TMalign.h

/* Functions for the core TMalign algorithm, including the entry function
 * TMalign_main */
#ifndef TMalign_h
#define TMalign_h 1

#include "param_set.h"
#include "NW.h"
#include "Kabsch.h"
#include "NWalign.h"

//     1, collect those residues with dis<d;
//     2, calculate TMscore
int score_fun8(double **xa, double **ya, int n_ali, double d, int i_ali[],
               double *score1, int score_sum_method, const double Lnorm,
               const double score_d8, const double d0)
{
    double score_sum = 0, di;
    double d_tmp = d * d;
    double d02 = d0 * d0;
    double score_d8_cut = score_d8 * score_d8;

    int i, n_cut, inc = 0;

    while (1)
    {
        n_cut = 0;
        score_sum = 0;
        for (i = 0; i < n_ali; i++)
        {
            di = dist(xa[i], ya[i]);
            if (di < d_tmp)
            {
                i_ali[n_cut] = i;
                n_cut++;
            }
            if (score_sum_method == 8)
            {
                if (di <= score_d8_cut)
                    score_sum += 1 / (1 + di / d02);
            }
            else
                score_sum += 1 / (1 + di / d02);
        }
        // there are not enough feasible pairs, relieve the threshold
        if (n_cut < 3 && n_ali > 3)
        {
            inc++;
            double dinc = (d + inc * 0.5);
            d_tmp = dinc * dinc;
        }
        else
            break;
    }

    *score1 = score_sum / Lnorm;
    return n_cut;
}

int score_fun8_standard(double **xa, double **ya, int n_ali, double d,
                        int i_ali[], double *score1, int score_sum_method,
                        double score_d8, double d0)
{
    double score_sum = 0, di;
    double d_tmp = d * d;
    double d02 = d0 * d0;
    double score_d8_cut = score_d8 * score_d8;

    int i, n_cut, inc = 0;
    while (1)
    {
        n_cut = 0;
        score_sum = 0;
        for (i = 0; i < n_ali; i++)
        {
            di = dist(xa[i], ya[i]);
            if (di < d_tmp)
            {
                i_ali[n_cut] = i;
                n_cut++;
            }
            if (score_sum_method == 8)
            {
                if (di <= score_d8_cut)
                    score_sum += 1 / (1 + di / d02);
            }
            else
            {
                score_sum += 1 / (1 + di / d02);
            }
        }
        // there are not enough feasible pairs, relieve the threshold
        if (n_cut < 3 && n_ali > 3)
        {
            inc++;
            double dinc = (d + inc * 0.5);
            d_tmp = dinc * dinc;
        }
        else
            break;
    }

    *score1 = score_sum / n_ali;
    return n_cut;
}

double TMscore8_search(double **r1, double **r2, double **xtm, double **ytm,
                       double **xt, int Lali, double t0[3], double u0[3][3], int simplify_step,
                       int score_sum_method, double *Rcomm, double local_d0_search, double Lnorm,
                       double score_d8, double d0)
{
    int i, m;
    double score_max, score, rmsd;
    const int kmax = Lali;
    int k_ali[kmax], ka, k;
    double t[3];
    double u[3][3];
    double d;

    // iterative parameters
    int n_it = 20;         // maximum number of iterations
    int n_init_max = 6;    // maximum number of different fragment length
    int L_ini[n_init_max]; // fragment lengths, Lali, Lali/2, Lali/4 ... 4
    int L_ini_min = 4;
    if (Lali < L_ini_min)
        L_ini_min = Lali;

    int n_init = 0, i_init;
    for (i = 0; i < n_init_max - 1; i++)
    {
        n_init++;
        L_ini[i] = (int)(Lali / pow(2.0, (double)i));
        if (L_ini[i] <= L_ini_min)
        {
            L_ini[i] = L_ini_min;
            break;
        }
    }
    if (i == n_init_max - 1)
    {
        n_init++;
        L_ini[i] = L_ini_min;
    }

    score_max = -1;
    // find the maximum score starting from local structures superposition
    int i_ali[kmax], n_cut;
    int L_frag; // fragment length
    int iL_max; // maximum starting position for the fragment

    for (i_init = 0; i_init < n_init; i_init++)
    {
        L_frag = L_ini[i_init];
        iL_max = Lali - L_frag;

        i = 0;
        while (1)
        {
            // extract the fragment starting from position i
            ka = 0;
            for (k = 0; k < L_frag; k++)
            {
                int kk = k + i;
                r1[k][0] = xtm[kk][0];
                r1[k][1] = xtm[kk][1];
                r1[k][2] = xtm[kk][2];

                r2[k][0] = ytm[kk][0];
                r2[k][1] = ytm[kk][1];
                r2[k][2] = ytm[kk][2];

                k_ali[ka] = kk;
                ka++;
            }

            // extract rotation matrix based on the fragment
            Kabsch(r1, r2, L_frag, 1, &rmsd, t, u);
            if (simplify_step != 1)
                *Rcomm = 0;
            do_rotation(xtm, xt, Lali, t, u);

            // get subsegment of this fragment
            d = local_d0_search - 1;
            n_cut = score_fun8(xt, ytm, Lali, d, i_ali, &score,
                               score_sum_method, Lnorm, score_d8, d0);
            if (score > score_max)
            {
                score_max = score;

                // save the rotation matrix
                for (k = 0; k < 3; k++)
                {
                    t0[k] = t[k];
                    u0[k][0] = u[k][0];
                    u0[k][1] = u[k][1];
                    u0[k][2] = u[k][2];
                }
            }

            // try to extend the alignment iteratively
            d = local_d0_search + 1;
            for (int it = 0; it < n_it; it++)
            {
                ka = 0;
                for (k = 0; k < n_cut; k++)
                {
                    m = i_ali[k];
                    r1[k][0] = xtm[m][0];
                    r1[k][1] = xtm[m][1];
                    r1[k][2] = xtm[m][2];

                    r2[k][0] = ytm[m][0];
                    r2[k][1] = ytm[m][1];
                    r2[k][2] = ytm[m][2];

                    k_ali[ka] = m;
                    ka++;
                }
                // extract rotation matrix based on the fragment
                Kabsch(r1, r2, n_cut, 1, &rmsd, t, u);
                do_rotation(xtm, xt, Lali, t, u);
                n_cut = score_fun8(xt, ytm, Lali, d, i_ali, &score,
                                   score_sum_method, Lnorm, score_d8, d0);
                if (score > score_max)
                {
                    score_max = score;

                    // save the rotation matrix
                    for (k = 0; k < 3; k++)
                    {
                        t0[k] = t[k];
                        u0[k][0] = u[k][0];
                        u0[k][1] = u[k][1];
                        u0[k][2] = u[k][2];
                    }
                }

                // check if it converges
                if (n_cut == ka)
                {
                    for (k = 0; k < n_cut; k++)
                    {
                        if (i_ali[k] != k_ali[k])
                            break;
                    }
                    if (k == n_cut)
                        break;
                }
            } // for iteration

            if (i < iL_max)
            {
                i = i + simplify_step; // shift the fragment
                if (i > iL_max)
                    i = iL_max; // do this to use the last missed fragment
            }
            else if (i >= iL_max)
                break;
        } // while(1)
        // end of one fragment
    } // for(i_init
    return score_max;
}

double TMscore8_search_standard(double **r1, double **r2,
                                double **xtm, double **ytm, double **xt, int Lali,
                                double t0[3], double u0[3][3], int simplify_step, int score_sum_method,
                                double *Rcomm, double local_d0_search, double score_d8, double d0)
{
    int i, m;
    double score_max, score, rmsd;
    const int kmax = Lali;
    int k_ali[kmax], ka, k;
    double t[3];
    double u[3][3];
    double d;

