Input nodes

An input node holds the values you supply to a pipeline: input file paths and scalar parameters. It runs no tool, its key/value dictionary is its output, fed to downstream nodes through their connectors.

rf_in = g.add_input_node(
    input_pdb="/vol/inputs/1l9h.pdb",
    contigs="[150-150]",
    num_designs="2",
)

Keys must match the downstream tool

For a value to reach a tool, its key must match one of that tool’s declared input name fields, and that name must appear as a {slot} in the tool’s command template. Read the names from the manifest:

bv show <tool> --format json

For example, bv show proteinmpnn --format json declares inputs pdb_path, num_seq_per_target, sampling_temp, so the input node uses exactly those keys. A value whose key matches no slot is silently dropped, which is the usual cause of a parameter “not taking effect.” See Tools and the registry for reading manifests in full.

Files vs. scalars

Both kinds of value are taken directly, biocomposer never rewrites a value you set yourself:

• File paths (values that exist on disk) are staged into the tool’s sandbox at run time and the command receives the staged filename.

• Scalars (numbers, short strings like "[150-150]" or "0.1") are substituted literally into the command line.

Input nodes override upstream outputs

A node’s inputs are merged with input-node values applied last, so a value you set on an input node overrides any value an upstream tool produced for the same key. For example, if a step receives a generated pdb from upstream but you also pass input_pdb=... on an input node into it, your input-node value is chosen. Only set a key when you intend that override. See Input merging and key clashes for the full rule (including which of two colliding tool outputs wins).

Multiple input nodes

A node may take several input nodes (plus one upstream tool). This is common with map and decision nodes, where one input node supplies the collection-producing tool and another supplies shared scalar parameters:

mpnn_in = g.add_input_node(num_seq_per_target="2", sampling_temp="0.1")
g.add_edge((rfdiffusion, proteinmpnn), (mpnn_in, proteinmpnn))

Reference

class biocomposer.InputNode

Bases: object

set_input(**kwargs)