Benchling Nucleotide Monomer API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Nucleotide Monomer API
  version: 2.0.0
  description: 'A building block component of modified oligonucleotides, representing a sugar, phosphate,

    or base subunit. Monomers are the chemical units that assemble to form nucleotides in

    therapeutic oligonucleotide design. Each monomer has a symbol identifier, chemical structure

    (SMILES), molecular weight, and attachment points defining where it bonds to other monomers.

    The naturalAnalog field links modified monomers to their natural counterparts (e.g., a

    2''-O-methyl ribose analog links to natural ribose ''r''). Monomers are referenced in

    ModifiedNucleotide and CustomNotationAlias to specify the exact chemistry of modified

    sequences. Also known as building blocks in oligonucleotide synthesis contexts.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: 'A building block component of modified oligonucleotides, representing a sugar, phosphate,

    or base subunit. Monomers are the chemical units that assemble to form nucleotides in

    therapeutic oligonucleotide design. Each monomer has a symbol identifier, chemical structure

    (SMILES), molecular weight, and attachment points defining where it bonds to other monomers.

    The naturalAnalog field links modified monomers to their natural counterparts (e.g., a

    2''-O-methyl ribose analog links to natural ribose ''r''). Monomers are referenced in

    ModifiedNucleotide and CustomNotationAlias to specify the exact chemistry of modified

    sequences. Also known as building blocks in oligonucleotide synthesis contexts.'
  name: NucleotideMonomer
  x-bnch-organization: Benchling
paths:
  /nucleotide-monomer/items:
    get:
      description: List NucleotideMonomer items.
      operationId: NucleotideMonomer.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/NucleotideMonomerPaginatedList'
          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 NucleotideMonomer items
      tags:
      - NucleotideMonomer
      x-bnch-rate-limit-tier: 4
  /nucleotide-monomer/{nucleotide_monomer_id}:
    get:
      description: Get a single NucleotideMonomer by ID.
      operationId: NucleotideMonomer.Get
      parameters:
      - description: ID of the NucleotideMonomer.
        in: path
        name: nucleotide_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/NucleotideMonomer'
          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 NucleotideMonomer by ID
      tags:
      - NucleotideMonomer
      x-bnch-rate-limit-tier: 5
components:
  parameters:
    pageSize:
      description: Number of results to return. Defaults to 50, maximum of 100.
      in: query
      name: pageSize
      schema:
        type: integer
    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
    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
    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
    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
    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.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
    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
    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
    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
    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
    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
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        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
    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
    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
  responses:
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Too Many Requests
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
  schemas:
    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
    NucleotideMonomerPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/NucleotideMonomer'
          type: array
        nextToken:
          type: string
      type: object
    NucleotideMonomer:
      description: 'A building block component of modified oligonucleotides, representing a sugar, phosphate,

        or base subunit. Monomers are the chemical units that assemble to form nucleotides in

        therapeutic oligonucleotide design. Each monomer has a symbol identifier, chemical structure

        (SMILES), molecular weight, and attachment points defining where it bonds to other monomers.

        The naturalAnalog field links modified monomers to their natural counterparts (e.g., a

        2''-O-methyl ribose analog links to natural ribose ''r''). Monomers are referenced in

        ModifiedNucleotide and CustomNotationAlias to specify the exact chemistry of modified

        sequences. Also known as building blocks in oligonucleotide synthesis contexts.'
      properties:
        __typename:
          type: string
        archiveReason:
          type:
          - 'null'
          - string
        archived:
          type: boolean
        attachmentPoints:
          description: A list of the capping group present at each location where the monomer can form a bond with other monomers.
          items:
            type: string
          type: array
        calculatedMolecularWeight:
          description: The molecular weight of the monomer as calculated by RDKit based on the monomer chemical structure.
          type:
          - 'null'
          - number
        canonicalSmiles:
          description: The SMILES representation of the monomer chemical structure after being standardized.
          type: string
        createdAt:
          format: datetime
          type: string
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated molecular weight.
          type:
          - 'null'
          - number
        exactMolecularWeight:
          description: The exact molecular weight of the monomer as calculated by RDKit based on the monomer chemical structure.
          type: number
        id:
          type: string
        modifiedAt:
          format: datetime
          type: string
        monomerType:
          description: The part of the nucleotide structure that the monomer fits into, i.e. backbone or branch.
          enum:
          - BACKBONE
          - BRANCH
          type: string
        name:
          type: string
        naturalAnalog:
          description: 'Natural equivalent of the monomer. For example, a modified ribose would have `r` as the natural analog,

            which is the symbol for natural ribose.'
          enum:
          - A
          - C
          - G
          - T
          - U
          - N
          - r
          - d
          - p
          - R
          - Y
          - M
          - K
          - W
          - S
          - B
          - D
          - H
          - V
          type: string
        originalSmiles:
          description: The SMILES string that was originally provided upon creation of the monomer.
          type:
          - 'null'
          - string
        polymerType:
          description: 'The polymer type of the monomer, per the HELM definition of polymer type. Because nucleotide monomers are only used in

            modified nucleotide sequences, the polymer type of a NucleotideMonomer is always `RNA`.'
          enum:
          - RNA
          type: string
        symbol:
          description: User-defined identifier of the monomer, unique on the monomer type.
          type: string
        visualColor:
          description: The color code of the monomer visual symbol.
          type:
          - 'null'
          - string
        visualSymbol:
          description: The shape of the monomer visual symbol.
          enum:
          - DIAMOND_FILLED
          - DIAMOND_HOLLOW
          - DIAMOND_DASHED
          - STAR_FILLED
          - STAR_HOLLOW
          - TRIANGLE_FILLED
          - TRIANGLE_HOLLOW
          - DYAD_FILLED
          - DYAD_HOLLOW
          - CLOVER_FILLED
          - CLOVER_HOLLOW
          - TRIAD_FILLED
          - TRIAD_HOLLOW
          - RECTANGLE_FILLED
          - RECTANGLE_HOLLOW
          - LETTERS_C
          - LETTERS_CO
          - LETTERS_M
          - LETTERS_MP
          - LETTERS_P
          - LETTERS_PS
          - LETTERS_R
          - LETTERS_RS
          - LETTERS_S
          - LETTERS_SP
          - null
          type:
          - 'null'
          - string
      type: object
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      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: /oauth/token
      type: oauth2