Make Secstruc Adj¶
Generates secondary structure (_ss.pt) and block adjacency (_adj.pt) tensors from provided PDB structures. It prepares scaffold conditioning artifacts required for fold-guided protein design workflows. The node validates input PDBs and returns a portable reference to the generated .pt files.
Usage¶
Use this node after assembling or loading one or more PDB structures. Connect the PDB output (e.g., from a PDB Combiner or PDB Loader) into this node to produce the scaffold .pt files. Then feed the returned scaffold_pt_files into downstream scaffold-guided configuration or generation nodes.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdbs | True | PDB | One or more PDB structures to process. Expects a mapping of names to PDB text content, typically provided by earlier nodes that load or combine PDBs. | {'scaffold_A': 'ATOM ... END', 'scaffold_B': 'ATOM ... END'} |
| timeout | False | INT | Maximum time in seconds to allow for generating the .pt files. Increase for larger or multiple PDBs. | 300 |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| scaffold_pt_files | SCAFFOLD_PT_FILES | Reference to the generated secondary structure and adjacency tensors for each input scaffold. Suitable for direct connection into scaffold-guided/fold conditioning nodes. | {'type': 'inline', 'pt_files': {'scaffold_A': {'ss': ' |
Important Notes¶
- At least one valid PDB structure is required; the input must be a mapping of names to PDB contents.
- The node produces two artifacts per scaffold: _ss.pt (secondary structure) and _adj.pt (block adjacency).
- Timeout is configurable between 60 and 1800 seconds; larger or more complex inputs may require higher values.
- Output is returned as a reference object that downstream nodes can consume directly for fold conditioning.
- Ensure upstream nodes provide correctly formatted PDB content; malformed or empty inputs will cause the operation to fail.
Troubleshooting¶
- No .pt files were generated: Verify that each provided PDB is valid and complete; try with a single known-good PDB to isolate issues.
- Operation timed out: Increase the timeout input value (e.g., to 600 or higher) for large or multiple PDBs.
- Invalid input type error: Confirm the 'pdbs' input is a dictionary-like mapping from scaffold names to PDB text.
- Downstream node rejects output: Ensure you connect the 'scaffold_pt_files' output directly into nodes expecting scaffold conditioning files.