aurekaresearch/opendde-harness/structure-analysis

Structure Analysis Skill

EvoReflect Direct Tool

Within ReflectAgent, call analyze_current_cycle_structure. It accepts trusted candidate IDs paired with the exact structure paths from Reflection's allowed catalog. The compute service validates that every path belongs to the active task output, invokes the packaged backend with validated arguments, parses the reports, and returns a bounded interaction summary. Do not invent paths or load raw PLIP reports into model context.

Call the tool at most once per Reflection and analyze no more than three informative complexes: the current parent, the best new candidate, and one contrasting candidate. Copy candidate IDs, structure paths, binder chains, target chains, and cycle number exactly from the trusted catalog. PLIP failure is non-fatal; continue from fold metrics and supplied contact-gate evidence and mark detailed interaction evidence unavailable.

Standalone Usage

python -m opendde_harness.plugin.protein_design.servers.backends.plip_runner \
    outputs/.../some_complex_structure.cif \
    --cyc-num 1 \
    --name cycle_1_mut_001 \
    --binder-chain <binder_chain_ids> \
    -o outputs/.../some_structure_interactions.txt

Pass a SINGLE predicted complex structure file. The file should already contain both target and binder chains. For protein-protein complexes, provide the binder chain IDs explicitly with --binder-chain.

Converts .cif/.mmcif to .pdb automatically when needed, runs PLIP on the given structure, and writes the interaction report to a txt file.

Do not split the complex into separate binder/target files. This wrapper expects one complex file and optional binder chain IDs.

Interpreting Results

Focus on the interaction summary PLIP reports:

• H-bonds / salt bridges — often strongest interaction signals
• Hydrophobic contacts — useful for interface packing
• Pi-stacking — notable for aromatic residues

Output is a text report with interaction type counts, residue identities, and distances per binding site.

Use interaction claims only for the exact analyzed complex. Do not infer hydrogen bonds, salt bridges, pi-stacking, or residue contacts from confidence scores alone.

Dependencies

The persistent configured compute service provides both runtime dependencies:

• PLIP: invoked inline through PLIP_COMMAND
• biotite: converts .cif/.mmcif structures to standard .pdb

No separate PLIP Docker image is required or launched by this skill.