Load PDB¶
Loads a protein structure from a raw PDB-formatted string and tags it with a user-provided ID. It produces a PDB-typed output as a dictionary mapping the given ID to the provided PDB string. The node performs no parsing or validation of PDB content; it simply packages the data for downstream nodes.
Usage¶
Use this node when you already have a PDB text block (e.g., from a file or external source) and need to introduce it into a workflow that operates on PDB structures. Commonly placed at the start of structure-processing pipelines, it allows you to assign a unique ID so later nodes can reference the structure consistently and correlate it with associated sequence or alignment data.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb_string | True | STRING | The full PDB-formatted text content of a protein structure. This should be the raw text of the PDB file. | ATOM 1 N MET A 1 38.428 13.337 2.441 1.00 54.69 N ... |
| pdb_id | True | STRING | A unique identifier to associate with this PDB structure. If a corresponding sequence (FASTA) is used elsewhere, ensure its sequence ID matches this value. | pdb1 |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| structure.pdb | PDB | A PDB-typed dictionary with the provided pdb_id as the key and the PDB string as the value. | {'pdb1': 'ATOM 1 N MET A 1 38.428 13.337 2.441 1.00 54.69 N ...'} |
Important Notes¶
- Uniqueness of IDs: Use unique pdb_id values if multiple PDBs are present in the same workflow to avoid collisions.
- Sequence alignment: If you provide a matching FASTA sequence elsewhere in the workflow, its sequence ID should match the pdb_id.
- No validation: The node does not validate or parse the PDB text; ensure the content is in valid PDB format if downstream nodes require it.
- Pass-through behavior: The output is a simple mapping {pdb_id: pdb_string}, intended for downstream nodes expecting a PDB-typed input.
Troubleshooting¶
- Downstream parse errors: If later nodes fail to read the structure, verify the pdb_string is complete, properly formatted PDB text.
- ID mismatch with FASTA: If a sequence-to-structure association fails, ensure the FASTA sequence ID matches the pdb_id used here.
- Overwritten or ambiguous structures: If multiple structures seem to conflict downstream, confirm all pdb_id values are unique within the workflow.
Example Pipelines¶