    // iterative parameters
    int n_it = 20;         // maximum number of iterations
    int n_init_max = 6;    // maximum number of different fragment length
    int L_ini[n_init_max]; // fragment lengths, Lali, Lali/2, Lali/4 ... 4
    int L_ini_min = 4;
    if (Lali < L_ini_min)
        L_ini_min = Lali;

    int n_init = 0, i_init;
    for (i = 0; i < n_init_max - 1; i++)
    {
        n_init++;
        L_ini[i] = (int)(Lali / pow(2.0, (double)i));
        if (L_ini[i] <= L_ini_min)
        {
            L_ini[i] = L_ini_min;
            break;
        }
    }
    if (i == n_init_max - 1)
    {
        n_init++;
        L_ini[i] = L_ini_min;
    }

    score_max = -1;
    // find the maximum score starting from local structures superposition
    int i_ali[kmax], n_cut;
    int L_frag; // fragment length
    int iL_max; // maximum starting position for the fragment

    for (i_init = 0; i_init < n_init; i_init++)
    {
        L_frag = L_ini[i_init];
        iL_max = Lali - L_frag;

        i = 0;
        while (1)
        {
            // extract the fragment starting from position i
            ka = 0;
            for (k = 0; k < L_frag; k++)
            {
                int kk = k + i;
                r1[k][0] = xtm[kk][0];
                r1[k][1] = xtm[kk][1];
                r1[k][2] = xtm[kk][2];

                r2[k][0] = ytm[kk][0];
                r2[k][1] = ytm[kk][1];
                r2[k][2] = ytm[kk][2];

                k_ali[ka] = kk;
                ka++;
            }
            // extract rotation matrix based on the fragment
            Kabsch(r1, r2, L_frag, 1, &rmsd, t, u);
            if (simplify_step != 1)
                *Rcomm = 0;
            do_rotation(xtm, xt, Lali, t, u);

            // get subsegment of this fragment
            d = local_d0_search - 1;
            n_cut = score_fun8_standard(xt, ytm, Lali, d, i_ali, &score,
                                        score_sum_method, score_d8, d0);

            if (score > score_max)
            {
                score_max = score;

                // save the rotation matrix
                for (k = 0; k < 3; k++)
                {
                    t0[k] = t[k];
                    u0[k][0] = u[k][0];
                    u0[k][1] = u[k][1];
                    u0[k][2] = u[k][2];
                }
            }

            // try to extend the alignment iteratively
            d = local_d0_search + 1;
            for (int it = 0; it < n_it; it++)
            {
                ka = 0;
                for (k = 0; k < n_cut; k++)
                {
                    m = i_ali[k];
                    r1[k][0] = xtm[m][0];
                    r1[k][1] = xtm[m][1];
                    r1[k][2] = xtm[m][2];

                    r2[k][0] = ytm[m][0];
                    r2[k][1] = ytm[m][1];
                    r2[k][2] = ytm[m][2];

                    k_ali[ka] = m;
                    ka++;
                }
                // extract rotation matrix based on the fragment
                Kabsch(r1, r2, n_cut, 1, &rmsd, t, u);
                do_rotation(xtm, xt, Lali, t, u);
                n_cut = score_fun8_standard(xt, ytm, Lali, d, i_ali, &score,
                                            score_sum_method, score_d8, d0);
                if (score > score_max)
                {
                    score_max = score;

                    // save the rotation matrix
                    for (k = 0; k < 3; k++)
                    {
                        t0[k] = t[k];
                        u0[k][0] = u[k][0];
                        u0[k][1] = u[k][1];
                        u0[k][2] = u[k][2];
                    }
                }

                // check if it converges
                if (n_cut == ka)
                {
                    for (k = 0; k < n_cut; k++)
                    {
                        if (i_ali[k] != k_ali[k])
                            break;
                    }
                    if (k == n_cut)
                        break;
                }
            } // for iteration

            if (i < iL_max)
            {
                i = i + simplify_step; // shift the fragment
                if (i > iL_max)
                    i = iL_max; // do this to use the last missed fragment
            }
            else if (i >= iL_max)
                break;
        } // while(1)
        // end of one fragment
    } // for(i_init
    return score_max;
}

// Comprehensive TMscore search engine
//  input:   two vector sets: x, y
//           an alignment invmap0[] between x and y
//           simplify_step: 1 or 40 or other integers
//           score_sum_method: 0 for score over all pairs
//                             8 for socre over the pairs with dist<score_d8
//  output:  the best rotaion matrix t, u that results in highest TMscore
double detailed_search(double **r1, double **r2, double **xtm, double **ytm,
                       double **xt, double **x, double **y, int xlen, int ylen,
                       int invmap0[], double t[3], double u[3][3], int simplify_step,
                       int score_sum_method, double local_d0_search, double Lnorm,
                       double score_d8, double d0)
{
    // x is model, y is template, try to superpose onto y
    int i, j, k;
    double tmscore;
    double rmsd;

    k = 0;
    for (i = 0; i < ylen; i++)
    {
        j = invmap0[i];
        if (j >= 0) // aligned
        {
            xtm[k][0] = x[j][0];
            xtm[k][1] = x[j][1];
            xtm[k][2] = x[j][2];

            ytm[k][0] = y[i][0];
            ytm[k][1] = y[i][1];
            ytm[k][2] = y[i][2];
            k++;
        }
    }

    // detailed search 40-->1
    tmscore = TMscore8_search(r1, r2, xtm, ytm, xt, k, t, u, simplify_step,
                              score_sum_method, &rmsd, local_d0_search, Lnorm, score_d8, d0);
    return tmscore;
}

double detailed_search_standard(double **r1, double **r2,
                                double **xtm, double **ytm, double **xt, double **x, double **y,
                                int xlen, int ylen, int invmap0[], double t[3], double u[3][3],
                                int simplify_step, int score_sum_method, double local_d0_search,
                                const bool &bNormalize, double Lnorm, double score_d8, double d0)
{
    // x is model, y is template, try to superpose onto y
    int i, j, k;
    double tmscore;
    double rmsd;

    k = 0;
    for (i = 0; i < ylen; i++)
    {
        j = invmap0[i];
        if (j >= 0) // aligned
        {
            xtm[k][0] = x[j][0];
            xtm[k][1] = x[j][1];
            xtm[k][2] = x[j][2];

            ytm[k][0] = y[i][0];
            ytm[k][1] = y[i][1];
            ytm[k][2] = y[i][2];
            k++;
        }
    }

    // detailed search 40-->1
    tmscore = TMscore8_search_standard(r1, r2, xtm, ytm, xt, k, t, u,
                                       simplify_step, score_sum_method, &rmsd, local_d0_search, score_d8, d0);
    if (bNormalize) // "-i", to use standard_TMscore, then bNormalize=true, else bNormalize=false;
        tmscore = tmscore * k / Lnorm;

    return tmscore;
}

// compute the score quickly in three iterations
double get_score_fast(double **r1, double **r2, double **xtm, double **ytm,
                      double **x, double **y, int xlen, int ylen, int invmap[],
                      double d0, double d0_search, double t[3], double u[3][3])
{
    double rms, tmscore, tmscore1, tmscore2;
    int i, j, k;

    k = 0;
    for (j = 0; j < ylen; j++)
    {
        i = invmap[j];
        if (i >= 0)
        {
            r1[k][0] = x[i][0];
            r1[k][1] = x[i][1];
            r1[k][2] = x[i][2];

            r2[k][0] = y[j][0];
            r2[k][1] = y[j][1];
            r2[k][2] = y[j][2];

            xtm[k][0] = x[i][0];
            xtm[k][1] = x[i][1];
            xtm[k][2] = x[i][2];

            ytm[k][0] = y[j][0];
            ytm[k][1] = y[j][1];
            ytm[k][2] = y[j][2];

            k++;
        }
        else if (i != -1)
            PrintErrorAndQuit("Wrong map!\n");
    }
    Kabsch(r1, r2, k, 1, &rms, t, u);

    // evaluate score
    double di;
    const int len = k;
    double dis[len];
    double d00 = d0_search;
    double d002 = d00 * d00;
    double d02 = d0 * d0;

    int n_ali = k;
    double xrot[3];
    tmscore = 0;
    for (k = 0; k < n_ali; k++)
    {
        transform(t, u, &xtm[k][0], xrot);
        di = dist(xrot, &ytm[k][0]);
        dis[k] = di;
        tmscore += 1 / (1 + di / d02);
    }

