{
"fields": [
{
"name": "inputs",
"label": "Inputs (JSON or YAML)",
"kind": "textarea",
"default": "{\n \"design\": {\n \"length\": \"150-150\",\n \"is_non_loopy\": true\n }\n}",
"required": false,
"help": "The path and file name of the JSON or YAML file where you have defined your inference constraints.",
"options": [],
"rows": 18,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inputs",
"input_modes": "text",
"help_note": "Enter the JSON or YAML contents here. Use \"input\": \"uploaded\" to reference the structure upload, or keep a bundled bio-tools://rfd3/ reference from a preset. Enter null with specification overrides for an override-only design."
},
{
"name": "spec_input_file",
"label": "Input structure (uploaded)",
"kind": "file",
"default": "",
"required": false,
"help": "Optional PDB or mmCIF for configurations with \"input\": \"uploaded\".",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": ".pdb,.cif,.ent",
"task": "",
"group": "Inputs",
"input_modes": "text,upload"
},
{
"name": "inputs_file",
"label": "Inputs file (JSON or YAML)",
"kind": "file",
"default": "",
"required": false,
"help": "The path and file name of the JSON or YAML file where you have defined your inference constraints.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": ".json,.yaml,.yml",
"task": "",
"group": "Inputs",
"input_modes": "upload",
"help_note": "Choose a JSON or YAML file. Use \"input\": \"uploaded\" to reference the structure upload, or keep a bundled bio-tools://rfd3/ reference from a preset."
},
{
"name": "input",
"label": "Input structure",
"kind": "file",
"default": "",
"required": false,
"help": "Path to and file name of PDB/CIF. Required if you provide contig+length.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": ".pdb,.cif,.ent",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters",
"help_note": "Choose a PDB or mmCIF file. Presets include their input structures; a new upload replaces the included file."
},
{
"name": "contig",
"label": "Contig",
"kind": "text",
"default": "",
"required": false,
"help": "(Can only pass a contig string.) Indexed motif specification, e.g., \"A1-80,10,/0,B5-12\".",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "unindex",
"label": "Unindex",
"kind": "textarea",
"default": "",
"required": false,
"help": "(Can only pass a contig string or dictionary.) Unindexed motif components, the specified residues can be anywhere in the final sequence. See Unindexing Specifics for more information.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "length",
"label": "Length",
"kind": "text",
"default": "150",
"required": false,
"help": "Total design length constraint; \"min-max\" or int for specified length.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "ligand",
"label": "Ligand",
"kind": "text",
"default": "",
"required": false,
"help": "Ligand(s) by chemical component name (from RSCB PDB) or index.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "cif_parser_args",
"label": "CIF parser args",
"kind": "textarea",
"default": "{}",
"required": false,
"help": "Optional args to CIF loader. See CIF parser options for more information.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters",
"help_note": "Enter a JSON object. The local cache_dir option is not available, and extra_fields is accepted only alongside an mmCIF structure because the PDB reader ignores it."
},
{
"name": "extra",
"label": "Extra",
"kind": "textarea",
"default": "{}",
"required": false,
"help": "Extra metadata (e.g., logs). Current options include sampled_contig.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "dialect",
"label": "Dialect",
"kind": "select",
"default": "2",
"required": false,
"help": "2=new (default), 1=legacy, Learn more about the legacy parsing system by looking at input_parsing.py.",
"options": [
{
"value": "2",
"label": "2 — current"
},
{
"value": "1",
"label": "1 — legacy"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_fixed_atoms",
"label": "Select fixed atoms",
"kind": "textarea",
"default": "",
"required": false,
"help": "Atoms with fixed coordinates. See the Select Fixed Atoms subsection for more information.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters",
"help_note": "Name a ligand by its chemical component code, such as NAI, rather than by chain and residue number. A ligand written into a chain that also holds polymer residues is moved onto a chain of its own while the structure is parsed, so a chain-and-number reference to it no longer matches."
