Load PDB¶

Loads a Protein Data Bank (PDB) structure provided as plain text and exposes it as a structured PDB output for downstream biotech nodes. It stores the content under a user-defined identifier without modifying or validating the text. Use this node to introduce existing PDB data directly into a workflow.

Usage¶

Use when you have a PDB structure in text form (e.g., copied from a file or fetched elsewhere) and want to feed it into a biotech workflow. Provide a unique ID for the structure; if you plan to pair it with a FASTA sequence later, ensure the FASTA sequence header ID matches this PDB ID. Connect the output to nodes that consume PDB inputs (e.g., visualization, sequence extraction, chain operations, or batch/combiner nodes).

Inputs¶

Field	Required	Type	Description	Example
pdb_string	True	STRING	The full PDB file content as a text string. The content is passed through unchanged to downstream nodes.	HEADER TEST STRUCTURE\nATOM 1 N MET A 1 11.104 13.207 9.101 1.00 20.00 N\nATOM 2 CA MET A 1 12.560 13.420 9.320 1.00 20.00 C\nEND
pdb_id	True	STRING	Identifier assigned to this PDB entry. Must be unique within the workflow if multiple PDBs are used. If pairing with a FASTA record, the FASTA sequence ID should match this value.	my_protein

Outputs¶

Field	Type	Description	Example
structure.pdb	PDB	A dictionary mapping the provided PDB ID to the PDB text content, suitable for use by nodes that accept PDB inputs.	{'my_protein': 'ATOM 1 N MET A 1 11.104 13.207 9.101 1.00 20.00 N\\n...\\nEND'}

Important Notes¶

IDs should be unique across the workflow to avoid collisions when combining or batching structures.
If you intend to pair this PDB with a FASTA sequence, ensure the FASTA header ID matches the provided pdb_id.
The node does not validate or correct PDB formatting; downstream nodes may fail if the content is malformed.
Content is treated as plain text; ensure it follows standard PDB conventions (e.g., ATOM/HETATM records, END line) for best compatibility.

Troubleshooting¶

Empty or missing output: Ensure pdb_string is not empty and contains valid PDB text.
Downstream node errors about parsing: Verify the PDB content is properly formatted (correct columns, ATOM/HETATM lines, and an END record).
ID mismatch when pairing with FASTA: Update either pdb_id here or the FASTA header so they match exactly.
Conflicts in combined workflows: If merging multiple PDB inputs later, make sure each pdb_id is unique to avoid overwriting entries.