    // second iteration
    double d002t = d002;
    vector<double> dis_vec(dis, dis + n_ali);
    sort(dis_vec.begin(), dis_vec.end());
    if (dis_vec.size()>2)
    {
        if (d002t < dis_vec[2])
            d002t = dis_vec[2];
    }
    else if (d002t < dis_vec.back())
        d002t = dis_vec.back();
    dis_vec.clear();
    while (1)
    {
        j = 0;
        for (k = 0; k < n_ali; k++)
        {
            if (dis[k] <= d002t)
            {
                r1[j][0] = xtm[k][0];
                r1[j][1] = xtm[k][1];
                r1[j][2] = xtm[k][2];

                r2[j][0] = ytm[k][0];
                r2[j][1] = ytm[k][1];
                r2[j][2] = ytm[k][2];

                j++;
            }
        }
        // there are not enough feasible pairs, relieve the threshold
        if (j < 3 && n_ali > 3)
            d002t += 0.5;
        else
            break;
    }

    if (n_ali != j)
    {
        Kabsch(r1, r2, j, 1, &rms, t, u);
        tmscore1 = 0;
        for (k = 0; k < n_ali; k++)
        {
            transform(t, u, &xtm[k][0], xrot);
            di = dist(xrot, &ytm[k][0]);
            dis[k] = di;
            tmscore1 += 1 / (1 + di / d02);
        }

        // third iteration
        d002t = d002 + 1;
        vector<double> dis_vec(dis, dis + n_ali);
        sort(dis_vec.begin(), dis_vec.end());
        if (dis_vec.size()>2)
        {
            if (d002t < dis_vec[2])
                d002t = dis_vec[2];
        }
        else if (d002t < dis_vec.back())
            d002t = dis_vec.back();

        dis_vec.clear();
        while (1)
        {
            j = 0;
            for (k = 0; k < n_ali; k++)
            {
                if (dis[k] <= d002t)
                {
                    r1[j][0] = xtm[k][0];
                    r1[j][1] = xtm[k][1];
                    r1[j][2] = xtm[k][2];

                    r2[j][0] = ytm[k][0];
                    r2[j][1] = ytm[k][1];
                    r2[j][2] = ytm[k][2];

                    j++;
                }
            }
            // there are not enough feasible pairs, relieve the threshold
            if (j < 3 && n_ali > 3)
                d002t += 0.5;
            else
                break;
        }

        // evaluate the score
        Kabsch(r1, r2, j, 1, &rms, t, u);
        tmscore2 = 0;
        for (k = 0; k < n_ali; k++)
        {
            transform(t, u, &xtm[k][0], xrot);
            di = dist(xrot, &ytm[k][0]);
            tmscore2 += 1 / (1 + di / d02);
        }
    }
    else
    {
        tmscore1 = tmscore;
        tmscore2 = tmscore;
    }

    if (tmscore1 >= tmscore)
        tmscore = tmscore1;
    if (tmscore2 >= tmscore)
        tmscore = tmscore2;
    return tmscore; // no need to normalize this score because it will not be used for latter scoring
}

// perform gapless threading to find the best initial alignment
// input: x, y, xlen, ylen
// output: y2x0 stores the best alignment: e.g.,
// y2x0[j]=i means:
// the jth element in y is aligned to the ith element in x if i>=0
// the jth element in y is aligned to a gap in x if i==-1
double get_initial(double **r1, double **r2, double **xtm, double **ytm,
                   double **x, double **y, int xlen, int ylen, int *y2x,
                   double d0, double d0_search, const bool fast_opt,
                   double t[3], double u[3][3])
{
    int min_len = getmin(xlen, ylen);
    if (min_len < 3)
        PrintErrorAndQuit("Sequence is too short <3!\n");

    int min_ali = min_len / 2; // minimum size of considered fragment
    if (min_ali <= 5)
        min_ali = 5;
    int n1, n2;
    n1 = -ylen + min_ali;
    n2 = xlen - min_ali;

    int i, j, k, k_best;
    double tmscore, tmscore_max = -1;

    k_best = n1;
    for (k = n1; k <= n2; k += (fast_opt) ? 5 : 1)
    {
        // get the map
        for (j = 0; j < ylen; j++)
        {
            i = j + k;
            if (i >= 0 && i < xlen)
                y2x[j] = i;
            else
                y2x[j] = -1;
        }

        // evaluate the map quickly in three iterations
        // this is not real tmscore, it is used to evaluate the goodness of the initial alignment
        tmscore = get_score_fast(r1, r2, xtm, ytm,
                                 x, y, xlen, ylen, y2x, d0, d0_search, t, u);
        if (tmscore >= tmscore_max)
        {
            tmscore_max = tmscore;
            k_best = k;
        }
    }

    // extract the best map
    k = k_best;
    for (j = 0; j < ylen; j++)
    {
        i = j + k;
        if (i >= 0 && i < xlen)
            y2x[j] = i;
        else
            y2x[j] = -1;
    }

    return tmscore_max;
}

void smooth(int *sec, int len)
{
    int i, j;
    // smooth single  --x-- => -----
    for (i = 2; i < len - 2; i++)
    {
        if (sec[i] == 2 || sec[i] == 4)
        {
            j = sec[i];
            if (sec[i - 2] != j && sec[i - 1] != j && sec[i + 1] != j && sec[i + 2] != j)
                sec[i] = 1;
        }
    }

    //   smooth double
    //   --xx-- => ------
    for (i = 0; i < len - 5; i++)
    {
        // helix
        if (sec[i] != 2 && sec[i + 1] != 2 && sec[i + 2] == 2 && sec[i + 3] == 2 &&
            sec[i + 4] != 2 && sec[i + 5] != 2)
        {
            sec[i + 2] = 1;
            sec[i + 3] = 1;
        }

        // beta
        if (sec[i] != 4 && sec[i + 1] != 4 && sec[i + 2] == 4 && sec[i + 3] == 4 &&
            sec[i + 4] != 4 && sec[i + 5] != 4)
        {
            sec[i + 2] = 1;
            sec[i + 3] = 1;
        }
    }

    // smooth connect
    for (i = 0; i < len - 2; i++)
    {
        if (sec[i] == 2 && sec[i + 1] != 2 && sec[i + 2] == 2)
            sec[i + 1] = 2;
        else if (sec[i] == 4 && sec[i + 1] != 4 && sec[i + 2] == 4)
            sec[i + 1] = 4;
    }
}

char sec_str(double dis13, double dis14, double dis15,
             double dis24, double dis25, double dis35)
{
    char s = 'C';

    double delta = 2.1;
    if (fabs(dis15 - 6.37) < delta && fabs(dis14 - 5.18) < delta &&
        fabs(dis25 - 5.18) < delta && fabs(dis13 - 5.45) < delta &&
        fabs(dis24 - 5.45) < delta && fabs(dis35 - 5.45) < delta)
    {
        s = 'H'; // helix
        return s;
    }

    delta = 1.42;
    if (fabs(dis15 - 13) < delta && fabs(dis14 - 10.4) < delta &&
        fabs(dis25 - 10.4) < delta && fabs(dis13 - 6.1) < delta &&
        fabs(dis24 - 6.1) < delta && fabs(dis35 - 6.1) < delta)
    {
        s = 'E'; // strand
        return s;
    }

    if (dis15 < 8)
        s = 'T'; // turn
    return s;
}

/* secondary structure assignment for protein:
 * 1->coil, 2->helix, 3->turn, 4->strand */
void make_sec(double **x, int len, char *sec)
{
    int j1, j2, j3, j4, j5;
    double d13, d14, d15, d24, d25, d35;
    for (int i = 0; i < len; i++)
    {
        sec[i] = 'C';
        j1 = i - 2;
        j2 = i - 1;
        j3 = i;
        j4 = i + 1;
        j5 = i + 2;

        if (j1 >= 0 && j5 < len)
        {
            d13 = sqrt(dist(x[j1], x[j3]));
            d14 = sqrt(dist(x[j1], x[j4]));
            d15 = sqrt(dist(x[j1], x[j5]));
            d24 = sqrt(dist(x[j2], x[j4]));
            d25 = sqrt(dist(x[j2], x[j5]));
            d35 = sqrt(dist(x[j3], x[j5]));
            sec[i] = sec_str(d13, d14, d15, d24, d25, d35);
        }
    }
    sec[len] = 0;
}

/* a c d b: a paired to b, c paired to d */
bool overlap(const int a1, const int b1, const int c1, const int d1,
             const int a2, const int b2, const int c2, const int d2)
{
    return (a2 >= a1 && a2 <= c1) || (c2 >= a1 && c2 <= c1) ||
           (d2 >= a1 && d2 <= c1) || (b2 >= a1 && b2 <= c1) ||
           (a2 >= d1 && a2 <= b1) || (c2 >= d1 && c2 <= b1) ||
           (d2 >= d1 && d2 <= b1) || (b2 >= d1 && b2 <= b1);
}

