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