ff_energy 0.4.1

fuzzyfold's nearest neighbor free energy evaluations.
Documentation 
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use crate::Base;

pub const T_REF: f64 = 37.0;
pub const MAX_LOOP: usize = 30;
pub const B: usize = 4;  // A, C, G, U
pub const P: usize = 6;  // AU, UA, CG, GC, GU, UG
                         
pub type StackParams = [[i32; P]; P]; 
pub type LoopParams = [i32; MAX_LOOP + 1];
pub type MismatchParams = [[[i32; B]; B]; P];
pub type DangleParams = [[i32; B]; P];

pub type Int11Params = [[[[i32; B]; B]; P]; P];
pub type Int21Params = [[[[[i32; B]; B]; B]; P]; P];
pub type Int22Params = [[[[[[i32; B]; B]; B]; B]; P]; P];

pub const E: usize = 8;  // AU, UA, CG, GC, GU, UG, AP, PA
pub type ExtendedStackParams = [[Option<i32>; E]; E];

#[derive(Copy, Clone, Debug)]
pub struct LoopEntry {
    pub seq: &'static [Base],
    pub val: i32,
}

/* NOTE: With the next modification, we may want to switch to a more
 * general format for end-penalties?:
 * ...but are these energies or penalties?
pub static CLOSING_PEN37: [i32; 8] = 
    /* [cl]:   AU     UA     CG     GC     GU     UG     AP     PA */
           [   50,    50,     0,     0,    50,    50,    31,    31];
*/

pub struct RNAThermoParams {
    pub stack_en37: &'static ExtendedStackParams,
    pub stack_enth: &'static ExtendedStackParams,
    pub mismatch_hairpin_en37: &'static MismatchParams,
    pub mismatch_hairpin_enth: &'static MismatchParams,
    pub mismatch_interior_en37: &'static MismatchParams,
    pub mismatch_interior_enth: &'static MismatchParams,
    pub mismatch_interior_1n_en37: &'static MismatchParams,
    pub mismatch_interior_1n_enth: &'static MismatchParams,
    pub mismatch_interior_23_en37: &'static MismatchParams,
    pub mismatch_interior_23_enth: &'static MismatchParams,
    pub mismatch_multi_en37: &'static MismatchParams,
    pub mismatch_multi_enth: &'static MismatchParams,
    pub mismatch_exterior_en37: &'static MismatchParams,
    pub mismatch_exterior_enth: &'static MismatchParams,
    pub dangle5_en37: &'static DangleParams,
    pub dangle5_enth: &'static DangleParams,
    pub dangle3_en37: &'static DangleParams,
    pub dangle3_enth: &'static DangleParams,
    pub int11_en37: &'static Int11Params,
    pub int11_enth: &'static Int11Params,
    pub int21_en37: &'static Int21Params,
    pub int21_enth: &'static Int21Params,
    pub int22_en37: &'static Int22Params,
    pub int22_enth: &'static Int22Params,
    pub hairpin_en37: &'static LoopParams,
    pub hairpin_enth: &'static LoopParams,
    pub bulge_en37: &'static LoopParams,
    pub bulge_enth: &'static LoopParams,
    pub interior_en37: &'static LoopParams,
    pub interior_enth: &'static LoopParams,
    // Misc parameters
    pub duplex_init_en37: i32,
    pub duplex_init_enth: i32,
    pub terminal_ru_en37: i32,
    pub terminal_ru_enth: i32,
    pub terminal_ap_en37: i32,
    pub terminal_ap_enth: i32,
    pub lxc: f64,
    // NINIO parameters
    pub ninio_en37: i32,
    pub ninio_enth: i32,
    pub ninio_max: i32,
    // Multi-loop parameters
    pub ml_base_en37: i32,
    pub ml_base_enth: i32,
    pub ml_closing_en37: i32,
    pub ml_closing_enth: i32,
    pub ml_intern_en37: i32,
    pub ml_intern_enth: i32,
    // Special haipin parameters
    pub triloops_en37: &'static [LoopEntry],
    pub triloops_enth: &'static [LoopEntry],
    pub tetraloops_en37: &'static [LoopEntry],
    pub tetraloops_enth: &'static [LoopEntry],
    pub hexaloops_en37: &'static [LoopEntry],
    pub hexaloops_enth: &'static [LoopEntry],
}