openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences Monomers 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: Monomers are chemical building blocks with specified structures used to compose modified nucleotides. Note that monomer write endpoints require tenant admin permissions.
  name: Monomers
paths:
  /monomers:
    get:
      description: List all available monomers
      operationId: listMonomers
      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
      - 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: monomers.id,monomers.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MonomersPaginatedList'
          description: OK
      summary: List Monomers
      tags:
      - Monomers
    post:
      description: Create a monomer.
      operationId: createMonomer
      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: monomers.id,monomers.symbol
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MonomerCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Monomer'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ForbiddenError'
          description: Forbidden
      summary: Create a monomer
      tags:
      - Monomers
  /monomers/{monomer_id}:
    patch:
      description: Update a Monomer.
      operationId: updateMonomer
      parameters:
      - in: path
        name: monomer_id
        required: true
        schema:
          type: string
      - 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: id, modifiedAt
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MonomerUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Monomer'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ForbiddenError'
          description: Forbidden
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Update a Monomer
      tags:
      - Monomers
  /monomers:archive:
    post:
      description: Archive Monomers.
      operationId: archiveMonomers
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MonomersArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MonomersArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive Monomers
      tags:
      - Monomers
  /monomers:unarchive:
    post:
      description: Unarchive Monomers.
      operationId: unarchiveMonomers
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MonomersUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MonomersArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive Monomers
      tags:
      - Monomers
components:
  schemas:
    MonomerType:
      description: The part of the nucleotide structure that the monomer fits into, i.e. backbone or branch
      enum:
      - BACKBONE
      - BRANCH
      type: string
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    ForbiddenError:
      properties:
        error:
          properties:
            invalidId:
              type: string
            message:
              type: string
            type:
              type: string
            userMessage:
              type: string
          type: object
      type: object
    MonomerBaseRequest:
      properties:
        color:
          description: The hex color code of the monomer visual symbol
          example: '#7051FC'
          nullable: true
          type: string
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated molecular weight
          example: 119.422
          nullable: true
          type: number
        name:
          description: Name of the monomer
          example: (Rp)-Phosphorothioate
          type: string
        smiles:
          description: The chemical structure in SMILES format.
          example: O[P@@](=S)([OH:1])[OH:2]
          type: string
        symbol:
          description: User-defined identifier of the monomer, unique on the monomer type.
          example: Rsp
          type: string
        visualSymbol:
          allOf:
          - $ref: '#/components/schemas/MonomerVisualSymbol'
      type: object
    NotFoundError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              invalidId:
                type: string
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    MonomersUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving Monomers.

        '
      properties:
        monomerIds:
          items:
            type: string
          maxItems: 100
          type: array
      required:
      - monomerIds
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    MonomersArchivalChange:
      additionalProperties: false
      description: 'IDs of all items that were archived or unarchived, grouped by resource type.

        '
      properties:
        batchIds:
          items:
            type: string
          type: array
        monomerIds:
          items:
            type: string
          type: array
      type: object
    MonomersArchive:
      additionalProperties: false
      description: 'The request body for archiving Monomers.

        '
      properties:
        monomerIds:
          items:
            type: string
          maxItems: 100
          type: array
        reason:
          description: 'The reason for archiving the provided Monomers. Accepted reasons may differ based on tenant configuration.

            '
          enum:
          - Made in error
          - Archived
          - Other
          type: string
      required:
      - reason
      - monomerIds
      type: object
    Pagination:
      properties:
        nextToken:
          type: string
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    MonomersPaginatedList:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          monomers:
            items:
              $ref: '#/components/schemas/Monomer'
            type: array
          nextToken:
            type: string
    Monomer:
      properties:
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        attachmentPoints:
          description: A list of the capping group present at each location where the monomer can form a bond with other monomers
          example:
          - OH
          - OH
          items:
            type: string
          type: array
        calculatedMolecularWeight:
          description: The molecular weight of the monomer as calculated by RDKit based on the monomer chemical structure
          example: 120.422
          type: number
        canonicalSmiles:
          description: The canonicalized chemical structure in SMILES format.
          example: O[P@@](=S)([OH:1])[OH:2]
          type: string
        createdAt:
          description: DateTime the monomer was created.
          format: date-time
          readOnly: true
          type: string
        customMolecularWeight:
          description: Optional molecular weight value that the user can provide to override the calculated molecular weight
          example: 119.422
          nullable: true
          type: number
        exactMolecularWeight:
          description: The exact molecular weight of the monomer as calculated by RDKit based on the monomer chemical structure
          example: 119.422
          type: number
        id:
          description: ID of the monomer
          example: mon_bhuDUw9D
          type: string
        modifiedAt:
          description: DateTime the monomer was last modified.
          format: date-time
          readOnly: true
          type: string
        monomerType:
          allOf:
          - $ref: '#/components/schemas/MonomerType'
        name:
          description: Name of the monomer
          example: (Rp)-Phosphorothioate
          type: string
        naturalAnalog:
          description: Symbol for the natural equivalent of the monomer. Acceptable natural analog values include IUPAC bases, r, and p.
          example: T
          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: O[P@@](=S)([OH:1])[OH:2]
          nullable: true
          type: string
        polymerType:
          allOf:
          - $ref: '#/components/schemas/MonomerPolymerType'
        symbol:
          description: User-defined identifier of the monomer, unique on the monomer type.
          example: Rsp
          type: string
        visualColor:
          description: The hex color code of the monomer visual symbol
          example: '#7051FC'
          nullable: true
          type: string
        visualSymbol:
          allOf:
          - $ref: '#/components/schemas/MonomerVisualSymbol'
          nullable: true
      type: object
    MonomerPolymerType:
      description: The polymer type of the monomer. Currently only RNA monomers are supported.
      enum:
      - RNA
      type: string
    MonomerVisualSymbol:
      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_P
      - LETTERS_PS
      type: string
    MonomerCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/MonomerBaseRequest'
      - properties:
          naturalAnalog:
            description: Symbol for the natural equivalent of the monomer. Acceptable natural analog values include IUPAC bases, r, and p.
            example: T
            type: string
      - required:
        - smiles
        - name
        - naturalAnalog
        - symbol
    MonomerUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/MonomerBaseRequest'
  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