# Application Flowchart

## Data Pipeline

```mermaid
flowchart TD
    A[Variant list CSV/XLSX] --> B[HGVS parse + NP_000537.3 QC]
    B --> C{Mutation class}
    C -->|Missense| D[Literature or physics ΔΔG]
    C -->|Stop-gain / splice| E[Alternative strategy]
    D --> F[Cavity volume + SiteMap-like Dscore]
    F -->|Gate open| G[Library + Lipinski/Veber/QED]
    F -->|Hold/closed| E
    G --> H[Complementarity / Kd→ΔG]
    H --> I[Matched WT vs mutant scores]
    I --> J[ADMET + occupancy MD proxies]
    J --> K["R(c,m) Rescue/Opportunity"]
    K --> M[Dashboard + PDF / CSV]
    E --> M
    U[Optional uploaded dock_mut/dock_wt] --> I
```

## Scoring

```mermaid
flowchart TD
    Kd[Published Kd] -->|ΔG = RT ln Kd| Bmut[Bmut]
    Emp[Volume/hydrophobic complementarity] --> Bmut
    WT[Matched WT protocol] --> Sel[Selectivity]
    Bmut --> R[Rescue / Opportunity Score]
    Sel --> R
    MD[Occupancy / RMSD / MMGBSA] --> R
    Fr[Cavity + mechanism] --> R
    AD[Lipinski Veber Egan QED hERG] --> R
    Ev[Evidence] --> R
    Risk[Liabilities + OOD] --> R
    R --> Rec{Go / Hold / No-go}
```