| """Fully fictional guided-engineering data for the public tutorial.""" |
| from __future__ import annotations |
|
|
| from casmd.engineering.io import build_design_report |
| from casmd.engineering.models import ( |
| EngineeringConfig, |
| NucleotideContact, |
| RegionFingerprint, |
| RegionObjective, |
| RegionSpec, |
| ResidueKey, |
| TruncationSpec, |
| ) |
|
|
|
|
| TUTORIAL_CONFIG = EngineeringConfig( |
| protein_selection="segid A", |
| regions=( |
| RegionSpec( |
| "target_region", |
| "Fictional RNA target segment", |
| "segid B and resid 5:16", |
| RegionObjective.WEAKEN, |
| 4.0, |
| ), |
| RegionSpec( |
| "protected_region", |
| "Fictional RNA functional segment", |
| "segid B and resid 17:30", |
| RegionObjective.PRESERVE, |
| 4.0, |
| ), |
| ), |
| mutation_budget=5, |
| min_occupancy=0.05, |
| preservation_weight=1.0, |
| risk_weight=1.0, |
| o2prime_bonus=0.25, |
| max_preservation_burden=0.45, |
| truncations=(TruncationSpec("Fictional flexible loop", "A", 230, 276),), |
| ) |
|
|
|
|
| def _fp(resid, resname, region, occupancy, pairs, *, o2=0.0): |
| return RegionFingerprint( |
| protein=ResidueKey("A", resid, resname), |
| region_id=region, |
| contact_occupancy=occupancy, |
| mean_contact_distance_A=3.35, |
| p10_contact_distance_A=2.95, |
| contact_events=12, |
| longest_run_frames=85, |
| o2prime_occupancy=o2, |
| nucleotide_contacts=tuple( |
| NucleotideContact(ResidueKey("B", nucleotide, "A"), pair_occupancy) |
| for nucleotide, pair_occupancy in pairs |
| ), |
| ) |
|
|
|
|
| _REFERENCE_FINGERPRINTS = ( |
| _fp(112, "ARG", "target_region", 0.86, ((5, 0.74), (6, 0.61)), o2=0.31), |
| _fp(112, "ARG", "protected_region", 0.06, ((17, 0.06),)), |
| _fp(176, "ASN", "target_region", 0.72, ((7, 0.63),), o2=0.27), |
| _fp(245, "ARG", "target_region", 0.18, ((8, 0.18),), o2=0.03), |
| _fp(245, "ARG", "protected_region", 0.10, ((18, 0.10),)), |
| _fp(318, "LEU", "target_region", 0.22, ((9, 0.20),)), |
| _fp(318, "LEU", "protected_region", 0.68, ((19, 0.62),)), |
| _fp(362, "TYR", "target_region", 0.78, ((10, 0.70), (11, 0.52)), o2=0.44), |
| _fp(362, "TYR", "protected_region", 0.04, ((20, 0.04),)), |
| _fp(409, "ASP", "target_region", 0.69, ((12, 0.61),), o2=0.39), |
| _fp(455, "LYS", "target_region", 0.58, ((13, 0.50),)), |
| _fp(455, "LYS", "protected_region", 0.12, ((21, 0.11),)), |
| ) |
|
|
|
|
| _VARIANT_A_FINGERPRINTS = ( |
| _fp(112, "ALA", "target_region", 0.13, ((5, 0.11),), o2=0.02), |
| _fp(112, "ALA", "protected_region", 0.05, ((17, 0.05),)), |
| _fp(176, "ALA", "target_region", 0.11, ((7, 0.09),), o2=0.02), |
| _fp(318, "ALA", "target_region", 0.09, ((9, 0.08),)), |
| _fp(318, "ALA", "protected_region", 0.61, ((19, 0.56),)), |
| _fp(362, "ALA", "target_region", 0.12, ((10, 0.10),), o2=0.02), |
| _fp(362, "ALA", "protected_region", 0.04, ((20, 0.04),)), |
| _fp(409, "ALA", "target_region", 0.10, ((12, 0.08),), o2=0.01), |
| _fp(455, "ALA", "target_region", 0.16, ((13, 0.14),)), |
| _fp(455, "ALA", "protected_region", 0.11, ((21, 0.10),)), |
| ) |
|
|
|
|
| def load_synthetic_engineering_tutorial(): |
| """Return reference and Variant A reports made entirely from invented values.""" |
| provenance = { |
| "data_status": "fictional_synthetic_tutorial", |
| "notice": ( |
| "Fictional construct, residue numbering, and measurements. This tutorial " |
| "is not derived from an unpublished project." |
| ), |
| } |
| baseline = build_design_report( |
| config=TUTORIAL_CONFIG, |
| fingerprints=_REFERENCE_FINGERPRINTS, |
| n_frames=1000, |
| frame_interval_ps=100.0, |
| source_label="Fictional reference", |
| provenance=provenance, |
| rmsf_by_residue={"A:245": 3.2, "A:112": 1.2, "A:362": 1.3}, |
| ) |
| variant = build_design_report( |
| config=TUTORIAL_CONFIG, |
| fingerprints=_VARIANT_A_FINGERPRINTS, |
| n_frames=1000, |
| frame_interval_ps=100.0, |
| source_label="Fictional Variant A", |
| provenance=provenance, |
| ) |
| return baseline, variant |
|
|
