Evaluate Prot Param¶
Evaluates physicochemical and sequence-derived parameters for one or more protein structures and returns a consolidated CSV. It computes protein charge at specified pH values and includes additional protein/sequence metrics. Supports three modes: PROD (service-backed), MOCK (predefined data), and TEST (minimal, faster evaluation).
Usage¶
Use this node after loading or generating protein structures to obtain a tabulated summary of properties, including charge at chosen pH values. Typical workflow: provide a set of PDB structures and a comma-separated list of pH values; consume the resulting CSV for ranking, filtering, or downstream analyses.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | Collection of named protein structures to evaluate. Each entry should be a name mapped to its PDB text content. | {"design_A": "ATOM ...\nEND", "design_B": "ATOM ...\nEND"} |
| pH_list | True | STRING | Comma-separated list of pH values (floats) at which to compute protein charge. Parsed into a float list internally. | 6.5, 7, 8.0 |
| mode | True | CHOICE[MOCK, PROD, TEST] | Execution mode. MOCK returns static demo output; PROD runs the live evaluation; TEST limits scope for a faster check. | PROD |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| score.csv | CSV | CSV summarizing evaluated parameters per structure, including charge at requested pH values and other protein/sequence metrics. | name,seq_len,gravy,instability_index,isoelectric_point,charge@pH6.5,charge@pH7,charge@pH8\ndesign_A,137,-0.42,32.1,6.8,-1.2,-2.0,-3.5\ndesign_B,141,-0.30,28.7,7.1,0.5,-0.3,-1.8 |
Important Notes¶
- Mode behavior: PROD calls the live evaluation service; MOCK loads predefined results; TEST uses only the first structure and sets pH_list to [7] for speed.
- pH parsing: pH_list must be numeric and comma-separated (e.g., "6.0,7,8.5"); spaces are allowed.
- Batch handling: Multiple PDB inputs are supported; the CSV will contain rows for each structure.
- Timeout scaling: Service timeout scales with the number of structures (about 300 seconds per structure). Large batches may run longer.
- Columns may vary: The exact set of metrics can evolve with the backing service; rely on the CSV headers returned at runtime.
Troubleshooting¶
- Invalid pH values: Ensure pH_list contains only numbers separated by commas (e.g., "6.5,7,8").
- Only one row returned: In TEST mode, the node uses only the first structure and forces pH to 7.
- Long runtimes or timeouts: Reduce the number of structures, try TEST mode for a quick sanity check, or run smaller batches.
- Unexpected columns: Check the header row in the returned CSV; metrics may change with service updates.
- Demo-like output: MOCK mode serves static sample data; switch to PROD for real evaluations.
Example Pipelines¶
