Benchling Aa Monomer API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Aa Monomer API
  version: 2.0.0
  description: 'An amino acid monomer is a building block for modified peptide sequences. Each

    AA monomer has a symbol identifier, chemical structure (SMILES/molfile), molecular

    weight, and attachment points defining where it bonds to other monomers. The

    naturalAnalog field links modified monomers to their standard amino acid counterpart

    (e.g., a modified alanine analog links to natural ''A''). AA monomers define the

    chemistry of non-standard amino acids used in peptide and protein engineering.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: 'An amino acid monomer is a building block for modified peptide sequences. Each

    AA monomer has a symbol identifier, chemical structure (SMILES/molfile), molecular

    weight, and attachment points defining where it bonds to other monomers. The

    naturalAnalog field links modified monomers to their standard amino acid counterpart

    (e.g., a modified alanine analog links to natural ''A''). AA monomers define the

    chemistry of non-standard amino acids used in peptide and protein engineering.'
  name: AaMonomer
  x-bnch-organization: Benchling
  x-displayName: Aa Monomer
paths:
  /aa-monomer:
    post:
      description: Create AaMonomer.
      operationId: AaMonomer.Create
      parameters:
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CreateAaMonomerInput'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaMonomer'
          description: Created
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Create AaMonomer
      tags:
      - AaMonomer
  /aa-monomer/items:
    get:
      description: List AaMonomer items.
      operationId: AaMonomer.List
      parameters:
      - $ref: '#/components/parameters/archiveReason.anyOf'
      - $ref: '#/components/parameters/archived.anyOf'
      - $ref: '#/components/parameters/createdAt.gt'
      - $ref: '#/components/parameters/createdAt.gte'
      - $ref: '#/components/parameters/createdAt.lt'
      - $ref: '#/components/parameters/createdAt.lte'
      - $ref: '#/components/parameters/id.anyOf'
      - $ref: '#/components/parameters/modifiedAt.gt'
      - $ref: '#/components/parameters/modifiedAt.gte'
      - $ref: '#/components/parameters/modifiedAt.lt'
      - $ref: '#/components/parameters/modifiedAt.lte'
      - $ref: '#/components/parameters/name.anyOf'
      - $ref: '#/components/parameters/name.anyOf.caseSensitive'
      - $ref: '#/components/parameters/nextToken'
      - $ref: '#/components/parameters/omit'
      - $ref: '#/components/parameters/pageSize'
      - $ref: '#/components/parameters/returning'
      - description: 'Method by which to order results. Valid sorts are: createdAt (created time, oldest first) and modifiedAt (modified time, oldest first). Use :asc or :desc to specify ascending or descending order. Default is modifiedAt:desc.'
        in: query
        name: sort
        schema:
          default: modifiedAt:desc
          enum:
          - createdAt:asc
          - createdAt:desc
          - modifiedAt:asc
          - modifiedAt:desc
          type: string
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaMonomerPaginatedList'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: List AaMonomer items
      tags:
      - AaMonomer
  /aa-monomer/{aa_monomer_id}:
    get:
      description: Get a single AaMonomer by ID.
      operationId: AaMonomer.Get
      parameters:
      - description: ID of the AaMonomer.
        in: path
        name: aa_monomer_id
        required: true
        schema:
          type: string
      - $ref: '#/components/parameters/returning'
      - $ref: '#/components/parameters/omit'
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaMonomer'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Get AaMonomer by ID
      tags:
      - AaMonomer
    patch:
      description: Update AaMonomer.
      operationId: AaMonomer.Update
      parameters:
      - description: ID of the AaMonomer.
        in: path
        name: aa_monomer_id
        required: true
        schema:
          type: string
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/UpdateAaMonomerInput'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaMonomer'
          description: OK
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Update AaMonomer
      tags:
      - AaMonomer
  /aa-monomer:batch-create:
    post:
      description: Batch create AaMonomer synchronously in one transaction. Maximum 25 items per request.
      operationId: AaMonomer.BatchCreate
      parameters:
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              additionalProperties: false
              properties:
                items:
                  items:
                    $ref: '#/components/schemas/CreateAaMonomerInput'
                  maxItems: 25
                  minItems: 1
                  type: array
              required:
              - items
              type: object
      responses:
        '201':
          content:
            application/json:
              schema:
                additionalProperties: false
                properties:
                  items:
                    items:
                      $ref: '#/components/schemas/AaMonomer'
                    type: array
                required:
                - items
                type: object
          description: Created
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Batch create AaMonomer
      tags:
      - AaMonomer
  /aa-monomer:batch-update:
    patch:
      description: Batch update AaMonomer synchronously in one transaction. Maximum 25 items per request.
      operationId: AaMonomer.BatchUpdate
      parameters:
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              additionalProperties: false
              properties:
                items:
                  items:
                    $ref: '#/components/schemas/UpdateAaMonomerInputWithPathParams'
                  maxItems: 25
                  minItems: 1
                  type: array
              required:
              - items
              type: object
      responses:
        '200':
          content:
            application/json:
              schema:
                additionalProperties: false
                properties:
                  items:
                    items:
                      $ref: '#/components/schemas/AaMonomer'
                    type: array
                required:
                - items
                type: object
          description: OK
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Batch update AaMonomer
      tags:
      - AaMonomer
  /aa-monomer:bulk-create:
    post:
      description: Bulk create AaMonomer.
      operationId: AaMonomer.BulkCreate
      parameters:
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/BulkImport'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: Task started
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Bulk create AaMonomer
      tags:
      - AaMonomer
  /aa-monomer:bulk-update:
    patch:
      description: Bulk update AaMonomer.
      operationId: AaMonomer.BulkUpdate
      parameters:
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/BulkImport'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: Task started
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '409':
          $ref: '#/components/responses/Conflict'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Bulk update AaMonomer
      tags:
      - AaMonomer
components:
  schemas:
    CreateAaMonomerInput:
      additionalProperties: false
      properties:
        chemicalStructure:
          $ref: '#/components/schemas/AaMonomerChemicalStructureInput'
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated value.
          type: number
        name:
          type: string
        naturalAnalog:
          description: The standard amino acid single-letter code that this monomer is an analog of.
          enum:
          - A
          - B
          - C
          - D
          - E
          - F
          - G
          - H
          - I
          - J
          - K
          - L
          - M
          - N
          - O
          - P
          - Q
          - R
          - S
          - T
          - U
          - V
          - W
          - X
          - Y
          - Z
          type: string
        symbol:
          description: User-defined identifier of the monomer, unique per tenant.
          type: string
      required:
      - symbol
      - name
      - naturalAnalog
      - chemicalStructure
      type: object
    PrincipalRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    AaMonomer:
      description: 'An amino acid monomer is a building block for modified peptide sequences. Each

