File size: 4,091 Bytes
4c02fbe | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 | """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
|