},
{
"name": "select_unfixed_sequence",
"label": "Select unfixed sequence",
"kind": "textarea",
"default": "",
"required": false,
"help": "Where sequence can change. Default is True - all input regions have fixed sequences. Contig string input specifies components to unfix the sequence for. Dictionary inputs are allowed but not recommended.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_buried",
"label": "Select buried",
"kind": "textarea",
"default": "",
"required": false,
"help": "Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_partially_buried",
"label": "Select partially buried",
"kind": "textarea",
"default": "",
"required": false,
"help": "Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_exposed",
"label": "Select exposed",
"kind": "textarea",
"default": "",
"required": false,
"help": "Selection of RASA (Relatively Accessible Surface Area) for buried, partially buried, and exposed conditioning, respectively. Only contig string and dictionary are acceptable inputs.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_hbond_donor",
"label": "Select hbond donor",
"kind": "textarea",
"default": "",
"required": false,
"help": "Atom-wise donor/acceptor flags. Atom-wise selection of hydrogen bond donors and acceptors, respectively. Only dictionary inputs allowed. See RFdiffusion3 — Nucleic acid binder design examples for an example.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_hbond_acceptor",
"label": "Select hbond acceptor",
"kind": "textarea",
"default": "",
"required": false,
"help": "Atom-wise donor/acceptor flags. Atom-wise selection of hydrogen bond donors and acceptors, respectively. Only dictionary inputs allowed. See RFdiffusion3 — Nucleic acid binder design examples for an example.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "select_hotspots",
"label": "Select hotspots",
"kind": "textarea",
"default": "",
"required": false,
"help": "Atom-level or residue-level hotspots. Hotspots will typically be at most 4.5 Ã… to any heavy atom in the designed structure. Typically used for designing binders.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "redesign_motif_sidechains",
"label": "Redesign motif sidechains",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Fixed backbone, redesigned sidechains for motifs (input structures).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "symmetry",
"label": "Symmetry",
"kind": "textarea",
"default": "",
"required": false,
"help": "See Overview of Symmetry in RFD3.",
"options": [],
"rows": 3,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters",
"help_note": "Enter SymmetryConfig as JSON, for example {\"id\": \"C3\", \"is_symmetric_motif\": true}."
},
{
"name": "ori_token",
"label": "Ori token",
"kind": "text",
"default": "",
"required": false,
"help": "[x,y,z] origin override to control COM (center of mass) placement of designed structure.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "infer_ori_strategy",
"label": "Infer ori strategy",
"kind": "select",
"default": "",
"required": false,
"help": "\"com\" or \"hotspots\". The center of mass of the diffused region will typically be within 5Ã… of the ORI token. Using hotspots will place the ORI token 10Ã… outward from the center of mass of the specified hotspots. Using com will place the token at the center of mass of the input structure.",
"options": [
{
"value": "",
"label": "Model default"
},
{
"value": "com",
"label": "com"
},
{
"value": "hotspots",
"label": "hotspots"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "plddt_enhanced",
"label": "pLDDT enhanced",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Default True. Enables pLDDT (predicted Local Distance Difference Test) enhancement.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "is_non_loopy",
"label": "Is non loopy",
"kind": "select",
"default": "",
"required": false,
"help": "Default None. If True/False, produces output structures with fewer/more loops.",
"options": [
{
"value": "",
"label": "Model default"
},
{
"value": "true",
"label": "True — fewer loops"
},
{
"value": "false",
"label": "False — more loops"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "partial_t",
"label": "Partial t (angstroms)",
"kind": "number",
"default": "",
"required": false,
"help": "Noise (Ã…) for partial diffusion, enables partial diffusion (sets the noise level.) Recommended values are 5.0-15.0 Ã…. See Partial Diffusion for more information.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.5,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters"
},
{
"name": "allow_ligand_on_existing_chain",
"label": "Allow ligand on existing chain",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Allow the shared ligand chains used by some official input structures. This is enabled in presets that require it.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "InputSpecification fields",
"input_modes": "parameters",
"help_note": "Accepting such a structure logs a warning that the shared chain is being separated, which is expected. The ligands end up on a chain of their own, so select them by chemical component code."