/* find base pairing stacks in RNA*/
void sec_str(int len, char *seq, const vector<vector<bool> > &bp,
             int a, int b, int &c, int &d)
{
    int i;

    for (i = 0; i < len; i++)
    {
        if (a + i < len - 3 && b - i > 0)
        {
            if (a + i < b - i && bp[a + i][b - i])
                continue;
            break;
        }
    }
    c = a + i - 1;
    d = b - i + 1;
}

/* secondary structure assignment for RNA:
 * 1->unpair, 2->paired with upstream, 3->paired with downstream */
void make_sec(char *seq, double **x, int len, char *sec, const string atom_opt)
{
    int ii, jj, i, j;

    float lb = 12.5; // lower bound for " C3'"
    float ub = 15.0; // upper bound for " C3'"
    if (atom_opt == " C4'")
    {
        lb = 14.0;
        ub = 16.0;
    }
    else if (atom_opt == " C5'")
    {
        lb = 16.0;
        ub = 18.0;
    }
    else if (atom_opt == " O3'")
    {
        lb = 13.5;
        ub = 16.5;
    }
    else if (atom_opt == " O5'")
    {
        lb = 15.5;
        ub = 18.5;
    }
    else if (atom_opt == " P  ")
    {
        lb = 16.5;
        ub = 21.0;
    }

    float dis;
    vector<bool> bp_tmp(len, false);
    vector<vector<bool> > bp(len, bp_tmp);
    bp_tmp.clear();
    for (i = 0; i < len; i++)
    {
        sec[i] = '.';
        for (j = i + 1; j < len; j++)
        {
            if (((seq[i] == 'u' || seq[i] == 't') && (seq[j] == 'a')) ||
                ((seq[i] == 'a') && (seq[j] == 'u' || seq[j] == 't')) ||
                ((seq[i] == 'g') && (seq[j] == 'c' || seq[j] == 'u')) ||
                ((seq[i] == 'c' || seq[i] == 'u') && (seq[j] == 'g')))
            {
                dis = sqrt(dist(x[i], x[j]));
                bp[j][i] = bp[i][j] = (dis > lb && dis < ub);
            }
        }
    }

    // From 5' to 3': A0_var C0_var D0_var B0_var: A0_var paired to B0_var, C0_var paired to D0_var
    vector<int> A0_var, B0_var, C0_var, D0_var;
    for (i = 0; i < len - 2; i++)
    {
        for (j = i + 3; j < len; j++)
        {
            if (!bp[i][j])
                continue;
            if (i > 0 && j + 1 < len && bp[i - 1][j + 1])
                continue;
            if (!bp[i + 1][j - 1])
                continue;
            sec_str(len, seq, bp, i, j, ii, jj);
            if (jj < i || j < ii)
            {
                ii = i;
                jj = j;
            }
            A0_var.push_back(i);
            B0_var.push_back(j);
            C0_var.push_back(ii);
            D0_var.push_back(jj);
        }
    }

    // int sign;
    for (i = 0; i < A0_var.size(); i++)
    {
        /*
        sign=0;
        if(C0_var[i]-A0_var[i]<=1)
        {
            for(j=0;j<A0_var.size();j++)
            {
                if(i==j) continue;

                if((A0_var[j]>=A0_var[i]&&A0_var[j]<=C0_var[i])||
                   (C0_var[j]>=A0_var[i]&&C0_var[j]<=C0_var[i])||
                   (D0_var[j]>=A0_var[i]&&D0_var[j]<=C0_var[i])||
                   (B0_var[j]>=A0_var[i]&&B0_var[j]<=C0_var[i])||
                   (A0_var[j]>=D0_var[i]&&A0_var[j]<=B0_var[i])||
                   (C0_var[j]>=D0_var[i]&&C0_var[j]<=B0_var[i])||
                   (D0_var[j]>=D0_var[i]&&D0_var[j]<=B0_var[i])||
                   (B0_var[j]>=D0_var[i]&&B0_var[j]<=B0_var[i]))
                {
                    sign=-1;
                    break;
                }
            }
        }
        if(sign!=0) continue;
        */

        for (j = 0;; j++)
        {
            if (A0_var[i] + j > C0_var[i])
                break;
            sec[A0_var[i] + j] = '<';
            sec[D0_var[i] + j] = '>';
        }
    }
    sec[len] = 0;

    /* clean up */
    A0_var.clear();
    B0_var.clear();
    C0_var.clear();
    D0_var.clear();
    bp.clear();
}

// get initial alignment from secondary structure alignment
// input: x, y, xlen, ylen
// output: y2x stores the best alignment: e.g.,
// y2x[j]=i means:
// the jth element in y is aligned to the ith element in x if i>=0
// the jth element in y is aligned to a gap in x if i==-1
void get_initial_ss(bool **path, double **val,
                    const char *secx, const char *secy, int xlen, int ylen, int *y2x)
{
    double gap_open = -1.0;
    NWDP_TM(path, val, secx, secy, xlen, ylen, gap_open, y2x);
}

// get_initial5 in TMalign fortran, get_initial_local in TMalign c by yangji
// get initial alignment of local structure superposition
// input: x, y, xlen, ylen
// output: y2x stores the best alignment: e.g.,
// y2x[j]=i means:
// the jth element in y is aligned to the ith element in x if i>=0
// the jth element in y is aligned to a gap in x if i==-1
bool get_initial5(double **r1, double **r2, double **xtm, double **ytm,
                  bool **path, double **val,
                  double **x, double **y, int xlen, int ylen, int *y2x,
                  double d0, double d0_search, const bool fast_opt, const double D0_MIN)
{
    double GL, rmsd;
    double t[3];
    double u[3][3];

    double d01 = d0 + 1.5;
    if (d01 < D0_MIN)
        d01 = D0_MIN;
    double d02 = d01 * d01;

    double GLmax = 0;
    int aL = getmin(xlen, ylen);
    int *invmap = new int[ylen + 1];

    // jump on sequence1-------------->
    int n_jump1 = 0;
    if (xlen > 250)
        n_jump1 = 45;
    else if (xlen > 200)
        n_jump1 = 35;
    else if (xlen > 150)
        n_jump1 = 25;
    else
        n_jump1 = 15;
    if (n_jump1 > (xlen / 3))
        n_jump1 = xlen / 3;

    // jump on sequence2-------------->
    int n_jump2 = 0;
    if (ylen > 250)
        n_jump2 = 45;
    else if (ylen > 200)
        n_jump2 = 35;
    else if (ylen > 150)
        n_jump2 = 25;
    else
        n_jump2 = 15;
    if (n_jump2 > (ylen / 3))
        n_jump2 = ylen / 3;

    // fragment to superimpose-------------->
    int n_frag[2] = {20, 100};
    if (n_frag[0] > (aL / 3))
        n_frag[0] = aL / 3;
    if (n_frag[1] > (aL / 2))
        n_frag[1] = aL / 2;

    // start superimpose search-------------->
    if (fast_opt)
    {
        n_jump1 *= 5;
        n_jump2 *= 5;
    }
    bool flag = false;
    for (int i_frag = 0; i_frag < 2; i_frag++)
    {
        int m1 = xlen - n_frag[i_frag] + 1;
        int m2 = ylen - n_frag[i_frag] + 1;

        for (int i = 0; i < m1; i = i + n_jump1) // index starts from 0, different from FORTRAN
        {
            for (int j = 0; j < m2; j = j + n_jump2)
            {
                for (int k = 0; k < n_frag[i_frag]; k++) // fragment in y
                {
                    r1[k][0] = x[k + i][0];
                    r1[k][1] = x[k + i][1];
                    r1[k][2] = x[k + i][2];

                    r2[k][0] = y[k + j][0];
                    r2[k][1] = y[k + j][1];
                    r2[k][2] = y[k + j][2];
                }

