Batch PDB¶

Combines multiple PDB inputs into a single batch dictionary. Each input is itself a dictionary mapping pdb_id to PDB content, and all keys must be unique across the batch. The node validates duplicate IDs and raises an error if a collision is found.

Usage¶

Use this node when you need to merge several PDB structures (from different loaders or generators) into one consolidated input for downstream biotech nodes that process batches. Connect pdb_1 first; additional inputs (pdb_2 to pdb_31) become available progressively after the previous one is connected.

Inputs¶

Field	Required	Type	Description	Example
pdb_1	True	PDB	First PDB dictionary to add to the batch. Must be a dict of {pdb_id: pdb_content}.	{"protein_A": "ATOM ...\nEND"}
pdb_2	False	PDB	Second PDB dictionary to merge. Appears after pdb_1 is connected.	{"protein_B": "ATOM ...\nEND"}
pdb_3	False	PDB	Third PDB dictionary to merge. Appears after pdb_2 is connected.	{"protein_C": "ATOM ...\nEND"}
pdb_4	False	PDB	Fourth PDB dictionary to merge. Appears after pdb_3 is connected.	{"protein_D": "ATOM ...\nEND"}
pdb_5	False	PDB	Fifth PDB dictionary to merge. Appears after pdb_4 is connected.	{"protein_E": "ATOM ...\nEND"}
pdb_6	False	PDB	Sixth PDB dictionary to merge. Appears after pdb_5 is connected.	{"protein_F": "ATOM ...\nEND"}
pdb_7	False	PDB	Seventh PDB dictionary to merge. Appears after pdb_6 is connected.	{"protein_G": "ATOM ...\nEND"}
pdb_8	False	PDB	Eighth PDB dictionary to merge. Appears after pdb_7 is connected.	{"protein_H": "ATOM ...\nEND"}
pdb_9	False	PDB	Ninth PDB dictionary to merge. Appears after pdb_8 is connected.	{"protein_I": "ATOM ...\nEND"}
pdb_10	False	PDB	Tenth PDB dictionary to merge. Appears after pdb_9 is connected.	{"protein_J": "ATOM ...\nEND"}
pdb_11	False	PDB	Eleventh PDB dictionary to merge. Appears after pdb_10 is connected.	{"protein_K": "ATOM ...\nEND"}
pdb_12	False	PDB	Twelfth PDB dictionary to merge. Appears after pdb_11 is connected.	{"protein_L": "ATOM ...\nEND"}
pdb_13	False	PDB	Thirteenth PDB dictionary to merge. Appears after pdb_12 is connected.	{"protein_M": "ATOM ...\nEND"}
pdb_14	False	PDB	Fourteenth PDB dictionary to merge. Appears after pdb_13 is connected.	{"protein_N": "ATOM ...\nEND"}
pdb_15	False	PDB	Fifteenth PDB dictionary to merge. Appears after pdb_14 is connected.	{"protein_O": "ATOM ...\nEND"}
pdb_16	False	PDB	Sixteenth PDB dictionary to merge. Appears after pdb_15 is connected.	{"protein_P": "ATOM ...\nEND"}
pdb_17	False	PDB	Seventeenth PDB dictionary to merge. Appears after pdb_16 is connected.	{"protein_Q": "ATOM ...\nEND"}
pdb_18	False	PDB	Eighteenth PDB dictionary to merge. Appears after pdb_17 is connected.	{"protein_R": "ATOM ...\nEND"}
pdb_19	False	PDB	Nineteenth PDB dictionary to merge. Appears after pdb_18 is connected.	{"protein_S": "ATOM ...\nEND"}
pdb_20	False	PDB	Twentieth PDB dictionary to merge. Appears after pdb_19 is connected.	{"protein_T": "ATOM ...\nEND"}
pdb_21	False	PDB	Twenty-first PDB dictionary to merge. Appears after pdb_20 is connected.	{"protein_U": "ATOM ...\nEND"}
pdb_22	False	PDB	Twenty-second PDB dictionary to merge. Appears after pdb_21 is connected.	{"protein_V": "ATOM ...\nEND"}
pdb_23	False	PDB	Twenty-third PDB dictionary to merge. Appears after pdb_22 is connected.	{"protein_W": "ATOM ...\nEND"}
pdb_24	False	PDB	Twenty-fourth PDB dictionary to merge. Appears after pdb_23 is connected.	{"protein_X": "ATOM ...\nEND"}
pdb_25	False	PDB	Twenty-fifth PDB dictionary to merge. Appears after pdb_24 is connected.	{"protein_Y": "ATOM ...\nEND"}
pdb_26	False	PDB	Twenty-sixth PDB dictionary to merge. Appears after pdb_25 is connected.	{"protein_Z": "ATOM ...\nEND"}
pdb_27	False	PDB	Twenty-seventh PDB dictionary to merge. Appears after pdb_26 is connected.	{"complex_1": "ATOM ...\nEND"}
pdb_28	False	PDB	Twenty-eighth PDB dictionary to merge. Appears after pdb_27 is connected.	{"complex_2": "ATOM ...\nEND"}
pdb_29	False	PDB	Twenty-ninth PDB dictionary to merge. Appears after pdb_28 is connected.	{"complex_3": "ATOM ...\nEND"}
pdb_30	False	PDB	Thirtieth PDB dictionary to merge. Appears after pdb_29 is connected.	{"complex_4": "ATOM ...\nEND"}
pdb_31	False	PDB	Thirty-first PDB dictionary to merge. Appears after pdb_30 is connected.	{"complex_5": "ATOM ...\nEND"}

Outputs¶

Field	Type	Description	Example
structure.pdb	PDB	A single merged PDB batch dictionary containing all input entries, formatted as {pdb_id: pdb_content}.	{"protein_A": "ATOM ...\nEND", "protein_B": "ATOM ...\nEND"}

Important Notes¶

Unique IDs required: All pdb_id keys across all inputs must be unique; duplicate IDs cause the node to raise an error.
Progressive inputs: Additional inputs (pdb_2 to pdb_31) become visible only after the previous one is connected.
Input format: Each input must be a dictionary mapping IDs to PDB strings; passing a raw string instead of a dict will fail.
Batch-friendly: Inputs can themselves be batches (dicts with multiple entries); the node merges all provided dictionaries.

Troubleshooting¶

Duplicate ID error: If you see an error about an ID repeating twice, rename the conflicting pdb_id in one of the inputs before merging.
Nothing happens for later ports: If pdb_2 (or later) is not visible, connect pdb_1 first; inputs appear sequentially.
Invalid input type: Ensure each connected input is a PDB dictionary (e.g., output of a PDB loader/combiner) rather than a plain string.
Empty output: At least pdb_1 is required; verify that each provided dictionary contains at least one entry.