132 lines
4.9 KiB
JSON
132 lines
4.9 KiB
JSON
{
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"params": {
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"pdb": {
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"type": "file",
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"description": "Path to input PDB file for protein sequence design",
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"default": "/mnt/OmicNAS/private/old/olamide/ligandmpnn/input/1BC8.pdb",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.pdb",
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"examples": [
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"/mnt/workflow/input/protein.pdb",
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"/mnt/workflow/input/*.pdb"
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],
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"pattern": ".*\\.pdb$",
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"enum": [],
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"validation": {},
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"notes": "Input PDB file containing the protein structure for sequence design."
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},
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"outdir": {
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"type": "folder",
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"description": "Directory for LigandMPNN output results",
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"default": "/mnt/OmicNAS/private/old/olamide/ligandmpnn/output",
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"required": true,
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"pipeline_io": "output",
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"var_name": "params.outdir",
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"examples": [
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"/mnt/workflow/output",
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"/path/to/results"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Directory where designed sequences and backbone PDBs will be saved."
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},
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"model_type": {
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"type": "string",
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"description": "Type of MPNN model to use for sequence design",
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"default": "ligand_mpnn",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.model_type",
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"examples": [
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"protein_mpnn",
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"ligand_mpnn",
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"soluble_mpnn"
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],
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"pattern": "^(protein_mpnn|ligand_mpnn|soluble_mpnn|global_label_membrane_mpnn|per_residue_label_membrane_mpnn)$",
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"enum": ["protein_mpnn", "ligand_mpnn", "soluble_mpnn", "global_label_membrane_mpnn", "per_residue_label_membrane_mpnn"],
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"validation": {},
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"notes": "protein_mpnn: Original ProteinMPNN. ligand_mpnn: Context-aware with ligands. soluble_mpnn: Trained on soluble proteins."
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},
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"temperature": {
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"type": "number",
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"description": "Sampling temperature for sequence generation",
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"default": 0.1,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.temperature",
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"examples": [0.05, 0.1, 0.2],
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"pattern": null,
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"enum": [],
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"validation": {},
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"notes": "Higher temperature gives more sequence diversity. Recommended range: 0.05-0.5"
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},
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"seed": {
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"type": "integer",
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"description": "Random seed for reproducibility",
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"default": 111,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.seed",
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"examples": [111, 42, 12345],
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"pattern": null,
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"enum": [],
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"validation": {},
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"notes": "Set for reproducible results."
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},
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"batch_size": {
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"type": "integer",
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"description": "Number of sequences to generate per batch",
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"default": 1,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.batch_size",
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"examples": [1, 3, 5],
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"pattern": null,
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"enum": [],
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"validation": {},
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"notes": "Higher batch sizes require more GPU memory."
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},
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"number_of_batches": {
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"type": "integer",
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"description": "Number of batches to run",
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"default": 1,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.number_of_batches",
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"examples": [1, 5, 10],
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"pattern": null,
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"enum": [],
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"validation": {},
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"notes": "Total sequences = batch_size × number_of_batches"
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},
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"chains_to_design": {
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"type": "string",
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"description": "Comma-separated chain IDs to redesign",
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"default": "",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.chains_to_design",
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"examples": ["A", "A,B", "A,B,C"],
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"pattern": "^([A-Z],?)*$",
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"enum": [],
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"validation": {},
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"notes": "Leave empty to design all chains."
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},
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"fixed_residues": {
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"type": "string",
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"description": "Space-separated list of residues to keep fixed",
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"default": "",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.fixed_residues",
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"examples": ["A1 A2 A3", "A12 B25 B26"],
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"pattern": null,
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"enum": [],
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"validation": {},
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"notes": "Format: ChainResidue (e.g., A12). Leave empty to design all residues."
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}
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}
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}
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