bio_tools 0.1.1

Install, run, and inspect computational biology and chemistry tools, e.g. AlphaFold, Boltz, RFdiffusion, and ProteinMPNN
Documentation 
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{
  "fields": [
    {
      "name": "job_name",
      "label": "Job name",
      "kind": "text",
      "default": "aggrescan3d-demo",
      "required": false,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "pdb",
      "label": "Protein PDB",
      "kind": "file",
      "default": "HEADER    PASTE A PROTEIN PDB HERE",
      "required": true,
      "help": "",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": ".pdb,.ent",
      "task": ""
    },
    {
      "name": "chain",
      "label": "Chain (optional)",
      "kind": "text",
      "default": "",
      "required": false,
      "help": "Restrict the analysis to one chain. Empty analyses the whole structure.",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": 4,
      "accept": "",
      "task": ""
    },
    {
      "name": "distance",
      "label": "Aggregation sphere radius (angstroms)",
      "kind": "number",
      "default": 10.0,
      "required": false,
      "help": "Residues within this radius of each alpha carbon contribute to its score.",
      "options": [],
      "rows": null,
      "minimum": 1.0,
      "maximum": 20.0,
      "step": 0.5,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "dynamic",
      "label": "Score over a CABS-flex ensemble",
      "kind": "checkbox",
      "default": false,
      "required": false,
      "help": "Much slower, but accounts for flexibility instead of scoring one conformation.",
      "options": [],
      "rows": null,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "mutate",
      "label": "Mutations to score (optional)",
      "kind": "textarea",
      "default": "",
      "required": false,
      "help": "One per line, as wild-type residue, mutant residue, position, and chain, for example MW1A. Needs FoldX.",
      "options": [],
      "rows": 3,
      "minimum": null,
      "maximum": null,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    },
    {
      "name": "auto_mutation",
      "label": "Solubility mutations to suggest",
      "kind": "number",
      "default": 0,
      "required": false,
      "help": "Ask A3D to propose this many stability-aware solubility mutations. 0 skips the search. Needs FoldX.",
      "options": [],
      "rows": null,
      "minimum": 0,
      "maximum": 10,
      "step": null,
      "maxlength": null,
      "accept": "",
      "task": ""
    }
  ],
  "tasks": []
}