        AA monomer has a symbol identifier, chemical structure (SMILES/molfile), molecular

        weight, and attachment points defining where it bonds to other monomers. The

        naturalAnalog field links modified monomers to their standard amino acid counterpart

        (e.g., a modified alanine analog links to natural ''A''). AA monomers define the

        chemistry of non-standard amino acids used in peptide and protein engineering.'
      properties:
        __typename:
          type: string
        archiveReason:
          type:
          - 'null'
          - string
        archived:
          type: boolean
        attachmentPoints:
          description: The capping groups present at each attachment point where the monomer bonds to other monomers.
          items:
            enum:
            - H
            - OH
            - NH2
            - CH3
            type: string
          type: array
        calculatedMolecularWeight:
          description: 'The molecular weight of the monomer with capping groups removed, computed using the

            average atomic weights of each element weighted by natural isotopic frequency.'
          type: number
        canonicalSmiles:
          description: The SMILES representation of the chemical structure after being standardized.
          type: string
        createdAt:
          format: datetime
          type: string
        creator:
          oneOf:
          - $ref: '#/components/schemas/PrincipalRef'
          - type: 'null'
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated value.
          type:
          - 'null'
          - number
        exactMolecularWeight:
          description: 'The exact (monoisotopic) molecular weight of the monomer with capping groups removed,

            computed using the atomic weight of the most frequent isotope of each element.'
          type: number
        id:
          type: string
        isNatural:
          description: 'Whether this monomer represents a natural (unmodified) amino acid, as opposed to a

            modified or synthetic variant.'
          type: boolean
        modifiedAt:
          format: datetime
          type: string
        molfile:
          description: The molfile representation of the chemical structure.
          type: string
        name:
          type: string
        naturalAnalog:
          description: The standard amino acid single-letter code that this monomer is an analog of.
          enum:
          - A
          - B
          - C
          - D
          - E
          - F
          - G
          - H
          - I
          - J
          - K
          - L
          - M
          - N
          - O
          - P
          - Q
          - R
          - S
          - T
          - U
          - V
          - W
          - X
          - Y
          - Z
          type: string
        originalSmiles:
          description: 'The SMILES string that was originally provided upon creation. Null if the