                // superpose the two structures and rotate it
                Kabsch(r1, r2, n_frag[i_frag], 1, &rmsd, t, u);

                double gap_open = 0.0;
                NWDP_TM(path, val, x, y, xlen, ylen,
                        t, u, d02, gap_open, invmap);
                GL = get_score_fast(r1, r2, xtm, ytm, x, y, xlen, ylen,
                                    invmap, d0, d0_search, t, u);
                if (GL > GLmax)
                {
                    GLmax = GL;
                    for (int ii = 0; ii < ylen; ii++)
                        y2x[ii] = invmap[ii];
                    flag = true;
                }
            }
        }
    }

    delete[] invmap;
    return flag;
}

void score_matrix_rmsd_sec(double **r1, double **r2, double **score,
                           const char *secx, const char *secy, double **x, double **y,
                           int xlen, int ylen, int *y2x, const double D0_MIN, double d0)
{
    double t[3], u[3][3];
    double rmsd, dij;
    double d01 = d0 + 1.5;
    if (d01 < D0_MIN)
        d01 = D0_MIN;
    double d02 = d01 * d01;

    double xx[3];
    int i, k = 0;
    for (int j = 0; j < ylen; j++)
    {
        i = y2x[j];
        if (i >= 0)
        {
            r1[k][0] = x[i][0];
            r1[k][1] = x[i][1];
            r1[k][2] = x[i][2];

            r2[k][0] = y[j][0];
            r2[k][1] = y[j][1];
            r2[k][2] = y[j][2];

            k++;
        }
    }
    Kabsch(r1, r2, k, 1, &rmsd, t, u);

    for (int ii = 0; ii < xlen; ii++)
    {
        transform(t, u, &x[ii][0], xx);
        for (int jj = 0; jj < ylen; jj++)
        {
            dij = dist(xx, &y[jj][0]);
            if (secx[ii] == secy[jj])
                score[ii + 1][jj + 1] = 1.0 / (1 + dij / d02) + 0.5;
            else
                score[ii + 1][jj + 1] = 1.0 / (1 + dij / d02);
        }
    }
}

// get initial alignment from secondary structure and previous alignments
// input: x, y, xlen, ylen
// output: y2x stores the best alignment: e.g.,
// y2x[j]=i means:
// the jth element in y is aligned to the ith element in x if i>=0
// the jth element in y is aligned to a gap in x if i==-1
void get_initial_ssplus(double **r1, double **r2, double **score, bool **path,
                        double **val, const char *secx, const char *secy, double **x, double **y,
                        int xlen, int ylen, int *y2x0, int *y2x, const double D0_MIN, double d0)
{
    // create score matrix for DP
    score_matrix_rmsd_sec(r1, r2, score, secx, secy, x, y, xlen, ylen,
                          y2x0, D0_MIN, d0);

    double gap_open = -1.0;
    NWDP_TM(score, path, val, xlen, ylen, gap_open, y2x);
}

void find_max_frag(double **x, int len, int *start_max,
                   int *end_max, double dcu0, const bool fast_opt)
{
    int r_min, fra_min = 4; // minimum fragment for search
    if (fast_opt)
        fra_min = 8;
    int start;
    int Lfr_max = 0;

    r_min = (int)(len * 1.0 / 3.0); // minimum fragment, in case too small protein
    if (r_min > fra_min)
        r_min = fra_min;

    int inc = 0;
    double dcu0_cut = dcu0 * dcu0;
    ;
    double dcu_cut = dcu0_cut;

    while (Lfr_max < r_min)
    {
        Lfr_max = 0;
        int j = 1; // number of residues at nf-fragment
        start = 0;
        for (int i = 1; i < len; i++)
        {
            if (dist(x[i - 1], x[i]) < dcu_cut)
            {
                j++;

                if (i == (len - 1))
                {
                    if (j > Lfr_max)
                    {
                        Lfr_max = j;
                        *start_max = start;
                        *end_max = i;
                    }
                    j = 1;
                }
            }
            else
            {
                if (j > Lfr_max)
                {
                    Lfr_max = j;
                    *start_max = start;
                    *end_max = i - 1;
                }

                j = 1;
                start = i;
            }
        } // for i;

        if (Lfr_max < r_min)
        {
            inc++;
            double dinc = pow(1.1, (double)inc) * dcu0;
            dcu_cut = dinc * dinc;
        }
    } // while <;
}

// perform fragment gapless threading to find the best initial alignment
// input: x, y, xlen, ylen
// output: y2x0 stores the best alignment: e.g.,
// y2x0[j]=i means:
// the jth element in y is aligned to the ith element in x if i>=0
// the jth element in y is aligned to a gap in x if i==-1
double get_initial_fgt(double **r1, double **r2, double **xtm, double **ytm,
                       double **x, double **y, int xlen, int ylen,
                       int *y2x, double d0, double d0_search,
                       double dcu0, const bool fast_opt, double t[3], double u[3][3])
{
    int fra_min = 4; // minimum fragment for search
    if (fast_opt)
        fra_min = 8;
    int fra_min1 = fra_min - 1; // cutoff for shift, save time

    int xstart = 0, ystart = 0, xend = 0, yend = 0;

    find_max_frag(x, xlen, &xstart, &xend, dcu0, fast_opt);
    find_max_frag(y, ylen, &ystart, &yend, dcu0, fast_opt);

    int Lx = xend - xstart + 1;
    int Ly = yend - ystart + 1;
    int *ifr, *y2x_;
    int L_fr = getmin(Lx, Ly);
    ifr = new int[L_fr];
    y2x_ = new int[ylen + 1];

    // select what piece will be used. The original implement may cause
    // asymetry, but only when xlen==ylen and Lx==Ly
    // if L1=Lfr1 and L2=Lfr2 (normal proteins), it will be the same as initial1

    if (Lx < Ly || (Lx == Ly && xlen < ylen))
    {
        for (int i = 0; i < L_fr; i++)
            ifr[i] = xstart + i;
    }
    else if (Lx > Ly || (Lx == Ly && xlen > ylen))
    {
        for (int i = 0; i < L_fr; i++)
            ifr[i] = ystart + i;
    }
    else // solve asymetric for 1x5gA vs 2q7nA5
    {
        /* In this case, L0==xlen==ylen; L_fr==Lx==Ly */
        int L0 = xlen;
        double tmscore, tmscore_max = -1;
        int i, j, k;
        int n1, n2;
        int min_len;
        int min_ali;

        /* part 1, normalized by xlen */
        for (i = 0; i < L_fr; i++)
            ifr[i] = xstart + i;

        if (L_fr == L0)
        {
            n1 = (int)(L0 * 0.1); // my index starts from 0
            n2 = (int)(L0 * 0.89);
            j = 0;
            for (i = n1; i <= n2; i++)
            {
                ifr[j] = ifr[i];
                j++;
            }
            L_fr = j;
        }

        int L1 = L_fr;
        min_len = getmin(L1, ylen);
        min_ali = (int)(min_len / 2.5); // minimum size of considered fragment
        if (min_ali <= fra_min1)
            min_ali = fra_min1;
        n1 = -ylen + min_ali;
        n2 = L1 - min_ali;

        for (k = n1; k <= n2; k += (fast_opt) ? 3 : 1)
        {
            // get the map
            for (j = 0; j < ylen; j++)
            {
                i = j + k;
                if (i >= 0 && i < L1)
                    y2x_[j] = ifr[i];
                else
                    y2x_[j] = -1;
            }

            // evaluate the map quickly in three iterations
            tmscore = get_score_fast(r1, r2, xtm, ytm, x, y, xlen, ylen, y2x_,
                                     d0, d0_search, t, u);

            if (tmscore >= tmscore_max)
            {
                tmscore_max = tmscore;
                for (j = 0; j < ylen; j++)
                    y2x[j] = y2x_[j];
            }
        }

        /* part 2, normalized by ylen */
        L_fr = Ly;
        for (i = 0; i < L_fr; i++)
            ifr[i] = ystart + i;

        if (L_fr == L0)
        {
            n1 = (int)(L0 * 0.1); // my index starts from 0
            n2 = (int)(L0 * 0.89);

            j = 0;
            for (i = n1; i <= n2; i++)
            {
                ifr[j] = ifr[i];
                j++;
            }
            L_fr = j;
        }

        int L2 = L_fr;
        min_len = getmin(xlen, L2);
        min_ali = (int)(min_len / 2.5); // minimum size of considered fragment
        if (min_ali <= fra_min1)
            min_ali = fra_min1;
        n1 = -L2 + min_ali;
        n2 = xlen - min_ali;

        for (k = n1; k <= n2; k++)
        {
            // get the map
            for (j = 0; j < ylen; j++)
                y2x_[j] = -1;

            for (j = 0; j < L2; j++)
            {
                i = j + k;
                if (i >= 0 && i < xlen)
                    y2x_[ifr[j]] = i;
            }

