naftiko: 1.0.0-alpha2
info:
  label: NVIDIA NIM Biology (BioNeMo)
  description: 'BioNeMo NIMs — protein structure, ligand docking, and molecule generation.'
  tags:
  - NVIDIA
  - NIM
  - BioNeMo
  - Biology
  created: '2026-05-25'
  modified: '2026-05-25'
binds:
- namespace: env
  keys:
    NVIDIA_API_KEY: NVIDIA_API_KEY
capability:
  consumes:
  - type: http
    namespace: biology
    baseUri: https://integrate.api.nvidia.com
    resources:
    - name: alphafold2
      path: /v1/biology/nvidia/alphafold2/predict-structure-from-sequence
      operations:
      - name: predictstructure
        method: POST
        description: Predict Protein Structure
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: body
          in: body
          type: object
          required: true
    - name: diffdock
      path: /v1/biology/mit/diffdock
      operations:
      - name: dockligand
        method: POST
        description: Dock Ligand To Protein
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: body
          in: body
          type: object
          required: true
    - name: molmim
      path: /v1/biology/nvidia/molmim/generate
      operations:
      - name: generatemolecules
        method: POST
        description: Generate Small Molecules
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: body
          in: body
          type: object
          required: true
    authentication:
      type: bearer
      value: '{{env.NVIDIA_API_KEY}}'
      placement: header
  exposes:
  - type: rest
    namespace: biology-rest
    port: 8080
    resources:
    - path: /v1/biology/alphafold2
      name: alphafold2
      operations:
      - method: POST
        name: predictstructure
        description: Predict Protein Structure
        call: biology.predictstructure
        with:
          body: rest.body
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/biology/diffdock
      name: diffdock
      operations:
      - method: POST
        name: dockligand
        description: Dock Ligand To Protein
        call: biology.dockligand
        with:
          body: rest.body
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/biology/molmim
      name: molmim
      operations:
      - method: POST
        name: generatemolecules
        description: Generate Small Molecules
        call: biology.generatemolecules
        with:
          body: rest.body
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: biology-mcp
    port: 9090
    transport: http
    tools:
    - name: nvidia-nim-alphafold
      description: Predict Protein Structure
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: biology.predictstructure
      with:
        body: tools.body
      outputParameters:
      - type: object
        mapping: $.
    - name: nvidia-nim-diffdock
      description: Dock Ligand To Protein
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: biology.dockligand
      with:
        body: tools.body
      outputParameters:
      - type: object
        mapping: $.
    - name: nvidia-nim-molmim
      description: Generate Small Molecules
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: biology.generatemolecules
      with:
        body: tools.body
      outputParameters:
      - type: object
        mapping: $.