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evo-design/proto-language/proto_language/constraint/protein_structure/structure_similarity_constraint.py
API Reference
Configuration for RMSD-based structure similarity.This configuration extends
StructureSimilarityConfig with specific parameters
for calculating the Root Mean Square Deviation (RMSD) between the target and
proposal structures. The raw RMSD value is transformed into a 0-1 constraint
score using a sigmoid function, where 0 represents a perfect match (low RMSD)
and 1 represents a poor match (high RMSD).Inherits target specification (target_chains, target_structure,
min_target_plddt) from StructureSimilarityConfig and tool selection
(structure_tool, esmfold_config, esmfold2_config, alphafold3_config,
boltz2_config, chai1_config, protenix_config, alphafold2_config,
alphafold2_binder_config) from StructureBasedConstraintConfig.number
default:"2.0"
RMSD in Ångströms where the sigmoid score equals 0.5; values below 2 Å are generally a good match.
number
default:"3.0"
Steepness of the penalty curve.
enum
default:"cealign"
PyMOL alignment routine for RMSD calculation.Options:
cealign, alignenum
default:"esmfold"
Predictor: esmfold/esmfold2/alphafold3/boltz2/chai1/protenix/alphafold2/alphafold2_binder.Options:
esmfold, esmfold2, alphafold3, boltz2, chai1, protenix, alphafold2, alphafold2_binderESMFoldConfig
Configuration for ESMFold structure prediction.
ESMFold2Config
Configuration for ESMFold2 structure prediction.
AlphaFold3Config
Configuration for AlphaFold3 structure prediction.
Boltz2Config
Configuration for Boltz2 structure prediction.
Chai1Config
Configuration for Chai1 structure prediction.
ProtenixConfig
Configuration for Protenix structure prediction.
AlphaFold2Config
Configuration for the general AlphaFold2 multimer structure predictor.
AlphaFold2BinderStructureConfig
Configuration for the AF2 binder-design backend.
array | Complex
Target chains: a tuple of sequence strings (entity types auto-detected).
Structure | string
Target structure: a Structure object, file path (.pdb/.cif), or raw PDB/CIF content string.
number
default:"0.6"
Min mean pLDDT (0-1 scale) for a target folded from sequence; ignored when target_structure is set.
Usage
python