RCSB PDB General API

openapi: 3.0.0
info:
  version: 0.9.12
  title: ModelServer General API
  description: The ModelServer is a service for accessing subsets of macromolecular model data.
tags:
- name: General
paths:
  /v1/{id}/assembly:
    get:
      tags:
      - General
      summary: Computes structural assembly.
      operationId: assembly
      parameters:
      - $ref: '#/components/parameters/id'
      - name: name
        in: query
        description: Assembly name.
        required: false
        schema:
          type: string
          default: '1'
        style: simple
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      responses:
        '200':
          description: Computes structural assembly.
          content:
            text/plain: {}
            application/octet-stream: {}
    post:
      tags:
      - General
      summary: Computes structural assembly.
      operationId: assembly-post
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      requestBody:
        content:
          application/json:
            schema:
              type: object
            example:
              name: '1'
      responses:
        '200':
          description: Computes structural assembly.
          content:
            text/plain: {}
            application/octet-stream: {}
  /v1/{id}/atoms:
    get:
      tags:
      - General
      summary: Atoms satisfying the given criteria.
      operationId: atoms
      parameters:
      - $ref: '#/components/parameters/id'
      - name: label_entity_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: auth_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: pdbx_PDB_ins_code
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: type_symbol
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      responses:
        '200':
          description: Atoms satisfying the given criteria.
          content:
            text/plain: {}
            application/octet-stream: {}
    post:
      tags:
      - General
      summary: Atoms satisfying the given criteria.
      operationId: atoms-post
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      requestBody:
        content:
          application/json:
            schema:
              type: object
            example:
              atom_site:
              - label_seq_id: 30
                label_asym_id: A
              - label_seq_id: 31
                label_asym_id: A
      responses:
        '200':
          description: Atoms satisfying the given criteria.
          content:
            text/plain: {}
            application/octet-stream: {}
  /v1/{id}/full:
    get:
      tags:
      - General
      summary: The full structure.
      operationId: full
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      responses:
        '200':
          description: The full structure.
          content:
            text/plain: {}
            application/octet-stream: {}
    post:
      tags:
      - General
      summary: The full structure.
      operationId: full-post
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      requestBody:
        content:
          application/json:
            schema:
              type: object
            example: {}
      responses:
        '200':
          description: The full structure.
          content:
            text/plain: {}
            application/octet-stream: {}
  /v1/{id}/ligand:
    get:
      tags:
      - General
      summary: Coordinates of the first group satisfying the given criteria.
      operationId: ligand
      parameters:
      - $ref: '#/components/parameters/id'
      - name: label_entity_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: auth_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: pdbx_PDB_ins_code
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: type_symbol
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      responses:
        '200':
          description: Coordinates of the first group satisfying the given criteria.
          content:
            text/plain: {}
            application/octet-stream: {}
    post:
      tags:
      - General
      summary: Coordinates of the first group satisfying the given criteria.
      operationId: ligand-post
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      requestBody:
        content:
          application/json:
            schema:
              type: object
            example:
              atom_site:
              - label_seq_id: 30
                label_asym_id: A
              - label_seq_id: 31
                label_asym_id: A
      responses:
        '200':
          description: Coordinates of the first group satisfying the given criteria.
          content:
            text/plain: {}
            application/octet-stream: {}
  /v1/{id}/residueInteraction:
    get:
      tags:
      - General
      summary: Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.
      operationId: residueInteraction
      parameters:
      - $ref: '#/components/parameters/id'
      - name: label_entity_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: auth_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: pdbx_PDB_ins_code
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: type_symbol
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: radius
        in: query
        description: Value in Angstroms.
        required: false
        schema:
          type: number
          default: 5
        style: simple
      - name: assembly_name
        in: query
        description: Assembly name. If none is provided, crystal symmetry (where available) or deposited model is used.
        required: false
        schema:
          type: string
        style: simple
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      responses:
        '200':
          description: Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.
          content:
            text/plain: {}
            application/octet-stream: {}
    post:
      tags:
      - General
      summary: Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.
      operationId: residueInteraction-post
      parameters:
      - $ref: '#/components/parameters/id'
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
          type: string
          default: ''
        style: simple
      - name: transform
        in: query
        description: Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values.
        required: false
        schema:
          type: string
        style: simple
      - name: download
        in: query
        description: If true, browser will download text files.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: filename
        in: query
        description: Controls the filename for downloaded files. Will force download if specified.
        required: false
        schema:
          type: string
          default: ''
        style: simple
      requestBody:
        content:
          application/json:
            schema:
              type: object
            example:
              atom_site:
              - label_seq_id: 30
                label_asym_id: A
              - label_seq_id: 31
                label_asym_id: A
              radius: 5
      responses:
        '200':
          description: Identifies all residues within the given radius from the source residue. Takes crystal symmetry into account.
          content:
            text/plain: {}
            application/octet-stream: {}
  /v1/{id}/residueSurroundings:
    get:
      tags:
      - General
      summary: Identifies all residues within the given radius from the source residue.
      operationId: residueSurroundings
      parameters:
      - $ref: '#/components/parameters/id'
      - name: label_entity_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_asym_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_comp_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: auth_seq_id
        in: query
        required: false
        schema:
          type: integer
        style: simple
      - name: pdbx_PDB_ins_code
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: label_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: auth_atom_id
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: type_symbol
        in: query
        required: false
        schema:
          type: string
        style: simple
      - name: radius
        in: query
        description: Value in Angstroms.
        required: false
        schema:
          type: number
          default: 5
        style: simple
      - name: model_nums
        in: query
        description: A comma-separated list of model ids (i.e. 1,2). If set, only include atoms with the corresponding '_atom_site.pdbx_PDB_model_num' field.
        required: false
        schema:
          type: string
        style: simple
      - name: encoding
        in: query
        description: Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'.
        required: false
        schema:
          type: string
          enum:
          - cif
          - bcif
          - sdf
          - mol
          - mol2
          default: cif
        style: simple
      - name: copy_all_categories
        in: query
        description: If true, copy all categories from the input file.
        required: false
        schema:
          type: boolean
          default: false
        style: simple
      - name: data_source
        in: query
        description: Allows to control how the provided data source ID maps to input file (as specified by the server instance config).
        required: false
        schema:
       

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# Full source: https://raw.githubusercontent.com/api-evangelist/pdb/refs/heads/main/openapi/pdb-general-api-openapi.yml