            // evaluate the map quickly in three iterations
            tmscore = get_score_fast(r1, r2, xtm, ytm,
                                     x, y, xlen, ylen, y2x_, d0, d0_search, t, u);
            if (tmscore >= tmscore_max)
            {
                tmscore_max = tmscore;
                for (j = 0; j < ylen; j++)
                    y2x[j] = y2x_[j];
            }
        }

        delete[] ifr;
        delete[] y2x_;
        return tmscore_max;
    }

    int L0 = getmin(xlen, ylen); // non-redundant to get_initial1
    if (L_fr == L0)
    {
        int n1 = (int)(L0 * 0.1); // my index starts from 0
        int n2 = (int)(L0 * 0.89);

        int j = 0;
        for (int i = n1; i <= n2; i++)
        {
            ifr[j] = ifr[i];
            j++;
        }
        L_fr = j;
    }

    // gapless threading for the extracted fragment
    double tmscore, tmscore_max = -1;

    if (Lx < Ly || (Lx == Ly && xlen <= ylen))
    {
        int L1 = L_fr;
        int min_len = getmin(L1, ylen);
        int min_ali = (int)(min_len / 2.5); // minimum size of considered fragment
        if (min_ali <= fra_min1)
            min_ali = fra_min1;
        int n1, n2;
        n1 = -ylen + min_ali;
        n2 = L1 - min_ali;

        int i, j, k;
        for (k = n1; k <= n2; k += (fast_opt) ? 3 : 1)
        {
            // get the map
            for (j = 0; j < ylen; j++)
            {
                i = j + k;
                if (i >= 0 && i < L1)
                    y2x_[j] = ifr[i];
                else
                    y2x_[j] = -1;
            }

            // evaluate the map quickly in three iterations
            tmscore = get_score_fast(r1, r2, xtm, ytm, x, y, xlen, ylen, y2x_,
                                     d0, d0_search, t, u);

            if (tmscore >= tmscore_max)
            {
                tmscore_max = tmscore;
                for (j = 0; j < ylen; j++)
                    y2x[j] = y2x_[j];
            }
        }
    }
    else
    {
        int L2 = L_fr;
        int min_len = getmin(xlen, L2);
        int min_ali = (int)(min_len / 2.5); // minimum size of considered fragment
        if (min_ali <= fra_min1)
            min_ali = fra_min1;
        int n1, n2;
        n1 = -L2 + min_ali;
        n2 = xlen - min_ali;

        int i, j, k;

        for (k = n1; k <= n2; k++)
        {
            // get the map
            for (j = 0; j < ylen; j++)
                y2x_[j] = -1;

            for (j = 0; j < L2; j++)
            {
                i = j + k;
                if (i >= 0 && i < xlen)
                    y2x_[ifr[j]] = i;
            }

            // evaluate the map quickly in three iterations
            tmscore = get_score_fast(r1, r2, xtm, ytm,
                                     x, y, xlen, ylen, y2x_, d0, d0_search, t, u);
            if (tmscore >= tmscore_max)
            {
                tmscore_max = tmscore;
                for (j = 0; j < ylen; j++)
                    y2x[j] = y2x_[j];
            }
        }
    }

    delete[] ifr;
    delete[] y2x_;
    return tmscore_max;
}

// heuristic run of dynamic programing iteratively to find the best alignment
// input: initial rotation matrix t, u
//        vectors x and y, d0
// output: best alignment that maximizes the TMscore, will be stored in invmap
double DP_iter(double **r1, double **r2, double **xtm, double **ytm,
               double **xt, bool **path, double **val, double **x, double **y,
               int xlen, int ylen, double t[3], double u[3][3], int invmap0[],
               int g1, int g2, int iteration_max, double local_d0_search,
               double D0_MIN, double Lnorm, double d0, double score_d8)
{
    double gap_open[2] = {-0.6, 0};
    double rmsd;
    int *invmap = new int[ylen + 1];

    int iteration, i, j, k;
    double tmscore, tmscore_max, tmscore_old = 0;
    int score_sum_method = 8, simplify_step = 40;
    tmscore_max = -1;

    // double d01=d0+1.5;
    double d02 = d0 * d0;
    for (int g = g1; g < g2; g++)
    {
        for (iteration = 0; iteration < iteration_max; iteration++)
        {
            NWDP_TM(path, val, x, y, xlen, ylen,
                    t, u, d02, gap_open[g], invmap);

            k = 0;
            for (j = 0; j < ylen; j++)
            {
                i = invmap[j];

                if (i >= 0) // aligned
                {
                    xtm[k][0] = x[i][0];
                    xtm[k][1] = x[i][1];
                    xtm[k][2] = x[i][2];

                    ytm[k][0] = y[j][0];
                    ytm[k][1] = y[j][1];
                    ytm[k][2] = y[j][2];
                    k++;
                }
            }

            tmscore = TMscore8_search(r1, r2, xtm, ytm, xt, k, t, u,
                                      simplify_step, score_sum_method, &rmsd, local_d0_search,
                                      Lnorm, score_d8, d0);

            if (tmscore > tmscore_max)
            {
                tmscore_max = tmscore;
                for (i = 0; i < ylen; i++)
                    invmap0[i] = invmap[i];
            }

            if (iteration > 0)
            {
                if (fabs(tmscore_old - tmscore) < 0.000001)
                    break;
            }
            tmscore_old = tmscore;
        } // for iteration

    } // for gapopen

    delete[] invmap;
    return tmscore_max;
}

/* script format: 0 - no script; 1 - pymol; 3 - chimerax */
void output_pymol(const string xname, const string yname,
                  const string fname_super, double t[3], double u[3][3], const int ter_opt,
                  const int mm_opt, const int split_opt, const int mirror_opt,
                  const char *seqM, const char *seqxA, const char *seqyA,
                  const vector<string> &resi_vec1, const vector<string> &resi_vec2,
                  const string chainID1, const string chainID2, const int o_opt = 1)
{
    int compress_type = 0; // uncompressed file
    ifstream fin;
#ifndef REDI_PSTREAM_H_SEEN
    ifstream fin_gz;
#else
    redi::ipstream fin_gz; // if file is compressed
    if (xname.size() >= 3 &&
        xname.substr(xname.size() - 3, 3) == ".gz")
    {
        fin_gz.open("gunzip -c " + xname);
        compress_type = 1;
    }
    else if (xname.size() >= 4 &&
             xname.substr(xname.size() - 4, 4) == ".bz2")
    {
        fin_gz.open("bzcat " + xname);
        compress_type = 2;
    }
    else
#endif
    fin.open(xname.c_str());

    stringstream buf;
    stringstream buf_pymol;
    string line;
    double x[3];  // before transform
    double x1[3]; // after transform

    /* for PDBx/mmCIF only */
    map<string, int> _atom_site;
    size_t atom_site_pos;
    vector<string> line_vec;
    int infmt = -1; // 0 - PDB, 3 - PDBx/mmCIF

    while (compress_type ? fin_gz.good() : fin.good())
    {
        if (compress_type)
            getline(fin_gz, line);
        else
            getline(fin, line);
        if (line.compare(0, 6, "ATOM  ") == 0 ||
            line.compare(0, 6, "HETATM") == 0) // PDB format
        {
            infmt = 0;
            x[0] = atof(line.substr(30, 8).c_str());
            x[1] = atof(line.substr(38, 8).c_str());
            x[2] = atof(line.substr(46, 8).c_str());
            if (mirror_opt)
                x[2] = -x[2];
            transform(t, u, x, x1);
            buf << line.substr(0, 30) << setiosflags(ios::fixed)
                << setprecision(3)
                << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2]
                << line.substr(54) << '\n';
        }
        else if (line.compare(0, 5, "loop_") == 0) // PDBx/mmCIF
        {
            infmt = 3;
            buf << line << '\n';
            while (1)
            {
                if (compress_type)
                {
                    if (fin_gz.good())
                        getline(fin_gz, line);
                    else
                        PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                }
                else
                {
                    if (fin.good())
                        getline(fin, line);
                    else
                        PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                }
                if (line.size())
                    break;
            }
            buf << line << '\n';
            if (line.compare(0, 11, "_atom_site."))
                continue;
            _atom_site.clear();
            atom_site_pos = 0;
            _atom_site[Trim(line.substr(11))] = atom_site_pos;
            while (1)
            {
                while (1)
                {
                    if (compress_type)
                    {
                        if (fin_gz.good())
                            getline(fin_gz, line);
                        else
                            PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                    }
                    else
                    {
                        if (fin.good())
                            getline(fin, line);
                        else
                            PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                    }
                    if (line.size())
                        break;
                }
                if (line.compare(0, 11, "_atom_site."))
                    break;
                _atom_site[Trim(line.substr(11))] = ++atom_site_pos;
                buf << line << '\n';
            }