},
{
"name": "job_name",
"label": "Job name",
"kind": "text",
"default": "rfd3-demo",
"required": false,
"help": "",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "n_batches",
"label": "Batches",
"kind": "number",
"default": 1,
"required": false,
"help": "number of batches to generate per input key (default: 1).",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 100,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "diffusion_batch_size",
"label": "Designs per batch",
"kind": "number",
"default": 8,
"required": false,
"help": "number of diffusion samples (designs) per batch (default: 8). If n_batches=1 and diffusion_batch_size=8 then 8 designs will be generated from the inference run.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 64,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "inference_sampler.num_timesteps",
"label": "inference_sampler.num_timesteps",
"kind": "number",
"default": 200,
"required": false,
"help": "diffusion timesteps for sampling (default: 200).",
"options": [],
"rows": null,
"minimum": 20,
"maximum": 1000,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "inference_sampler.step_scale",
"label": "inference_sampler.step_scale",
"kind": "number",
"default": 1.5,
"required": false,
"help": "scales diffusion step size; higher → less diverse, more designable (default: 1.5).",
"options": [],
"rows": null,
"minimum": 0.1,
"maximum": 10,
"step": 0.1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "low_memory_mode",
"label": "Low-memory mode",
"kind": "checkbox",
"default": false,
"required": false,
"help": "memory-efficient tokenization mode; set True if GPU RAM is tight (default: False).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "dump_trajectories",
"label": "Save trajectories",
"kind": "checkbox",
"default": false,
"required": false,
"help": "If True, the trajectory files are also saved to the specified output directory (default: False).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "out_dir",
"label": "Out dir",
"kind": "text",
"default": "output",
"required": false,
"help": "The directory that output files from the inference run will be stored in. If the directory does not exist it will be created. This does not change how the output files are named.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": "",
"help_note": "Enter a directory name within this run. The results page collects its files; absolute server paths are not accepted."
},
{
"name": "specification",
"label": "Specification overrides (JSON)",
"kind": "textarea",
"default": "{}",
"required": false,
"help": "JSON overrides for the per-example InputSpecification (default: {}). For example, you can run rfd3 design inputs=null specification.length=200 for a quick debug of creating a 200-length protein.",
"options": [],
"rows": 4,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "ckpt_path",
"label": "Ckpt path",
"kind": "text",
"default": "rfd3",
"required": false,
"help": "String containing he path and file name of the checkpoint path you want to use (default: rfd3)",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": "",
"help_note": "Use rfd3 for the configured default, or a .ckpt filename in the configured checkpoint directory."
},
{
"name": "skip_existing",
"label": "Skip existing",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Skip designing any systems whose output files already exist in the specified out_dir (default: True).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "global_prefix",
"label": "Global prefix",
"kind": "text",
"default": "",
"required": false,
"help": "This setting allows you to change the beginning of the name of the output files from the name of the input JSON or YAML file to your own string (default: null).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": "",
"help_note": "Leave blank for the default. Enter \"\" to omit the prefix. Use letters, digits, dots, underscores or hyphens."
