Spaces:
Running
Running
| { | |
| "edges": [ | |
| { | |
| "id": "Import file 2 Query GenMol 1", | |
| "source": "Import file 2", | |
| "sourceHandle": "output", | |
| "target": "Query GenMol 1", | |
| "targetHandle": "bundle" | |
| }, | |
| { | |
| "id": "Import file 1 MSA-search 1", | |
| "source": "Import file 1", | |
| "sourceHandle": "output", | |
| "target": "MSA-search 1", | |
| "targetHandle": "bundle" | |
| }, | |
| { | |
| "id": "Query GenMol 1 Query DiffDock 1", | |
| "source": "Query GenMol 1", | |
| "sourceHandle": "output", | |
| "target": "Query DiffDock 1", | |
| "targetHandle": "ligands" | |
| }, | |
| { | |
| "id": "Query DiffDock 1 View molecules 1", | |
| "source": "Query DiffDock 1", | |
| "sourceHandle": "output", | |
| "target": "View molecules 1", | |
| "targetHandle": "bundle" | |
| }, | |
| { | |
| "id": "MSA-search 1 Query OpenFold2 1", | |
| "source": "MSA-search 1", | |
| "sourceHandle": "output", | |
| "target": "Query OpenFold2 1", | |
| "targetHandle": "bundle" | |
| }, | |
| { | |
| "id": "Query OpenFold2 1 View molecules 3", | |
| "source": "Query OpenFold2 1", | |
| "sourceHandle": "output", | |
| "target": "View molecules 3", | |
| "targetHandle": "bundle" | |
| }, | |
| { | |
| "id": "Query OpenFold2 1 Query DiffDock 1", | |
| "source": "Query OpenFold2 1", | |
| "sourceHandle": "output", | |
| "target": "Query DiffDock 1", | |
| "targetHandle": "proteins" | |
| } | |
| ], | |
| "env": "LynxKite Graph Analytics", | |
| "nodes": [ | |
| { | |
| "data": { | |
| "__execution_delay": 0.0, | |
| "collapsed": null, | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": {}, | |
| "name": "Import file", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "file_format": { | |
| "default": "csv", | |
| "groups": { | |
| "csv": [ | |
| { | |
| "default": "<from file>", | |
| "name": "columns", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| { | |
| "default": "<auto>", | |
| "name": "separator", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| ], | |
| "excel": [ | |
| { | |
| "default": "Sheet1", | |
| "name": "sheet_name", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| ], | |
| "json": [], | |
| "parquet": [] | |
| }, | |
| "name": "file_format", | |
| "selector": { | |
| "default": "csv", | |
| "name": "file_format", | |
| "type": { | |
| "enum": [ | |
| "csv", | |
| "parquet", | |
| "json", | |
| "excel" | |
| ] | |
| } | |
| }, | |
| "type": "group" | |
| }, | |
| "file_path": { | |
| "default": null, | |
| "name": "file_path", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "table_name": { | |
| "default": null, | |
| "name": "table_name", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "columns": "<from file>", | |
| "file_format": "csv", | |
| "file_path": "uploads/protein.csv", | |
| "separator": "<auto>", | |
| "table_name": "" | |
| }, | |
| "status": "done", | |
| "title": "Import file" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 487.0, | |
| "id": "Import file 1", | |
| "position": { | |
| "x": -755.0582906538923, | |
| "y": 543.770372030674 | |
| }, | |
| "type": "basic", | |
| "width": 439.0 | |
| }, | |
| { | |
| "data": { | |
| "__execution_delay": 0.0, | |
| "collapsed": null, | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": {}, | |
| "name": "Import file", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "file_format": { | |
| "default": "csv", | |
| "groups": { | |
| "csv": [ | |
| { | |
| "default": "<from file>", | |
| "name": "columns", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| { | |
| "default": "<auto>", | |
| "name": "separator", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| ], | |
| "excel": [ | |
| { | |
| "default": "Sheet1", | |
| "name": "sheet_name", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| ], | |
| "json": [], | |
| "parquet": [] | |
| }, | |
| "name": "file_format", | |
| "selector": { | |
| "default": "csv", | |
| "name": "file_format", | |
| "type": { | |
| "enum": [ | |
| "csv", | |
| "parquet", | |
| "json", | |
| "excel" | |
| ] | |
| } | |
| }, | |
| "type": "group" | |
| }, | |
| "file_path": { | |
| "default": null, | |
| "name": "file_path", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "table_name": { | |
| "default": null, | |
| "name": "table_name", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "columns": "<from file>", | |
| "file_format": "csv", | |
| "file_path": "uploads/molecules.csv", | |
| "separator": "<auto>", | |
| "table_name": null | |
| }, | |
| "status": "done", | |
| "title": "Import file" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 436.0, | |
| "id": "Import file 2", | |
| "position": { | |
| "x": 62.887657256500006, | |
| "y": 1380.6697994924546 | |
| }, | |
| "type": "basic", | |
| "width": 311.0 | |
| }, | |
| { | |
| "data": { | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "bundle": { | |
| "name": "bundle", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "Query GenMol", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "molecule_column": { | |
| "default": null, | |
| "name": "molecule_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "molecule_table": { | |