            if (_atom_site.count("group_PDB") *
                    _atom_site.count("Cartn_x") *
                    _atom_site.count("Cartn_y") *
                    _atom_site.count("Cartn_z") ==
                0)
            {
                buf << line << '\n';
                cerr << "Warning! Missing one of the following _atom_site data items: group_PDB, Cartn_x, Cartn_y, Cartn_z" << endl;
                continue;
            }

            while (1)
            {
                line_vec.clear();
                split(line, line_vec);
                if (line_vec[_atom_site["group_PDB"]] != "ATOM" &&
                    line_vec[_atom_site["group_PDB"]] != "HETATM")
                    break;

                x[0] = atof(line_vec[_atom_site["Cartn_x"]].c_str());
                x[1] = atof(line_vec[_atom_site["Cartn_y"]].c_str());
                x[2] = atof(line_vec[_atom_site["Cartn_z"]].c_str());
                if (mirror_opt)
                    x[2] = -x[2];
                transform(t, u, x, x1);

                for (atom_site_pos = 0; atom_site_pos < _atom_site.size(); atom_site_pos++)
                {
                    if (atom_site_pos == _atom_site["Cartn_x"])
                        buf << setiosflags(ios::fixed) << setprecision(3)
                            << setw(8) << x1[0] << ' ';
                    else if (atom_site_pos == _atom_site["Cartn_y"])
                        buf << setiosflags(ios::fixed) << setprecision(3)
                            << setw(8) << x1[1] << ' ';
                    else if (atom_site_pos == _atom_site["Cartn_z"])
                        buf << setiosflags(ios::fixed) << setprecision(3)
                            << setw(8) << x1[2] << ' ';
                    else
                        buf << line_vec[atom_site_pos] << ' ';
                }
                buf << '\n';

                if (compress_type && fin_gz.good())
                    getline(fin_gz, line);
                else if (!compress_type && fin.good())
                    getline(fin, line);
                else
                    break;
            }
            if (compress_type ? fin_gz.good() : fin.good())
                buf << line << '\n';
        }
        else if (line.size())
        {
            buf << line << '\n';
            if (ter_opt >= 1 && line.compare(0, 3, "END") == 0)
                break;
        }
    }
    if (compress_type)
        fin_gz.close();
    else
        fin.close();

    string fname_super_full = fname_super;
    if (infmt == 0)
        fname_super_full += ".pdb";
    else if (infmt == 3)
        fname_super_full += ".cif";
    ofstream fp;
    fp.open(fname_super_full.c_str());
    fp << buf.str();
    fp.close();
    buf.str(string()); // clear stream

    string chain1_sele;
    string chain2_sele;
    int i;
    if (!mm_opt)
    {
        if (split_opt == 2 && ter_opt >= 1) // align one chain from model 1
        {
            if (o_opt == 1)
            {
                chain1_sele = " and c. " + chainID1.substr(1);
                chain2_sele = " and c. " + chainID2.substr(1);
            }
            else if (o_opt == 3)
            {
                chain1_sele = "/" + chainID1.substr(1);
                chain2_sele = "/" + chainID2.substr(1);
            }
        }
        else if (split_opt == 2 && ter_opt == 0) // align one chain from each model
        {
            for (i = 1; i < chainID1.size(); i++)
                if (chainID1[i] == ',')
                    break;
            if (o_opt == 1)
                chain1_sele = " and c. " + chainID1.substr(i + 1);
            else if (o_opt == 3)
                chain1_sele = "/" + chainID1.substr(i + 1);
            for (i = 1; i < chainID2.size(); i++)
                if (chainID2[i] == ',')
                    break;
            if (o_opt == 1)
                chain2_sele = " and c. " + chainID2.substr(i + 1);
            else if (o_opt == 3)
                chain2_sele = "/" + chainID2.substr(i + 1);
        }
    }

    /* extract aligned region */
    int i1 = -1;
    int i2 = -1;
    string resi1_sele;
    string resi2_sele;
    string resi1_bond;
    string resi2_bond;
    string prev_resi1;
    string prev_resi2;
    string curr_resi1;
    string curr_resi2;
    if (mm_opt)
    {
        ;
    }
    else
    {
        for (i = 0; i < strlen(seqM); i++)
        {
            i1 += (seqxA[i] != '-' && seqxA[i] != '*');
            i2 += (seqyA[i] != '-');
            if (seqM[i] == ' ' || seqxA[i] == '*')
                continue;
            curr_resi1 = resi_vec1[i1].substr(0, 4);
            curr_resi2 = resi_vec2[i2].substr(0, 4);
            if (resi1_sele.size() == 0)
            {
                if (o_opt == 1)
                    resi1_sele = "i. " + curr_resi1;
                else if (o_opt == 3)
                    resi1_sele = ":" + Trim(curr_resi1);
            }
            else
            {
                if (o_opt == 1)
                {
                    resi1_sele += " or i. " + curr_resi1;
                    resi1_bond += "bond structure1 and i. " + prev_resi1 +
                                  ", structure1 and i. " + curr_resi1 + "\n";
                }
                else if (o_opt == 3)
                    resi1_sele += "," + Trim(curr_resi1);
            }
            if (resi2_sele.size() == 0)
            {
                if (o_opt == 1)
                    resi2_sele = "i. " + curr_resi2;
                else if (o_opt == 3)
                    resi2_sele = ":" + Trim(curr_resi2);
            }
            else
            {
                if (o_opt == 1)
                {
                    resi2_sele += " or i. " + curr_resi2;
                    resi2_bond += "bond structure2 and i. " + prev_resi2 +
                                  ", structure2 and i. " + curr_resi2 + "\n";
                }
                else if (o_opt == 3)
                    resi2_sele += "," + Trim(curr_resi2);
            }
            prev_resi1 = curr_resi1;
            prev_resi2 = curr_resi2;
            // if (seqM[i]!=':') continue;
        }
        if (o_opt == 1)
        {
            if (resi1_sele.size())
                resi1_sele = " and ( " + resi1_sele + ")";
            if (resi2_sele.size())
                resi2_sele = " and ( " + resi2_sele + ")";
        }
    }

    /* write pymol script */
    vector<string> pml_list;
    pml_list.push_back(fname_super + "");
    pml_list.push_back(fname_super + "_atm");
    pml_list.push_back(fname_super + "_all");
    pml_list.push_back(fname_super + "_all_atm");
    pml_list.push_back(fname_super + "_all_atm_lig");