},
{
"name": "prevalidate_inputs",
"label": "Prevalidate inputs",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Check that your inputs (JSON or YAML file) are valid before running inference (default: False).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Most useful CLI arguments",
"input_modes": ""
},
{
"name": "inference_sampler.gamma_0",
"label": "inference_sampler.gamma_0",
"kind": "number",
"default": 0.6,
"required": false,
"help": "This value (default: 0.6) influences the diversity of the designs from RFD3. A lower value increases designability but decreases diversity.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": 1,
"step": 0.05,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "json_keys_subset",
"label": "JSON keys subset",
"kind": "textarea",
"default": "",
"required": false,
"help": "Allows the user to extract only a subset of the JSON keys provided in the inputs file (default: null).",
"options": [],
"rows": 4,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.n_recycle",
"label": "inference_sampler.n_recycle",
"kind": "number",
"default": "",
"required": false,
"help": "Number of recycling iterations per diffusion step (default: null, uses the model checkpoint default of 2). Recycling allows the network to refine its predictions iteratively within each denoising step.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.kind",
"label": "inference_sampler.kind",
"kind": "select",
"default": "auto",
"required": false,
"help": "Change this value to symmetry (default: default) to turn on symmetry mode for the inference sampler.",
"options": [
{
"value": "auto",
"label": "Automatic from inputs"
},
{
"value": "default",
"label": "default"
},
{
"value": "symmetry",
"label": "symmetry"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": "",
"help_note": "Automatic selects the sampler from the input specification."
},
{
"name": "inference_sampler.cfg_features",
"label": "inference_sampler.cfg_features",
"kind": "textarea",
"default": "active_donor, active_acceptor, ref_atomwise_rasa",
"required": false,
"help": "The values specified (options are active_donor, active_acceptor, or ref_atomwise_rasa) are set to 0 for classifier-free guidance. Classifier-free guidance is how the diffusion model can steer the calculation towards a condition without training a separate classifier.",
"options": [],
"rows": 4,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.use_classifier_free_guidance",
"label": "inference_sampler.use_classifier_free_guidance",
"kind": "checkbox",
"default": false,
"required": false,
"help": "If set to True, RFD3 can use classifier-free guidance to guide the system towards a condition without training a separate classifier (default: False).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.cfg_t_max",
"label": "inference_sampler.cfg_t_max",
"kind": "number",
"default": "",
"required": false,
"help": "The maximum time to apply classifier-free guidance to the inference run (default: null).",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.cfg_scale",
"label": "inference_sampler.cfg_scale",
"kind": "number",
"default": 1.5,
"required": false,
"help": "Controls the influence of the classifier-free guidance adjustment (default: 1.5).",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.center_option",
"label": "inference_sampler.center_option",
"kind": "select",
"default": "all",
"required": false,
"help": "Specifies how to center the coordinates during the inference run to ensure that structures are alined around a specific point. Options include: all — (default) Uses the center of mass (COM) of all atoms motif — Uses the COM of the motif atoms with fixed coordinates diffuse — Uses the COM of all fixed coordinates that are not part of motif atoms",
"options": [
{
"value": "all",
"label": "all"
},
{
"value": "motif",
"label": "motif"
},
{
"value": "diffuse",
"label": "diffuse"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.s_trans",
"label": "inference_sampler.s_trans",
"kind": "number",
"default": 1.0,
"required": false,
"help": "Translational noise scale for augmentation during inference (default: 1.0).",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.allow_realignment",
"label": "inference_sampler.allow_realignment",
"kind": "checkbox",
"default": false,
"required": false,
"help": "If set to True (default: False) then the noised structure can be realigned during inference based on the location of a given motif. From Issue #154: It is generally not needed to include this option, there are fewer ‘weird’ interactions with motif scaffolding when it’s set to False.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.noise_scale",
"label": "inference_sampler.noise_scale",
"kind": "number",
"default": 1.003,
"required": false,
"help": "This parameter sets the scaling for the noise during inference (default 1.003). A smaller value will lead to less noise in your system leading to less diversity in the outputs.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.p",