| "default": null, | |
| "name": "molecule_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "noise": { | |
| "default": 0.2, | |
| "name": "noise", | |
| "type": { | |
| "type": "<class 'float'>" | |
| } | |
| }, | |
| "num_molecules": { | |
| "default": 5.0, | |
| "name": "num_molecules", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| }, | |
| "scoring": { | |
| "default": "QED", | |
| "name": "scoring", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "step_size": { | |
| "default": 4.0, | |
| "name": "step_size", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| }, | |
| "temperature": { | |
| "default": 1.0, | |
| "name": "temperature", | |
| "type": { | |
| "type": "<class 'float'>" | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 594.0, | |
| "y": 633.0 | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "molecule_column": null, | |
| "molecule_table": null, | |
| "noise": 0.2, | |
| "num_molecules": 5.0, | |
| "scoring": "QED", | |
| "step_size": 4.0, | |
| "temperature": 1.0 | |
| }, | |
| "status": "done", | |
| "title": "Query GenMol" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 601.0, | |
| "id": "Query GenMol 1", | |
| "position": { | |
| "x": 663.3333333333335, | |
| "y": 1283.3333333333335 | |
| }, | |
| "type": "basic", | |
| "width": 358.0 | |
| }, | |
| { | |
| "data": { | |
| "collapsed": null, | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "bundle": { | |
| "name": "bundle", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "MSA-search", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "databases": { | |
| "default": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]", | |
| "name": "databases", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "e_value": { | |
| "default": 0.0001, | |
| "name": "e_value", | |
| "type": { | |
| "type": "<class 'float'>" | |
| } | |
| }, | |
| "iterations": { | |
| "default": 1.0, | |
| "name": "iterations", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| }, | |
| "output_alignment_formats": { | |
| "default": [ | |
| "fasta", | |
| "a3m" | |
| ], | |
| "name": "output_alignment_formats", | |
| "type": { | |
| "type": "list[lynxkite_bio.nims.AlignmentFormats]" | |
| } | |
| }, | |
| "protein_column": { | |
| "default": null, | |
| "name": "protein_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "protein_table": { | |
| "default": null, | |
| "name": "protein_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "search_type": { | |
| "default": "ALPHAFOLD2", | |
| "name": "search_type", | |
| "type": { | |
| "enum": [ | |
| "ALPHAFOLD2", | |
| "ESM2" | |
| ] | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 576.0, | |
| "y": 228.0 | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "databases": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]", | |
| "e_value": 0.0001, | |
| "iterations": 1.0, | |
| "output_alignment_formats": [ | |
| "fasta", | |
| "a3m" | |
| ], | |
| "protein_column": null, | |
| "protein_table": null, | |
| "search_type": "ALPHAFOLD2" | |
| }, | |
| "status": "done", | |
| "title": "MSA-search" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 550.0, | |
| "id": "MSA-search 1", | |
| "position": { | |
| "x": -45.0, | |
| "y": 570.0 | |
| }, | |
| "type": "basic", | |
| "width": 531.0 | |
| }, | |
| { | |
| "data": { | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "ligands": { | |
| "name": "ligands", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| }, | |
| "proteins": { | |
| "name": "proteins", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "Query DiffDock", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "ligand_column": { | |
| "default": null, | |
| "name": "ligand_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "ligand_table": { | |
| "default": null, | |
| "name": "ligand_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "num_poses": { | |
| "default": 10.0, | |
| "name": "num_poses", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| }, | |
| "num_steps": { | |
| "default": 18.0, | |
| "name": "num_steps", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| }, | |
| "protein_column": { | |
| "default": null, | |
| "name": "protein_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "protein_table": { | |
| "default": null, | |
| "name": "protein_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "time_divisions": { | |
| "default": 20.0, | |
| "name": "time_divisions", | |
| "type": { | |
| "type": "<class 'int'>" | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 852.0, | |
| "y": 432.0 | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "ligand_column": null, | |
| "ligand_table": null, | |
| "num_poses": 10.0, | |
| "num_steps": 18.0, | |
| "protein_column": null, | |
| "protein_table": null, | |
| "time_divisions": 20.0 | |
| }, | |
| "status": "done", | |
| "title": "Query DiffDock" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 635.0, | |
| "id": "Query DiffDock 1", | |
| "position": { | |
| "x": 1543.010053920781, | |
| "y": 1167.386382170133 | |
| }, | |
| "type": "basic", | |
| "width": 408.0 | |
| }, | |
| { | |
