USalign/param_set.h at master · pylelab/USalign · GitHub

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/* These functions implement d0 normalization. The d0 for final TM-score
 * output is implemented by parameter_set4final. For both RNA alignment
 * and protein alignment, using d0 set by parameter_set4search yields
 * slightly better results during initial alignment-superposition iteration.
 */
#include <math.h>
#include "basic_fun.h"

void parameter_set4search(const int xlen, const int ylen,
                          double &D0_MIN, double &Lnorm,
                          double &score_d8, double &d0, double &d0_search, double &dcu0)
{
    // parameter initialization for searching: D0_MIN, Lnorm, d0, d0_search, score_d8
    D0_MIN = 0.5;
    dcu0 = 4.25; // update 3.85-->4.25

    Lnorm = getmin(xlen, ylen); // normalize TMscore by this in searching
    if (Lnorm <= 19)            // update 15-->19
        d0 = 0.168;             // update 0.5-->0.168
    else
        d0 = (1.24 * pow((Lnorm * 1.0 - 15), 1.0 / 3) - 1.8);
    D0_MIN = d0 + 0.8; // this should be moved to above
    d0 = D0_MIN;       // update: best for search

    d0_search = d0;
    if (d0_search > 8)
        d0_search = 8;
    if (d0_search < 4.5)
        d0_search = 4.5;

    score_d8 = 1.5 * pow(Lnorm * 1.0, 0.3) + 3.5; // remove pairs with dis>d8 during search & final
}

void parameter_set4final_C3prime(const double len, double &D0_MIN,
                                 double &Lnorm, double &d0, double &d0_search)
{
    D0_MIN = 0.3;

    Lnorm = len; // normalize TMscore by this in searching
    if (Lnorm <= 11)
        d0 = 0.3;
    else if (Lnorm > 11 && Lnorm <= 15)
        d0 = 0.4;
    else if (Lnorm > 15 && Lnorm <= 19)
        d0 = 0.5;
    else if (Lnorm > 19 && Lnorm <= 23)
        d0 = 0.6;
    else if (Lnorm > 23 && Lnorm < 30)
        d0 = 0.7;
    else
        d0 = (0.6 * pow((Lnorm * 1.0 - 0.5), 1.0 / 2) - 2.5);

    d0_search = d0;
    if (d0_search > 8)
        d0_search = 8;
    if (d0_search < 4.5)
        d0_search = 4.5;
}

void parameter_set4final(const double len, double &D0_MIN, double &Lnorm,
                         double &d0, double &d0_search, const int mol_type)
{
    if (mol_type > 0) // RNA
    {
        parameter_set4final_C3prime(len, D0_MIN, Lnorm,
                                    d0, d0_search);
        return;
    }
    D0_MIN = 0.5;

    Lnorm = len; // normalize TMscore by this in searching
    if (Lnorm <= 21)
        d0 = 0.5;
    else
        d0 = (1.24 * pow((Lnorm * 1.0 - 15), 1.0 / 3) - 1.8);
    if (d0 < D0_MIN)
        d0 = D0_MIN;
    d0_search = d0;
    if (d0_search > 8)
        d0_search = 8;
    if (d0_search < 4.5)
        d0_search = 4.5;
}

void parameter_set4scale(const int len, const double d_s, double &Lnorm,
                         double &d0, double &d0_search)
{
    d0 = d_s;
    Lnorm = len; // normalize TMscore by this in searching
    d0_search = d0;
    if (d0_search > 8)
        d0_search = 8;
    if (d0_search < 4.5)
        d0_search = 4.5;
}