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### pDockQ2 Interface Quality (`pdockq2`) Scores the per-interface quality of a cofolded protein complex by computing pDockQ2 for each chain pair and aggregating the per-chain scores into a single overall score. The tool takes a `Structure` with per-residue pLDDT in the B-factor column and the PAE matrix attached at `structure.metrics["pae"]`, identifies CA-CA contacts between every pair of chains within a configurable distance cutoff, applies the published sigmoid, and returns the overall score together with a per-chain interface breakdown. #### API Reference

Source Cofolded complex with per-residue pLDDT in the B-factor column (`b_factor_type` must be `PLDDT` or `NORMALIZED_PLDDT`) and the PAE matrix attached at `structure.metrics['pae']` as a square `list[list[float]]` whose dimension matches the structure's total residue count. Raw structure content in PDB or CIF format. Format of the content string (auto-detected if omitted). What the B-factor column represents. Optional source identifier (filepath or tool name). Associated metrics (e.g., pLDDT, pTM scores, per-chain lists, pairwise matrices). None values are stripped at construction. Single-character chain ID of the binder (e.g. VHH). The selected chain ID. Target chain IDs (single character each). Chain IDs in the selection.

Source CA-CA distance cutoff in Å for interface residue detection. Defaults to 10.0, matching germinal's `pDockQ.pDockQ2` wrapper default. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Scalar pDockQ2 metrics plus per-chain interface breakdown. Per-target-chain breakdown kept as a Pydantic field so it stays out of metric iteration. Name of the metric that best summarizes the result overall (e.g. `"avg_plddt"` for AlphaFold2). Used by downstream UI and reporting to pick a headline value. Concrete Metrics subclass tag; enables typed reconstruction after a serialization round-trip. **Metrics** | Metric | Type | Range | Availability | | ------------------------ | ----- | ------------ | ------------ | | `pdockq2` | float | 0.0 to 1.0 | always | | `avg_interface_plddt` | float | 0.0 to 100.0 | always | | `avg_interface_pae` | float | 0.0 to 1.0 | always | | `num_interface_contacts` | int | ≥ 0.0 | always |

#### Applications This tool is appropriate for filtering and ranking cofolded complexes from structure-prediction tools such as AlphaFold-Multimer, AlphaFold 3, Chai-1, Boltz-2, and Protenix. Representative applications include gating candidate protein binders from a design pipeline by predicted interface quality, ranking the most promising poses in a multi-chain prediction ensemble, and screening large sets of predicted complexes before committing to more expensive downstream analyses. #### Usage Tips * **The PAE matrix is required and must be attached at `structure.metrics["pae"]` as a square `list[list[float]]` whose dimension matches the total residue count of the structure.** The input is rejected when the matrix is missing, not square, or of the wrong dimension. * **Per-residue pLDDT must be supplied via the B-factor column.** Structure predictors in proto-tools return the correct `b_factor_type` automatically, and `Structure.from_file()` auto-detects it for AlphaFold DB and ModelArchive files. For manually provided structures from other sources, pass `b_factor_type=BFactorType.PLDDT` (raw 0 to 100) or `BFactorType.NORMALIZED_PLDDT` (0 to 1) explicitly. The input is rejected when `b_factor_type` is any other value, since the published sigmoid was fit on a 0 to 100 pLDDT scale. * **A pDockQ2 score above 0.23 corresponds to the "Acceptable" DockQ quality class.** The thresholds derive from the underlying DockQ measure ([Basu and Wallner, 2016](https://doi.org/10.1371/journal.pone.0161879)): scores above 0.49 correspond to "Medium" quality and scores above 0.80 to "High" quality. Scores below 0.23 typically reflect either low interface pLDDT or high cross-chain PAE. * **The overall score is the mean of `pmidockq` over target chains that contact the binder chain.** When no target chain in `target_chains` is within the distance cutoff of `binder_chain`, the overall score is set to `0.0`, `num_interface_contacts` is reported as `0`, and a warning is logged. Verify the chain identifiers and the cutoff before interpreting an all-zero result as a poor interface. * **`distance_cutoff` controls the CA-CA contact distance used to define interface residues.** The wrapper default of `10.0` Å is more permissive than the `8.0` Å default used by the Elofsson Lab reference implementation against which the published sigmoid was calibrated. The qualitative DockQ-quality interpretation still applies at `10.0` Å, but quantitative scores will not exactly match the published values. Set `distance_cutoff=8.0` for scores that match the original pDockQ2 calibration. The PAE normalisation distance inside the sigmoid is independently fixed at 10 Å per the published formula and is not affected by this setting. * **The interface pLDDT is contact-pair weighted, not residue-deduplicated.** A residue that contacts `k` cross-chain partners contributes its pLDDT `k` times to the interface mean. This matches the published pDockQ2 definition and is preserved by the wrapper. * **The per-chain breakdown is available on `result.metrics.interfaces`.** Each `InterfacePDockQ2` entry exposes `chain_id`, `neighbor_chains`, `if_plddt` (0 to 100 pLDDT scale), `norm_pae` (0 to 1 normalised confidence, higher is more confident), and `pmidockq` (0 to 1 DockQ-scale prediction) for one chain. Inspect this list when debugging multi-chain targets or when the overall mean masks variation across interfaces.