            user did not originally provide SMILES.'
          type:
          - 'null'
          - string
        symbol:
          description: User-defined identifier of the monomer, unique per tenant.
          type: string
      type: object
    AaMonomerChemicalStructureInput:
      additionalProperties: false
      properties:
        structureFormat:
          enum:
          - smiles
          type: string
        value:
          type: string
      required:
      - structureFormat
      - value
      type: object
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    UpdateAaMonomerInputWithPathParams:
      additionalProperties: false
      properties:
        archiveReason:
          type: string
        archived:
          type: boolean
        chemicalStructure:
          $ref: '#/components/schemas/AaMonomerChemicalStructureInput'
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated value.
          type:
          - 'null'
          - number
        id:
          type: string
        name:
          type: string
        symbol:
          description: User-defined identifier of the monomer, unique per tenant.
          type: string
      required:
      - id
      type: object
    TooManyRequestsError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    AaMonomerPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/AaMonomer'
          type: array
        nextToken:
          type:
          - string
          - 'null'
      type: object
    AsyncTaskLink:
      properties:
        pollingUri:
          format: uri
          type: string
        taskId:
          type: string
      type: object
    BulkImport:
      example:
        fileId: scrfile_jdf8BV24kLmN
      properties:
        fileId:
          description: The API ID of the scratch file (`scrfile_XXXXXXXX`) containing the items to import. The referenced file must be a scratch file whose upload has completed successfully.
          type: string
      required:
      - fileId
      type: object
    InternalServerError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        errorId:
          type: string
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    UpdateAaMonomerInput:
      additionalProperties: false
      properties:
        archiveReason:
          type: string
        archived:
          type: boolean
        chemicalStructure:
          $ref: '#/components/schemas/AaMonomerChemicalStructureInput'
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated value.
          type:
          - 'null'
          - number
        name:
          type: string
        symbol:
          description: User-defined identifier of the monomer, unique per tenant.
          type: string
      type: object
  responses:
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    Conflict:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Conflict
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/TooManyRequestsError'
      description: Too Many Requests
      headers:
        Retry-After:
          description: Minimum number of seconds to wait before retrying. Only included when the request exceeded a rate limit specific to the caller. Limits shared with other callers, such as tenant-wide limits, omit this header because the wait depends on their traffic.
          required: false
          schema:
            minimum: 1
            type: integer
  parameters:
    modifiedAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: modifiedAt.gte
      schema:
        format: datetime
        type: string
    createdAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: createdAt.lte
      schema:
        format: datetime
        type: string
    omit:
      description: Comma-separated list of top-level fields to omit from each returned item. Cannot overlap with returning.
      explode: false
      in: query
      name: omit
      schema:
        items:
          type: string
        type: array
    modifiedAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: modifiedAt.lte
      schema:
        format: datetime
        type: string
    name.anyOf:
      description: Restricts results to those that match any of the specified names. Case insensitive. Warning - this filter can be non-performant due to case insensitivity. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    createdAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created after the specified time. e.g. > 2017-04-30.
      in: query
      name: createdAt.gt
      schema:
        format: datetime
        type: string
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        type: string
    name.anyOf.caseSensitive:
      description: Restricts results to those that match any of the specified names. Case sensitive. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf.caseSensitive
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    archived.anyOf:
      description: If true, returns archived items. If false, returns unarchived items. If both true and false, returns archived and unarchived items. Comma-separated list.
      explode: false
      in: query
      name: archived.anyOf
      schema:
        items:
          type: boolean
        maxItems: 2
        type: array
    modifiedAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified after the specified time. e.g. > 2017-04-30.
      in: query
      name: modifiedAt.gt
      schema:
        format: datetime
        type: string
    pageSize:
      description: Number of results to return. Defaults to 50, maximum of 100.
      in: query
      name: pageSize
      schema:
        type: integer
    modifiedAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified before the specified time. e.g. < 2017-04-30.
      in: query
      name: modifiedAt.lt
      schema:
        format: datetime
        type: string
    returning:
      description: Comma-separated list of top-level fields to include in each returned item. Cannot overlap with omit.
      explode: false
      in: query
      name: returning
      schema:
        items:
          type: string
        type: array
    createdAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: createdAt.gte
      schema:
        format: datetime
        type: string
    archiveReason.anyOf:
      description: Restricts items to those with any of the specified archive reasons. Use "NOT_ARCHIVED" to filter for unarchived items. Use "ANY_ARCHIVED" to filter for archived items regardless of reason. Use "ANY_ARCHIVED_OR_NOT_ARCHIVED" to return items for both archived and unarchived. Comma-separated list.
      explode: false
      in: query
      name: archiveReason.anyOf
      schema:
        items:
          type: string
        maxItems: 10
        type: array
    createdAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created before the specified time. e.g. < 2017-04-30.
      in: query
      name: createdAt.lt
      schema:
        format: datetime
        type: string
    id.anyOf:
      description: Restricts results to those matching any of the specified IDs. Comma-separated list.
      explode: false
      in: query
      name: id.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
  securitySchemes:
    BearerAuth:
      description: Use a short-lived V3 API Explorer token.
      scheme: bearer
      type: http
      x-fern-playground-description: Copy a short-lived V3 API Explorer token from the user's settings page
    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: /oauth/token
      type: oauth2