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: 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. content: text/plain: {} application/octet-stream: {} post: tags: - General summary: Identifies all residues within the given radius from the source residue. operationId: residueSurroundings-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. content: text/plain: {} application/octet-stream: {} /v1/{id}/surroundingLigands: get: tags: - General summary: Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account. operationId: surroundingLigands 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: omit_water in: query required: false schema: type: boolean default: false 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 (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account. content: text/plain: {} application/octet-stream: {} post: tags: - General summary: Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account. operationId: surroundingLigands-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 (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account. content: text/plain: {} application/octet-stream: {} /v1/{id}/symmetryMates: get: tags: - General summary: Computes crystal symmetry mates within the specified radius. operationId: symmetryMates parameters: - $ref: '#/components/parameters/id' - 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: 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 crystal symmetry mates within the specified radius. content: text/plain: {} application/octet-stream: {} post: tags: - General summary: Computes crystal symmetry mates within the specified radius. operationId: symmetryMates-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: radius: 5 responses: '200': description: Computes crystal symmetry mates within the specified radius. content: text/plain: {} application/octet-stream: {} /v1/query-many: get: tags: - General summary: Executes multiple queries at the same time and writes them as separate data blocks. operationId: query-many parameters: - name: query in: query description: URI encoded JSON object with the query definiton. required: true schema: type: string example: '{"queries":[{"entryId":"1cbs","query":"residueInteraction","params":{"atom_site":[{"label_comp_id":"REA"}],"radius":5}},{"entryId":"1tqn","query":"full","copy_all_categories":true}],"encoding":"cif","asTarGz":false}' style: simple responses: '200': description: Separate CIF data blocks with the result content: text/plain: {} application/octet-stream: {} post: tags: - General summary: Executes multiple queries at the same time and writes them as separate data blocks. operationId: query-many-post parameters: [] requestBody: content: application/json: schema: type: object example: queries: - entryId: 1cbs query: residueInteraction params: atom_site: - label_comp_id: REA radius: 5 - entryId: 1tqn query: full copy_all_categories: true encoding: cif asTarGz: false responses: '200': description: Separate CIF data blocks with the result content: text/plain: {} application/octet-stream: {} /{source}/{id}/: get: tags: - General summary: Returns a JSON response specifying if data is available and the maximum region that can be queried. operationId: getInfo parameters: - $ref: '#/components/parameters/source' - $ref: '#/components/parameters/id_2' responses: '200': description: Volume availability and info content: application/json: schema: $ref: '#/components/schemas/info' /{source}/{id}/box/{a1,a2,a3}/{b1,b2,b3}/: get: tags: - General summary: Returns density data inside the specified box for the given entry. For X-ray data, returns 2Fo-Fc and Fo-Fc volumes in a single response. operationId: getBox parameters: - $ref: '#/components/parameters/source' - $ref: '#/components/parameters/id_2' - name: bottomLeftCorner in: path description: Bottom left corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter). required: true schema: type: list items: type: float style: simple - name: topRightCorner in: path description: Top right corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter). required: true schema: type: list items: type: float style: simple - $ref: '#/components/parameters/encoding' - $ref: '#/components/parameters/detail' - name: space in: query description: Determines the coordinate space the query is in. Can be cartesian or fractional. An optional argument, default values is cartesian. schema: type: string enum: - cartesian - fractional style: form responses: '200': description: Volume box content: text/plain: {} application/octet-stream: {} /{source}/{id}/cell/: get: tags: - General summary: Returns (downsampled) volume data for the entire "data cell". For X-ray data, returns unit cell of 2Fo-Fc and Fo-Fc volumes, for EM data returns everything. operationId: getCell parameters: - $ref: '#/components/parameters/source' - $ref: '#/components/parameters/id_2' - $ref: '#/components/parameters/encoding' - $ref: '#/components/parameters/detail' responses: '200': description: Volume cell content: text/plain: {} application/octet-stream: {} components: parameters: id: name: id in: path description: Id of the entry (i.e. 1tqn). required: true schema: type: string style: simple encoding: name: encoding in: query description: Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding. schema: type: string enum: - cif - bcif style: form detail: name: detail in: query description: 'Determines the maximum number of voxels the query can return. Possible values are in the range from 0 (0.52M voxels) to 6 (25.17M voxels). Default value is 0. Note: different detail levels might lead to the same result.' schema: type: integer style: form id_2: name: id in: path description: Id of the entry. For x-ray, use PDB ID (i.e. 1cbs) and for em use EMDB id (i.e. emd-8116). required: true schema: type: string style: simple source: name: source in: path description: 'Specifies the data source (determined by the experiment method). Currently supported sources are: x-ray, em.' required: true schema: type: string enum: - x-ray - em style: simple schemas: info: properties: formatVersion: type: string description: Format version number axisOrder: type: array items: type: number description: Axis order from the slowest to fastest moving, same as in CCP4 origin: type: array items: type: number description: Origin in fractional coordinates, in axisOrder dimensions: type: array items: type: number description: Dimensions in fractional coordinates, in axisOrder spacegroup: properties: number: type: number size: type: array items: type: number angles: type: array items: type: number isPeriodic: type: boolean description: Determine if the data should be treated as periodic or not. (e.g. X-ray = periodic, EM = not periodic) channels: type: array items: type: string valueType: type: string enum: - float32 - int16 - int8 description: Determines the data type of the values blockSize: type: number description: The value are stored in blockSize^3 cubes sampling: type: array items: properties: byteOffset: type: number rate: type: number description: How many values along each axis were collapsed into 1 valuesInfo: properties: mean: type: number sigma: type: number min: type: number max: type: number sampleCount: type: array items: type: number description: Number of samples along each axis, in axisOrder