> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # DNA Base Contact Quality > Score protein-DNA base contact quality from PDB geometry. Rewards bidentate contacts, diverse readout residues (GLN/ASN/SER/THR/HIS/TYR/TRP over ARG-only), and sufficient base-specific H-bond contacts. Does not require Rosetta relaxation.
DNA Base Contact Quality
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evo-design/proto-language/proto\_language/constraint/protein\_structure/dna\_base\_contact\_quality\_constraint.py
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Score protein-DNA base contact quality from a predicted complex PDB. Resolves (reuses or predicts) a protein-operator complex PDB per candidate tuple, then scores base-specific contact quality directly from heavy-atom geometry. The score is a weighted combination of bidentate deficit (0.35), base-contact deficit (0.30), unique-residue deficit (0.15), and a diversity deficit weighted by `config.diversity_bonus_weight` (default 0.3), all in `[0, 1]` where 0 is best. ## API Reference
ConfigDNABaseContactQualityConfig Source
Config for geometry-based DNA base contact quality scoring. Scores protein-DNA complexes based on the quality of base-specific contacts, measured directly from heavy-atom distances in a predicted complex PDB without requiring Rosetta relaxation. Inherits the structure-prediction tool selection and per-tool configs from `StructureBasedConstraintConfig`. Heavy-atom distance cutoff for base contacts. Target bidentate-contact count (one residue H-bonding 2+ atoms on a base); 0 component when met. Target number of polar sidechain-to-base contacts. Target number of unique protein residues contacting bases. Weight of the diversity term rewarding base-specific readout over nonspecific ARG/LYS charge. Predictor for the protein-DNA complex; must be DNA-capable (alphafold3/boltz2/protenix). Options: `esmfold`, `esmfold2`, `alphafold3`, `boltz2`, `chai1`, `protenix`, `alphafold2`, `alphafold2_binder` Configuration for ESMFold structure prediction. Configuration for ESMFold2 structure prediction. Configuration for AlphaFold3 structure prediction. Configuration for Boltz2 structure prediction. Configuration for Chai1 structure prediction. Configuration for Protenix structure prediction. Configuration for the general AlphaFold2 multimer structure predictor. Configuration for the AF2 binder-design backend.
ReturnsConstraintOutput
Per-candidate score in `[0, 1]` (lower is better) with contact-quality metadata (`n_base_contacts`, `n_bidentate`, `n_unique_residues`, `n_specific_residues`, `pct_arg`, `diversity_score`, per-component deficits, and `pdb_path`). Candidates whose structure could not be resolved, or whose PDB is empty/unparseable, receive `MAX_ENERGY`.
## Usage ```python python icon="python" theme={null} from proto_language.core import Constraint from proto_language.constraint import dna_base_contact_quality_constraint, DNABaseContactQualityConfig constraint = Constraint( inputs=[segment], function=dna_base_contact_quality_constraint, function_config=DNABaseContactQualityConfig( # Configure parameters here ), ) scores = constraint.evaluate() ``` ## Metadata | Property | Value | | --------------- | ------------------------------------- | | Key | `dna-base-contact-quality` | | Function | `dna_base_contact_quality_constraint` | | Category | `protein_structure` | | Mode | `discrete` | | Uses GPU | `True` | | Supported Types | `protein`, `dna` |