> ## Documentation Index > Fetch the complete documentation index at: https://docs.biohub.ai/llms.txt > Use this file to discover all available pages before exploring further. # encode > (ESM3, ESMC) Tokenize sequence, structure, or function annotations ## OpenAPI ````yaml openapi/biohub-platform-openapi.json POST /api/v1/encode openapi: 3.1.0 info: title: Biohub Platform API version: 1.0.0 servers: - url: https://biohub.ai security: [] paths: /api/v1/encode: post: tags: - v1 summary: (ESM3, ESMC) Tokenize sequence, structure, or function annotations operationId: encode_api_v1_encode_post parameters: - name: accept in: header required: false schema: anyOf: - type: string - type: 'null' title: Accept requestBody: content: application/json: schema: $ref: '#/components/schemas/EncodeRequest' required: true responses: '200': description: Successful Response content: application/json: schema: $ref: '#/components/schemas/EncodeResponse' application/vnd.evolutionaryscale.pickle: schema: type: string format: binary '422': description: Validation Error content: application/json: schema: $ref: '#/components/schemas/HTTPValidationError' security: - HTTPBearer: [] components: schemas: EncodeRequest: properties: model: type: string enum: - esm3-open-2024-03 - esmc-300m-2024-12 - esmc-600m-2024-12 - esmc-6b-2024-12 description: >- You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console potential_sequence_of_concern: type: boolean description: >- Disclose potential sequences of concern. For approved users, such sequences will not go through additional safety filtering. Reach out if you are interested in using this. default: false inputs: $ref: '#/components/schemas/Tracks' type: object required: - model - inputs EncodeResponse: properties: model: type: string enum: - esm3-open-2024-03 - esmc-300m-2024-12 - esmc-600m-2024-12 - esmc-6b-2024-12 description: >- You may have access to additional, private models as well. These will be visible on the Rate Limits page under the Developer Console created: type: string description: ISO formatted date time potential_sequence_of_concern: type: boolean description: Indicate that the returned sequence may be of potential concerns. default: false warning_messages: anyOf: - items: type: string type: array - type: 'null' description: Warning messages returned by FastAPI. outputs: $ref: '#/components/schemas/Tokens' type: object required: - model - created - tokens_used - outputs HTTPValidationError: properties: detail: items: $ref: '#/components/schemas/ValidationError' type: array type: object Tracks: properties: sequence: anyOf: - type: string - type: 'null' description: >- Sequence of amino acids. As input, this can be partially masked out with `_`, for example to get logprob over masked positions secondary_structure: anyOf: - type: string - type: 'null' description: Secondary structure in 8-class DSSP format. sasa: anyOf: - items: anyOf: - type: integer - type: number - type: 'null' type: array - type: 'null' description: >- Solvent accessible surface area (SASA) as a list of floats. Nones are replaced with padding. 03/18/2025: A bug was fixed where 'inf' prior to this date was returned encoded as '-1', it will instead be 1000 going forward function: anyOf: - items: prefixItems: - type: string - type: integer - type: integer type: array maxItems: 3 minItems: 3 type: array - type: 'null' description: >- Function annotations, as a list of 3-tuples: (interpro tag, start, end). Start and end are 1-indexed, inclusive. We support interpro tags from version 95.0. coordinates: anyOf: - items: items: items: anyOf: - type: number - type: 'null' type: array type: array type: array - type: 'null' description: Coordinates of the N, CA, C atom sequence as a Nx37x3 array. plddt: anyOf: - items: type: number type: array - type: 'null' description: >- Per position plddt predictions for a protein. Usually produced by structure decoder. ptm: anyOf: - type: number - type: 'null' description: >- Predicted TM score of a protein. Usually produced by structure decoder. crmsd: anyOf: - type: number - type: 'null' description: >- Constrained RMSD between the generated protein coordinates and the input protein coordinates. Produced by the generate endpoint. globularity: anyOf: - type: number - type: 'null' description: >- Globularity of the generated protein. Produced by the generate endpoint. interface: anyOf: - items: type: string type: array - type: 'null' description: Annotations on residues that participate in a multimer interface. interface_ptm: anyOf: - type: number - type: 'null' description: Interface TM score of a protein. pae: anyOf: - items: items: type: number type: array type: array - type: 'null' description: >- Predicted Aligned Error matrix for the protein. Shape is L x L. Values are rounded to 2 decimals (well within 0.5 A bin width) type: object Tokens: properties: sequence: anyOf: - items: type: integer type: array - type: 'null' description: Sequence as a list of tokens as integers. coordinates: anyOf: - items: items: items: anyOf: - type: number - type: 'null' type: array type: array type: array - type: 'null' description: Coordinates of the N, CA, C atom sequence as a Nx37x3 array. structure: anyOf: - items: type: integer type: array - type: 'null' description: Structure output from the model as a list of integer tokens. secondary_structure: anyOf: - items: type: integer type: array - type: 'null' description: Secondary structure in 8-class DSSP format. sasa: anyOf: - items: anyOf: - type: integer - type: 'null' type: array - type: 'null' description: Solvent accessible surface area (SASA) as a list of integers. function: anyOf: - items: items: type: integer type: array type: array - type: 'null' description: Function annotations, as a list of integers. residue_annotation: anyOf: - items: items: type: integer type: array type: array - type: 'null' description: Residue annotations tokens, as a list of integers. type: object ValidationError: properties: loc: items: anyOf: - type: string - type: integer type: array msg: type: string type: type: string input: {} ctx: type: object type: object required: - loc - msg - type securitySchemes: HTTPBearer: type: http scheme: bearer ````