
          entityRegistryId:
            type: string
        type: object
      - $ref: '#/components/schemas/MoleculeBaseRequest'
    MoleculesPaginatedList:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          molecules:
            items:
              $ref: '#/components/schemas/Molecule'
            type: array
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    MoleculesArchive:
      additionalProperties: false
      description: 'The request body for archiving Molecules.

        '
      properties:
        moleculeIds:
          items:
            type: string
          type: array
        reason:
          description: 'The reason for archiving the provided Molecules. Accepted reasons may differ based on tenant configuration.

            '
          enum:
          - Made in error
          - Retired
          - Expended
          - Shipped
          - Contaminated
          - Expired
          - Missing
          - Other
          type: string
      required:
      - reason
      - moleculeIds
      type: object
    FieldWithResolution:
      allOf:
      - $ref: '#/components/schemas/Field'
      - properties:
          value:
            allOf:
            - $ref: '#/components/schemas/FieldValueWithResolution'
            nullable: true
        type: object
    MoleculesArchivalChange:
      additionalProperties: false
      description: 'IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of Molecules along with any IDs of batches that were archived / unarchived.

        '
      properties:
        batchIds:
          items:
            type: string
          type: array
        moleculeIds:
          items:
            type: string
          type: array
      type: object
    CustomField:
      properties:
        value:
          type: string
      type: object
    MoleculesBulkUpdateRequest:
      additionalProperties: false
      properties:
        molecules:
          items:
            $ref: '#/components/schemas/MoleculeBulkUpdate'
          type: array
      type: object
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    ArchiveRecordSet:
      additionalProperties: false
      description: Currently, we only support setting a null value for archiveRecord, which unarchives the item
      example: null
      nullable: true
      type: object
    MoleculesBulkCreateRequest:
      additionalProperties: false
      properties:
        molecules:
          items:
            $ref: '#/components/schemas/MoleculeCreate'
          type: array
      type: object
    SchemaFieldsQueryParam:
      additionalProperties: true
      example:
        schemaField.Cell Count: '>= 10 AND <= 50'
        schemaField.Experiment: MyExperiment
        schemaField.Started On: <= 2023-05-23T00:00:00Z
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    Pagination:
      properties:
        nextToken:
          type: string
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    MoleculeStructure:
      additionalProperties: false
      properties:
        structureFormat:
          description: 'Format of the chemical structure.

            - smiles

            - molfile

            '
          enum:
          - smiles
          - molfile
          type: string
        value:
          description: Chemical structure in SMILES or molfile format.
          example: Nc1nc(=O)n([H:1])cc1C1CC1
          type: string
      type: object
    MoleculesUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving Molecules.

        '
      properties:
        moleculeIds:
          items:
            type: string
          type: array
      required:
      - moleculeIds
      type: object
    FieldType:
      enum:
      - dna_sequence_link
      - aa_sequence_link
      - custom_entity_link
      - entity_link
      - mixture_link
      - molecule_link
      - dropdown
      - part_link
      - translation_link
      - aa_part_link
      - base_molecule_link
      - blob_link
      - text
      - long_text
      - batch_link
      - storage_link
      - entry_link
      - assay_request_link
      - assay_result_link
      - assay_run_link
      - boolean
      - float
      - integer
      - datetime
      - date
      - json
      type: string
    MoleculeBulkUpdate:
      additionalProperties: false
      allOf:
      - properties:
          id:
            type: string
        type: object
      - $ref: '#/components/schemas/MoleculeUpdate'
    FieldsWithResolution:
      additionalProperties:
        $ref: '#/components/schemas/FieldWithResolution'
      example:
        Linked Peptide:
          value: prtn_ObbdtGhC
        Linked Sequence:
          value:
            entityRegistryId: DNA001
        Linked Strains:
          value:
          - entityRegistryId: STRAIN001
          - entityRegistryId: STRAIN002
      type: object
    FieldValueWithResolution:
      oneOf:
      - type: string
      - type: boolean
      - type: number
      - items:
          type: string
        type: array
      - additionalProperties: false
        description: Look up an entity by its entity registry ID
        properties:
          entityRegistryId:
            type: string
        required:
        - entityRegistryId
        type: object
    MoleculeBulkUpsertRequest:
      allOf:
      - $ref: '#/components/schemas/EntityBulkUpsertBaseRequest'
      - $ref: '#/components/schemas/MoleculeBaseRequestForCreate'
    NamingStrategy:
      description: 'Specifies the behavior for automatically generated names when registering an entity.