"label": "inference_sampler.p",
"kind": "number",
"default": 7,
"required": false,
"help": "Determines the ‘shape’ of the noise schedule (default: 7).",
"options": [],
"rows": null,
"minimum": 0.001,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.gamma_min",
"label": "inference_sampler.gamma_min",
"kind": "number",
"default": 1.0,
"required": false,
"help": "Controls when gamma_0 is used, if t>gamma_min, gamma_0 is used as the value of gamma, which influences the diversity of the designs from RFD3.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "inference_sampler.s_jitter_origin",
"label": "inference_sampler.s_jitter_origin",
"kind": "number",
"default": 0.0,
"required": false,
"help": "Controls the standard deviation of the Gaussian distribution that is used to ‘jitter’ the motif offset (default: 0.0, no jitter).",
"options": [],
"rows": null,
"minimum": 0,
"maximum": null,
"step": 0.001,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "cleanup_guideposts",
"label": "Cleanup guideposts",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Set to False (default: True) to save the guideposts used during inference, see Debugging recommendations for more information.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "cleanup_virtual_atoms",
"label": "Cleanup virtual atoms",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Set to False (default: True) to save information about the diffused virtual atoms used during inference. RFD3 uses virtual atoms to account for the different number of atoms in side chains during the design process. RFD3 is atom based, however the number of atoms in a residue will differ based on its side chain, which is only determined after some diffusion steps have occurred, meaning virtual atoms are necessary for those steps. See Debugging recommendations for more information.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "read_sequence_from_sequence_head",
"label": "Read sequence from sequence head",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Used during training, it is not recommended to change this setting (default: True).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "output_full_json",
"label": "Output full JSON",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Output all specification information to the JSON file that gets created for each design (default: True).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "dump_prediction_metadata_json",
"label": "Dump prediction metadata JSON",
"kind": "checkbox",
"default": true,
"required": false,
"help": "If True, the metadata for the inference run will be included in the output JSON file (default: True).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
},
{
"name": "align_trajectory_structures",
"label": "Align trajectory structures",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Aligns the structures in the output trajectories (default: False).",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Other CLI options",
"input_modes": ""
}
],
"tasks": [],
"references": {
"cli_arguments": "https://rosettacommons.github.io/foundry/models/rfd3/input.html#cli-arguments",
"input_specification": "https://rosettacommons.github.io/foundry/models/rfd3/input.html",
"official_examples": "https://github.com/RosettaCommons/foundry/tree/production/models/rfd3/docs/examples"
},
"input_modes": {
"name": "input_mode",
"label": "Input mode",
"default": "parameters",
"options": [
{
"value": "upload",
"label": "Upload YAML or JSON"
},
{
"value": "text",
"label": "Enter YAML or JSON"
},
{
"value": "parameters",
"label": "Set parameters here"
}
]
},
"task_group": "",
"field_groups": [
{
"label": "Inputs",
"docs_url": "https://rosettacommons.github.io/foundry/models/rfd3/input.html#cli-arguments"
},
{
"label": "InputSpecification fields",
"docs_url": "https://rosettacommons.github.io/foundry/models/rfd3/input.html#inputspecification-fields"
},
{
"label": "Most useful CLI arguments",
"docs_url": "https://rosettacommons.github.io/foundry/models/rfd3/input.html#cli-arguments"
},
{
"label": "Other CLI options",
"docs_url": "https://rosettacommons.github.io/foundry/models/rfd3/input.html#other-cli-options"
}
],
"web_adaptations": {
"input": "PDB/mmCIF contents or bundled asset reference instead of an arbitrary local path.",
"atom_array_input": "Internal Python AtomArray; not a web/JSON input.",
"out_dir": "Directory name inside the isolated run.",
"ckpt_path": "Filename inside the configured checkpoint directory.",
"cif_parser_args": "cache_dir is excluded because it refers to a server path; extra_fields is rejected without an mmCIF structure instead of being silently dropped."
},
"_comment": "Field help is transcribed from the official input documentation (BSD-3-Clause): https://rosettacommons.github.io/foundry/models/rfd3/input.html . Formatting is plain text; help_note describes web input adaptations. See ../presets/rfd3/LICENSE.md for the upstream license."
}