Sign NIM skills

[ohadmo]

No description provided.

[ohadmo]

/nvskills-ci

[greptile-apps]

Confidence Score: 4/5

The PR is not yet safe to merge because multichain structure preflight can incorrectly reject or crop valid target chains by counting partner residues.

Findings

1.  Partner Chains Inflate Target Length ▶

Summary

This PR signs and standardizes the BioNeMo NIM skill set, restructures evaluation assertions, strengthens credential-handling guidance, and extends binder-design validation and preflight behavior.

• Adds explicit secret-handling and missing-credential instructions to hosted NIM workflows.
• Converts evaluation assertions to the format expected by the signing and validation system.
• Adds PDB/mmCIF author-chain interface support to Complexa preflight.
• Makes protein-binder filtering reject missing, invalid, and non-finite required metrics.
• Adds regression tests and evaluation configuration for the binder-design workflows.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  A[Target name, accession, PDB ID, or structure path] --> B{UniProt target?}
  B -->|Yes| C[Fetch AlphaFold structure and functional hotspots]
  B -->|No| D[Load PDB or mmCIF and select author chain]
  D --> E[Detect target-partner interface contacts]
  C --> F[Align hotspots to structure]
  E --> F
  F --> G[Calculate conditioned target length]
  G --> H{Complex residue budget satisfied?}
  H -->|Yes| I[READY]
  H -->|No| J[Crop or report NEEDS ATTENTION]

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_{Reviews (5) · Last reviewed commit: "reconfig harbor"}

[ohadmo]

/nvskills-ci

[ohadmo]

/nvskills-ci

[ohadmo]

/nvskills-ci

[ohadmo]

/nvskills-ci

[greptile-apps]

Partner Chains Inflate Target Length

For a multichain PDB or mmCIF, _pdb_target() selects the requested target chain, but plan() assigns the full structure back to model and calculates full_length from every chain. Because PDB inputs then derive conditioned_length from that value, partner chains count against the 500-residue budget. This can incorrectly reject or crop a valid target chain. The mirrored workflow implementation has the same issue.