        - NEW_IDS: Generate new registry IDs

        - IDS_FROM_NAMES: Generate registry IDs based on entity names

        - DELETE_NAMES: Generate new registry IDs and replace name with registry ID

        - SET_FROM_NAME_PARTS: Generate new registry IDs, rename according to name template, and keep old name as alias

        - REPLACE_NAMES_FROM_PARTS: Generate new registry IDs, and replace name according to name template

        - KEEP_NAMES: Keep existing entity names as registry IDs

        - REPLACE_ID_AND_NAME_FROM_PARTS: Generate registry IDs and names according to name template

        '
      enum:
      - NEW_IDS
      - IDS_FROM_NAMES
      - DELETE_NAMES
      - SET_FROM_NAME_PARTS
      - REPLACE_NAMES_FROM_PARTS
      - KEEP_NAMES
      - REPLACE_ID_AND_NAME_FROM_PARTS
      type: string
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    Field:
      properties:
        displayValue:
          nullable: true
          readOnly: true
          type: string
        isMulti:
          readOnly: true
          type: boolean
        textValue:
          example: Amp
          nullable: true
          readOnly: true
          type: string
        type:
          allOf:
          - $ref: '#/components/schemas/FieldType'
          readOnly: true
        value:
          description: 'For single link fields, use the id of the item you want to link (eg. "seq_jdf8BV24").

            For multi-link fields, use an array of ids of the items you want to link (eg. ["seq_jdf8BV24"])

            '
          nullable: true
          oneOf:
          - type: string
          - type: boolean
          - type: number
          - type: object
          - items:
              type: string
            type: array
      required:
      - value
      type: object
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    MoleculeCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/MoleculeBaseRequestForCreate'
      - $ref: '#/components/schemas/CreateEntityIntoRegistry'
    MoleculesBulkUpsertRequest:
      additionalProperties: false
      maxItems: 1000
      properties:
        molecules:
          items:
            $ref: '#/components/schemas/MoleculeBulkUpsertRequest'
          type: array
      required:
      - molecules
      type: object
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    EntityBulkUpsertBaseRequest:
      allOf:
      - $ref: '#/components/schemas/EntityUpsertBaseRequest'
      - properties:
          entityRegistryId:
            description: Registry ID of the entity in Benchling.
            type: string
      - required:
        - entityRegistryId
    CustomFields:
      additionalProperties:
        $ref: '#/components/schemas/CustomField'
      example:
        Legacy ID:
          value: STR100
      type: object
    MoleculeBaseRequest:
      additionalProperties: false
      properties:
        aliases:
          description: Aliases to add to the Molecule.
          items:
            type: string
          type: array
        authorIds:
          description: IDs of users to set as the Molecule's authors.
          items:
            type: string
          type: array
        chemicalStructure:
          allOf:
          - $ref: '#/components/schemas/MoleculeStructure'
          description: 'Chemical structure of the Molecule.

            '
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: 'Custom fields to add to the Molecule. Every field should have its name as a key, mapping to an object with information about the value of the field.

            '
        fields:
          allOf:
          - $ref: '#/components/schemas/Fields'
          description: 'Fields to set on the Molecule. Must correspond with the schema''s field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.

            '
        folderId:
          description: 'ID of the folder containing the Molecule.

            '
          type: string
        name:
          description: 'Name of the Molecule.

            '
          type: string
        schemaId:
          description: 'ID of the Molecule''s schema.

            '
          type: string
      type: object
    MoleculeUpsertRequest:
      allOf:
      - $ref: '#/components/schemas/EntityUpsertBaseRequest'
      - $ref: '#/components/schemas/MoleculeBaseRequestForCreate'
    RegistrationOrigin:
      properties:
        originEntryId:
          nullable: true
          readOnly: true
          type: string
        registeredAt:
          format: date-time
          readOnly: true
          type: string
      type: object
    EntityUpsertBaseRequest:
      properties:
        archiveRecord:
          $ref: '#/components/schemas/ArchiveRecordSet'
        fields:
          $ref: '#/components/schemas/FieldsWithResolution'
        name:
          type: string
        registryId:
          type: string
        schemaId:
          type: string
      required:
      - registryId
      - name
      - schemaId
      type: object
    CreateEntityIntoRegistry:
      properties:
        entityRegistryId:
          description: 'Entity registry ID to set for the registered entity. Cannot specify both entityRegistryId and namingStrategy at the same time.

            '
          type: string
        folderId:
          description: ID of the folder containing the entity. Can be left empty when registryId is present.
          type: string
        namingStrategy:
          $ref: '#/components/schemas/NamingStrategy'
        registryId:
          description: 'Registry ID into which entity should be registered. this is the ID of the registry which was configured for a particular organization

            To get available registryIds, use the [/registries endpoint](#/Registry/listRegistries)


            Required in order for entities to be created directly in the registry.

            '
          type: string
      type: object
    SchemaSummary:
      properties:
        id:
          type: string
        name:
          type: string
      type: object
  securitySchemes:
    basicApiKeyAuth:
      description: Use issued API key for standard access to the API
      scheme: basic
      type: http
    basicClientIdSecretAuth:
      description: Auth used as part of client credentials OAuth flow prior to receiving a bearer token.
      scheme: basic
      type: http
    oAuth:
      description: OAuth2 Client Credentials flow intended for service access
      flows:
        clientCredentials:
          scopes: {}
          tokenUrl: /api/v2/token
      type: oauth2
externalDocs:
  description: Additional API Documentation
  url: https://docs.benchling.com