| """Fully fictional example content shown in the public StrandMD UI.""" |
| from __future__ import annotations |
|
|
| from casmd.project import Condition, GuideMode, Project, Replicate, SystemClass |
|
|
|
|
| VARIANT_PROJECT = Project( |
| project_id="fictional-variant-a", |
| title="Fictional Variant A interface-engineering tutorial", |
| system_class=SystemClass.PROTEIN_NUCLEIC_ACID_TERNARY, |
| hypothesis=( |
| "Can a designed protein variant weaken one RNA interface while preserving " |
| "global stability and a protected protein–nucleic-acid interface?" |
| ), |
| conditions=tuple( |
| Condition( |
| condition_id=f"{variant.lower().replace(' ', '-')}-{mode.value.lower()}", |
| label=f"{variant} · {mode.value}", |
| variant=variant, |
| guide_mode=mode, |
| replicates=(Replicate("run-1"),), |
| ) |
| for variant, modes in ( |
| ("Reference", (GuideMode.RNA, GuideMode.DNA)), |
| ("Loop control", (GuideMode.RNA,)), |
| ("Linker control", (GuideMode.RNA,)), |
| ("Variant A", (GuideMode.RNA, GuideMode.DNA)), |
| ) |
| for mode in modes |
| ), |
| evidence_status="fictional_synthetic_tutorial", |
| ) |
|
|
|
|
| VARIANT_CONSTRUCTS = [ |
| { |
| "Construct": "Reference", |
| "Engineering": "Fictional full-length reference", |
| "Role": "Global-stability and interface reference", |
| }, |
| { |
| "Construct": "Loop control", |
| "Engineering": "Invented loop edit", |
| "Role": "Tests whether the loop edit alone changes the target interface", |
| }, |
| { |
| "Construct": "Linker control", |
| "Engineering": "Invented loop edit with neutral linker", |
| "Role": "Controls for geometry restoration", |
| }, |
| { |
| "Construct": "Variant A", |
| "Engineering": "Invented interface substitutions", |
| "Role": "Fictional optimization candidate", |
| }, |
| ] |
|
|
|
|
| VARIANT_METRICS = [ |
| { |
| "Synthetic metric": "Protein Cα RMSD", |
| "Reference": "2.40 ± 0.18 Å", |
| "Variant A": "2.47 ± 0.20 Å", |
| "Illustrative interpretation": "Similar simulated global stability", |
| }, |
| { |
| "Synthetic metric": "Radius of gyration", |
| "Reference": "34.8 ± 0.2 Å", |
| "Variant A": "34.6 ± 0.2 Å", |
| "Illustrative interpretation": "Comparable compactness", |
| }, |
| { |
| "Synthetic metric": "Target-region contacts", |
| "Reference": "1000 ± 40", |
| "Variant A": "420 ± 30", |
| "Illustrative interpretation": "42% retained", |
| }, |
| { |
| "Synthetic metric": "Protected-region contacts", |
| "Reference": "1200 ± 35", |
| "Variant A": "1050 ± 32", |
| "Illustrative interpretation": "88% retained", |
| }, |
| { |
| "Synthetic metric": "Second-guide contacts", |
| "Reference": "1500 ± 45", |
| "Variant A": "1470 ± 41", |
| "Illustrative interpretation": "98% retained", |
| }, |
| ] |
|
|
|
|
| VARIANT_RETENTION = { |
| "Target-region contacts": 42, |
| "Protected-region contacts": 88, |
| "Second-guide contacts": 98, |
| } |
|
|
|
|
| CONTROL_RETENTION = { |
| "Reference": 100, |
| "Loop control": 94, |
| "Linker control": 90, |
| "Variant A": 42, |
| } |
|
|
