Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths
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params.json
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202
params.json
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{
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"params": {
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"protein_fasta": {
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"type": "file",
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"description": "Path to protein FASTA file for structure prediction",
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"default": "s3://omic/eureka/rosettafold-all-atom/input/protein.fasta",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.protein_fasta",
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"examples": [
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"s3://omic/eureka/rosettafold-all-atom/input/protein.fasta"
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],
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"pattern": ".*\\.(fasta|fa)$",
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"enum": [],
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"validation": {},
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"notes": "FASTA file containing protein sequence(s). Required for all prediction modes."
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},
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"na_fasta": {
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"type": "file",
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"description": "Path to nucleic acid FASTA file (DNA or RNA)",
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"default": "",
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"required": false,
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"pipeline_io": "input",
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"var_name": "params.na_fasta",
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"examples": [
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"s3://omic/eureka/rosettafold-all-atom/input/dna_strand.fasta"
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],
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"pattern": ".*\\.(fasta|fa)$",
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"enum": [],
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"validation": {},
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"notes": "Optional. For protein-nucleic acid complex prediction."
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},
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"na_type": {
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"type": "string",
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"description": "Type of nucleic acid input",
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"default": "dna",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.na_type",
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"examples": [
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"dna",
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"rna"
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],
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"pattern": "^(dna|rna)$",
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"enum": ["dna", "rna"],
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"validation": {},
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"notes": "Specify whether the nucleic acid is DNA or RNA."
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},
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"sm_file": {
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"type": "file",
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"description": "Path to small molecule file (SDF format)",
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"default": "",
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"required": false,
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"pipeline_io": "input",
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"var_name": "params.sm_file",
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"examples": [
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"s3://omic/eureka/rosettafold-all-atom/input/ligand.sdf"
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],
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"pattern": ".*\\.sdf$",
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"enum": [],
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"validation": {},
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"notes": "Optional. For protein-small molecule complex prediction."
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},
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"sm_type": {
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"type": "string",
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"description": "Type of small molecule input",
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"default": "sdf",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.sm_type",
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"examples": [
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"sdf",
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"smiles"
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],
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"pattern": "^(sdf|smiles)$",
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"enum": ["sdf", "smiles"],
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"validation": {},
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"notes": "Format of small molecule input. SDF recommended for covalent modifications."
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},
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"covale_inputs": {
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"type": "string",
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"description": "Covalent bond specifications for modified proteins",
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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.covale_inputs",
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"examples": [
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"[((\"A\", \"74\", \"ND2\"), (\"B\", \"1\"), (\"CW\", \"null\"))]"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Format: [((chain, residue, atom), (sm_chain, atom_idx), (chirality1, chirality2))]"
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},
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"outdir": {
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"type": "folder",
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"description": "Directory for RFAA prediction results",
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"default": "s3://omic/eureka/rosettafold-all-atom/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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"s3://omic/eureka/rosettafold-all-atom/output"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Output directory for PDB structures and confidence metrics."
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},
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"job_name": {
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"type": "string",
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"description": "Name for the prediction job",
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"default": "rfaa_prediction",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.job_name",
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"examples": [
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"rfaa_prediction",
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"my_protein"
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],
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"pattern": "^[a-zA-Z0-9_-]+$",
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"enum": [],
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"validation": {},
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"notes": "Used to name output files."
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},
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"max_cycle": {
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"type": "integer",
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"description": "Number of inference cycles for structure refinement",
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"default": 4,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.max_cycle",
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"examples": [
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4,
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10
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],
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"enum": [],
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"validation": {},
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"notes": "Default is 4. Increase to 10 for difficult cases."
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},
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"db_uniref30": {
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"type": "folder",
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"description": "Path to UniRef30_2020_06 database directory",
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"default": "/mnt/databases/UniRef30_2020_06",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.db_uniref30",
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"examples": [
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"/mnt/databases/UniRef30_2020_06"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Required for MSA generation. ~46GB."
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},
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"db_bfd": {
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"type": "folder",
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"description": "Path to BFD database directory",
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"default": "/mnt/databases/bfd",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.db_bfd",
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"examples": [
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"/mnt/databases/bfd"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Required for MSA generation. ~272GB."
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},
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"db_pdb100": {
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"type": "folder",
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"description": "Path to pdb100_2021Mar03 template database",
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"default": "/mnt/databases/pdb100_2021Mar03",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.db_pdb100",
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"examples": [
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"/mnt/databases/pdb100_2021Mar03"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Required for template search. ~81GB."
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},
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"weights": {
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"type": "file",
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"description": "Path to RFAA model weights file",
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"default": "/mnt/databases/RFAA_paper_weights.pt",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.weights",
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"examples": [
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"/mnt/databases/RFAA_paper_weights.pt"
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],
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"pattern": ".*\\.pt$",
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"enum": [],
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"validation": {},
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"notes": "Download from: http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt"
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}
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}
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}
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