{ "opencollection": "1.0.0", "info": { "name": "ModelServer General API", "version": "0.9.12" }, "items": [ { "info": { "name": "General", "type": "folder" }, "items": [ { "info": { "name": "Computes structural assembly.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/:id/assembly", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "name", "value": "", "type": "query", "description": "Assembly name." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). 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Will force download if specified." } ] }, "docs": "Computes structural assembly." }, { "info": { "name": "Computes structural assembly.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/:id/assembly", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. 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Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ] }, "docs": "Atoms satisfying the given criteria." }, { "info": { "name": "Atoms satisfying the given criteria.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/:id/atoms", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ], "body": { "type": "json", "data": "{}" } }, "docs": "Atoms satisfying the given criteria." }, { "info": { "name": "The full structure.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/:id/full", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ] }, "docs": "The full structure." }, { "info": { "name": "The full structure.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/:id/full", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ], "body": { "type": "json", "data": "{}" } }, "docs": "The full structure." }, { "info": { "name": "Coordinates of the first group satisfying the given criteria.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/:id/ligand", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "label_entity_id", "value": "", "type": "query" }, { "name": "label_asym_id", "value": "", "type": "query" }, { "name": "auth_asym_id", "value": "", "type": "query" }, { "name": "label_comp_id", "value": "", "type": "query" }, { "name": "auth_comp_id", "value": "", "type": "query" }, { "name": "label_seq_id", "value": "", "type": "query" }, { "name": "auth_seq_id", "value": "", "type": "query" }, { "name": "pdbx_PDB_ins_code", "value": "", "type": "query" }, { "name": "label_atom_id", "value": "", "type": "query" }, { "name": "auth_atom_id", "value": "", "type": "query" }, { "name": "type_symbol", "value": "", "type": "query" }, { "name": "model_nums", "value": "", "type": "query", "description": "A comma-separated list of model ids (i.e. 1,2). 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Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ], "body": { "type": "json", "data": "{}" } }, "docs": "Identifies all residues within the given radius from the source residue." }, { "info": { "name": "Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/:id/surroundingLigands", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "label_entity_id", "value": "", "type": "query" }, { "name": "label_asym_id", "value": "", "type": "query" }, { "name": "auth_asym_id", "value": "", "type": "query" }, { "name": "label_comp_id", "value": "", "type": "query" }, { "name": "auth_comp_id", "value": "", "type": "query" }, { "name": "label_seq_id", "value": "", "type": "query" }, { "name": "auth_seq_id", "value": "", "type": "query" }, { "name": "pdbx_PDB_ins_code", "value": "", "type": "query" }, { "name": "label_atom_id", "value": "", "type": "query" }, { "name": "auth_atom_id", "value": "", "type": "query" }, { "name": "type_symbol", "value": "", "type": "query" }, { "name": "radius", "value": "", "type": "query", "description": "Value in Angstroms." }, { "name": "omit_water", "value": "", "type": "query" }, { "name": "assembly_name", "value": "", "type": "query", "description": "Assembly name. 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Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ] }, "docs": "Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account." }, { "info": { "name": "Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/:id/surroundingLigands", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "query", "description": "A comma-separated list of model ids (i.e. 1,2). 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Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ], "body": { "type": "json", "data": "{}" } }, "docs": "Identifies (complete) ligands within the given radius from the source atom set. Takes crystal symmetry into account." }, { "info": { "name": "Computes crystal symmetry mates within the specified radius.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/:id/symmetryMates", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "radius", "value": "", "type": "query", "description": "Value in Angstroms." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ] }, "docs": "Computes crystal symmetry mates within the specified radius." }, { "info": { "name": "Computes crystal symmetry mates within the specified radius.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/:id/symmetryMates", "params": [ { "name": "id", "value": "", "type": "path", "description": "Id of the entry (i.e. 1tqn)." }, { "name": "model_nums", "value": "", "type": "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." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines the output encoding (text based 'CIF' or binary 'BCIF'). Ligands can also be exported as 'SDF', 'MOL', or 'MOL2'." }, { "name": "copy_all_categories", "value": "", "type": "query", "description": "If true, copy all categories from the input file." }, { "name": "data_source", "value": "", "type": "query", "description": "Allows to control how the provided data source ID maps to input file (as specified by the server instance config)." }, { "name": "transform", "value": "", "type": "query", "description": "Transformation to apply to coordinates in '_atom_site'. Accepts a 4x4 transformation matrix, provided as array of 16 float values." }, { "name": "download", "value": "", "type": "query", "description": "If true, browser will download text files." }, { "name": "filename", "value": "", "type": "query", "description": "Controls the filename for downloaded files. Will force download if specified." } ], "body": { "type": "json", "data": "{}" } }, "docs": "Computes crystal symmetry mates within the specified radius." }, { "info": { "name": "Executes multiple queries at the same time and writes them as separate data blocks.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/v1/query-many", "params": [ { "name": "query", "value": "{\"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}", "type": "query", "description": "URI encoded JSON object with the query definiton." } ] }, "docs": "Executes multiple queries at the same time and writes them as separate data blocks." }, { "info": { "name": "Executes multiple queries at the same time and writes them as separate data blocks.", "type": "http" }, "http": { "method": "POST", "url": "{{baseUrl}}/v1/query-many", "body": { "type": "json", "data": "{}" } }, "docs": "Executes multiple queries at the same time and writes them as separate data blocks." }, { "info": { "name": "Returns a JSON response specifying if data is available and the maximum region that can be queried.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/:source/:id/", "params": [ { "name": "source", "value": "", "type": "path", "description": "Specifies the data source (determined by the experiment method). Currently supported sources are: x-ray, em." }, { "name": "id", "value": "", "type": "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)." } ] }, "docs": "Returns a JSON response specifying if data is available and the maximum region that can be queried." }, { "info": { "name": "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.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/:source/:id/box/:a1,a2,a3/:b1,b2,b3/", "params": [ { "name": "source", "value": "", "type": "path", "description": "Specifies the data source (determined by the experiment method). Currently supported sources are: x-ray, em." }, { "name": "id", "value": "", "type": "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)." }, { "name": "bottomLeftCorner", "value": "", "type": "path", "description": "Bottom left corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter)." }, { "name": "topRightCorner", "value": "", "type": "path", "description": "Top right corner of the query region in Cartesian or fractional coordinates (determined by the `space` query parameter)." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding." }, { "name": "detail", "value": "", "type": "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." }, { "name": "space", "value": "", "type": "query", "description": "Determines the coordinate space the query is in. Can be cartesian or fractional. An optional argument, default values is cartesian." } ] }, "docs": "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." }, { "info": { "name": "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.", "type": "http" }, "http": { "method": "GET", "url": "{{baseUrl}}/:source/:id/cell/", "params": [ { "name": "source", "value": "", "type": "path", "description": "Specifies the data source (determined by the experiment method). Currently supported sources are: x-ray, em." }, { "name": "id", "value": "", "type": "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)." }, { "name": "encoding", "value": "", "type": "query", "description": "Determines if text based CIF or binary BinaryCIF encoding is used. An optional argument, default is BinaryCIF encoding." }, { "name": "detail", "value": "", "type": "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." } ] }, "docs": "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." } ] } ], "bundled": true }