| "data": { | |
| "display": { | |
| "series": [ | |
| { | |
| "data": [ | |
| { | |
| "name": "Hydrogen", | |
| "value": 2 | |
| }, | |
| { | |
| "name": "Sulfur", | |
| "value": 1 | |
| }, | |
| { | |
| "name": "Oxygen", | |
| "value": 4 | |
| } | |
| ], | |
| "itemStyle": { | |
| "borderColor": "#fff", | |
| "borderRadius": 10, | |
| "borderWidth": 2 | |
| }, | |
| "radius": [ | |
| "40%", | |
| "70%" | |
| ], | |
| "type": "pie" | |
| } | |
| ] | |
| }, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "bundle": { | |
| "name": "bundle", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "View molecules", | |
| "outputs": {}, | |
| "params": { | |
| "color": { | |
| "default": "spectrum", | |
| "name": "color", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "molecule_column": { | |
| "default": null, | |
| "name": "molecule_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "molecule_table": { | |
| "default": null, | |
| "name": "molecule_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 1009.0, | |
| "y": 124.0 | |
| }, | |
| "type": "visualization" | |
| }, | |
| "params": { | |
| "color": "spectrum", | |
| "molecule_column": null, | |
| "molecule_table": null | |
| }, | |
| "status": "done", | |
| "title": "View molecules" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 200.0, | |
| "id": "View molecules 3", | |
| "position": { | |
| "x": 1545.0, | |
| "y": 585.0 | |
| }, | |
| "type": "visualization", | |
| "width": 200.0 | |
| }, | |
| { | |
| "data": { | |
| "display": { | |
| "series": [ | |
| { | |
| "data": [ | |
| { | |
| "name": "Hydrogen", | |
| "value": 2 | |
| }, | |
| { | |
| "name": "Sulfur", | |
| "value": 1 | |
| }, | |
| { | |
| "name": "Oxygen", | |
| "value": 4 | |
| } | |
| ], | |
| "itemStyle": { | |
| "borderColor": "#fff", | |
| "borderRadius": 10, | |
| "borderWidth": 2 | |
| }, | |
| "radius": [ | |
| "40%", | |
| "70%" | |
| ], | |
| "type": "pie" | |
| } | |
| ] | |
| }, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "bundle": { | |
| "name": "bundle", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "View molecules", | |
| "outputs": {}, | |
| "params": { | |
| "color": { | |
| "default": "spectrum", | |
| "name": "color", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "molecule_column": { | |
| "default": null, | |
| "name": "molecule_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "molecule_table": { | |
| "default": null, | |
| "name": "molecule_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 859.0, | |
| "y": 225.0 | |
| }, | |
| "type": "visualization" | |
| }, | |
| "params": { | |
| "color": "spectrum", | |
| "molecule_column": null, | |
| "molecule_table": null | |
| }, | |
| "status": "done", | |
| "title": "View molecules" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 200.0, | |
| "id": "View molecules 1", | |
| "position": { | |
| "x": 2230.0, | |
| "y": 1598.3333333333333 | |
| }, | |
| "type": "visualization", | |
| "width": 200.0 | |
| }, | |
| { | |
| "data": { | |
| "display": null, | |
| "error": null, | |
| "meta": { | |
| "inputs": { | |
| "bundle": { | |
| "name": "bundle", | |
| "position": "left", | |
| "type": { | |
| "type": "<class 'lynxkite_graph_analytics.core.Bundle'>" | |
| } | |
| } | |
| }, | |
| "name": "Query OpenFold2", | |
| "outputs": { | |
| "output": { | |
| "name": "output", | |
| "position": "right", | |
| "type": { | |
| "type": "None" | |
| } | |
| } | |
| }, | |
| "params": { | |
| "alignment_column": { | |
| "default": null, | |
| "name": "alignment_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "alignment_table": { | |
| "default": null, | |
| "name": "alignment_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "databases": { | |
| "default": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]", | |
| "name": "databases", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "protein_column": { | |
| "default": null, | |
| "name": "protein_column", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "protein_table": { | |
| "default": null, | |
| "name": "protein_table", | |
| "type": { | |
| "type": "<class 'str'>" | |
| } | |
| }, | |
| "relaxed_prediction": { | |
| "default": false, | |
| "name": "relaxed_prediction", | |
| "type": { | |
| "type": "<class 'bool'>" | |
| } | |
| }, | |
| "use_templates": { | |
| "default": false, | |
| "name": "use_templates", | |
| "type": { | |
| "type": "<class 'bool'>" | |
| } | |
| } | |
| }, | |
| "position": { | |
| "x": 628.0, | |
| "y": 184.0 | |
| }, | |
| "type": "basic" | |
| }, | |
| "params": { | |
| "alignment_column": null, | |
| "alignment_table": null, | |
| "databases": "[\"Uniref30_2302\", \"colabfold_envdb_202108\", \"PDB70_220313\"]", | |
| "protein_column": null, | |
| "protein_table": null, | |
| "relaxed_prediction": false, | |
| "use_templates": false | |
| }, | |
| "status": "done", | |
| "title": "Query OpenFold2" | |
| }, | |
| "dragHandle": ".bg-primary", | |
| "height": 653.0, | |
| "id": "Query OpenFold2 1", | |
| "position": { | |
| "x": 750.0, | |
| "y": 480.0 | |
| }, | |
| "type": "basic", | |
| "width": 523.0 | |
| } | |
| ] | |
| } | |