    for (int p = 0; p < pml_list.size(); p++)
    {
        if (mm_opt && p <= 1)
            continue;
        if (o_opt == 1)
            buf_pymol
                << "#!/usr/bin/env pymol\n"
                << "cmd.load(\"" << fname_super_full << "\", \"structure1\")\n"
                << "cmd.load(\"" << yname << "\", \"structure2\")\n"
                << "hide all\n"
                << "set all_states, " << ((ter_opt == 0) ? "on" : "off") << '\n';
        else if (o_opt == 3)
            buf_pymol
                << "#!/usr/bin/env chimerax --script\n"
                << "open \"" << fname_super_full << "\" name structure1\n"
                << "open \"" << yname << "\" name structure2\n";
        if (p == 0) // .pml
        {
            if (o_opt == 1)
            {
                if (chain1_sele.size())
                    buf_pymol
                        << "remove structure1 and not " << chain1_sele.substr(4) << "\n";
                if (chain2_sele.size())
                    buf_pymol
                        << "remove structure2 and not " << chain2_sele.substr(4) << "\n";
                buf_pymol
                    << "remove not n. CA and not n. C3'\n"
                    << resi1_bond
                    << resi2_bond
                    << "show stick, structure1" << chain1_sele << resi1_sele << "\n"
                    << "show stick, structure2" << chain2_sele << resi2_sele << "\n";
            }
            else if (o_opt == 3)
            {
                buf_pymol
                    << "hide all cartoon\n"
                    << "hide all atoms\n"
                    << "hide all bonds\n"
                    << "show #1" << chain1_sele << resi1_sele << " cartoon\n"
                    << "show #2" << chain2_sele << resi2_sele << " cartoon\n"
                    << "cartoon style protein modeh default arrows f xsect oval width 1 thick 1\n"
                    << "cartoon style nucleic xsect oval width 1 thick 1\n";
            }
        }
        else if (p == 1) // _atm.pml
        {
            if (o_opt == 1)
                buf_pymol
                    << "show cartoon, structure1" << chain1_sele << resi1_sele << "\n"
                    << "show cartoon, structure2" << chain2_sele << resi2_sele << "\n";
            else if (o_opt == 3)
                buf_pymol
                    << "hide all cartoon\n"
                    << "hide all atoms\n"
                    << "hide all bonds\n"
                    << "show #1" << chain1_sele << resi1_sele << " & protein cartoon\n"
                    << "show #1" << chain1_sele << resi1_sele << " & nucleic cartoon,bonds\n"
                    << "show #2" << chain2_sele << resi2_sele << " & protein cartoon\n"
                    << "show #2" << chain2_sele << resi2_sele << " & nucleic cartoon,bonds\n";
        }
        else if (p == 2) // _all.pml
        {
            if (o_opt == 1)
                buf_pymol
                    << "show ribbon, structure1" << chain1_sele << "\n"
                    << "show ribbon, structure2" << chain2_sele << "\n";
            else if (o_opt == 3)
                buf_pymol
                    << "hide all atoms\n"
                    << "hide all bonds\n"
                    << "cartoon style protein modeh default arrows f xsect oval width 1 thick 1\n"
                    << "cartoon style nucleic xsect oval width 1 thick 1\n"
                    << "hide all cartoon\n"
                    << "show #1" << chain1_sele << " cartoon\n"
                    << "show #2" << chain2_sele << " cartoon\n";
        }
        else if (p == 3) // _all_atm.pml
        {
            if (o_opt == 1)
                buf_pymol
                    << "show cartoon, structure1" << chain1_sele << "\n"
                    << "show cartoon, structure2" << chain2_sele << "\n";
            else if (o_opt == 3)
                buf_pymol
                    << "hide all bonds\n"
                    << "hide all atoms\n"
                    << "hide all cartoon\n"
                    << "show #1" << chain1_sele << " cartoon\n"
                    << "show #1" << chain1_sele << " & nucleic cartoon,bonds\n"
                    << "show #2" << chain2_sele << " cartoon\n"
                    << "show #2" << chain2_sele << " & nucleic cartoon,bonds\n";
        }
        else if (p == 4) // _all_atm_lig.pml
        {
            if (o_opt == 1)
                buf_pymol
                    << "show cartoon, structure1\n"
                    << "show cartoon, structure2\n"
                    << "show stick, not polymer\n"
                    << "show sphere, not polymer\n";
            else if (o_opt == 3)
                buf_pymol
                    << "show solvent atoms,bonds\n";
        }
        if (o_opt == 1)
            buf_pymol
                << "color blue, structure1\n"
                << "color red, structure2\n"
                << "set ribbon_width, 6\n"
                << "set stick_radius, 0.3\n"
                << "set sphere_scale, 0.25\n"
                << "set ray_shadow, 0\n"
                << "bg_color white\n"
                << "set transparency=0.2\n"
                << "zoom polymer and ((structure1" << chain1_sele
                << ") or (structure2" << chain2_sele << "))\n"
                << endl;
        else if (o_opt == 3)
            buf_pymol
                << "color #1 blue\n"
                << "color #2 red\n"
                << "set bgColor white\n"
                << endl;

        if (o_opt == 1) // pymol
            fp.open((pml_list[p] + ".pml").c_str());
        else if (o_opt == 3) // chimerax
            fp.open((pml_list[p] + ".cxc").c_str());
        fp << buf_pymol.str();
        fp.close();
        buf_pymol.str(string());
    }

    /* clean up */
    pml_list.clear();

    resi1_sele.clear();
    resi2_sele.clear();

    resi1_bond.clear();
    resi2_bond.clear();

    prev_resi1.clear();
    prev_resi2.clear();

    curr_resi1.clear();
    curr_resi2.clear();

    chain1_sele.clear();
    chain2_sele.clear();
}

void output_mTMalign_pymol(const vector<string> &chain_list,
                           const int infmt_opt, double **ut_mat, const string &fname_super,
                           const int o_opt = 1)
{
    int compress_type = 0; // uncompressed file
    size_t m;
    string name;
    double t[3];
    double u[3][3];
    int ui, uj;
    string filename;
    vector<string> color_list;
    color_list.push_back("red");
    color_list.push_back("green");
    color_list.push_back("blue");
    color_list.push_back("yellow");
    color_list.push_back("violet");
    color_list.push_back("cyan");
    color_list.push_back("salmon");
    color_list.push_back("lime");
    color_list.push_back("pink");
    color_list.push_back("slate");
    color_list.push_back("magenta");
    color_list.push_back("orange");
    color_list.push_back("marine");
    color_list.push_back("olive");
    color_list.push_back("purple");
    color_list.push_back("teal");
    color_list.push_back("forest");
    color_list.push_back("firebrick");
    color_list.push_back("chocolate");
    color_list.push_back("wheat");
    color_list.push_back("white");
    color_list.push_back("grey");

    stringstream buf_pymol;
    if (o_opt == 1)
        buf_pymol << "#!/usr/bin/env pymol\n";
    else if (o_opt == 3)
        buf_pymol << "#!/usr/bin/env chimerax --script\n";
    for (m = 0; m < chain_list.size(); m++)
    {
        name = chain_list[m];

        ifstream fin;
#ifndef REDI_PSTREAM_H_SEEN
        ifstream fin_gz;
#else
        redi::ipstream fin_gz; // if file is compressed
        if (name.size() >= 3 &&
            name.substr(name.size() - 3, 3) == ".gz")
        {
            fin_gz.open("gunzip -c " + name);
            compress_type = 1;
        }
        else if (name.size() >= 4 &&
                 name.substr(name.size() - 4, 4) == ".bz2")
        {
            fin_gz.open("bzcat " + name);
            compress_type = 2;
        }
        else
#endif
        fin.open(name.c_str());

        stringstream buf;
        buf << fname_super << '.' << m << ".pdb";
        filename = buf.str();
        buf.str(string());
        for (ui = 0; ui < 3; ui++)
            for (uj = 0; uj < 3; uj++)
                u[ui][uj] = ut_mat[m][ui * 3 + uj];
        for (uj = 0; uj < 3; uj++)
            t[uj] = ut_mat[m][9 + uj];

        string line;
        double x[3];  // before transform
        double x1[3]; // after transform

        /* for PDBx/mmCIF only */
        map<string, int> _atom_site;
        size_t atom_site_pos;
        vector<string> line_vec;
        int infmt = -1; // 0 - PDB, 3 - PDBx/mmCIF

        while (compress_type ? fin_gz.good() : fin.good())
        {
            if (compress_type)
                getline(fin_gz, line);
            else
                getline(fin, line);
            if (line.compare(0, 6, "ATOM  ") == 0 ||
                line.compare(0, 6, "HETATM") == 0) // PDB format
            {
                infmt = 0;
                x[0] = atof(line.substr(30, 8).c_str());
                x[1] = atof(line.substr(38, 8).c_str());
                x[2] = atof(line.substr(46, 8).c_str());
                transform(t, u, x, x1);
                buf << line.substr(0, 30) << setiosflags(ios::fixed)
                    << setprecision(3)
                    << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2]
                    << line.substr(54) << '\n';
            }
            else if (line.compare(0, 5, "loop_") == 0) // PDBx/mmCIF
            {
                infmt = 3;
                buf << line << '\n';
                while (1)
                {
                    if (compress_type)
                    {
                        if (fin_gz.good())
                            getline(fin_gz, line);
                        else
                            PrintErrorAndQuit("ERROR! Unexpected end of " + name);
                    }
                    else
                    {
                        if (fin.good())
                            getline(fin, line);
                        else
                            PrintErrorAndQuit("ERROR! Unexpected end of " + name);
                    }
                    if (line.size())
                        break;
                }
                buf << line << '\n';
                if (line.compare(0, 11, "_atom_site."))
                    continue;
                _atom_site.clear();
                atom_site_pos = 0;
                _atom_site[Trim(line.substr(11))] = atom_site_pos;
                while (1)
                {
                    while (1)
                    {
                        if (compress_type)
                        {
                            if (fin_gz.good())
                                getline(fin_gz, line);
                            else
                                PrintErrorAndQuit("ERROR! Unexpected end of " + name);
                        }
                        else
                        {
                            if (fin.good())
                                getline(fin, line);
                            else
                                PrintErrorAndQuit("ERROR! Unexpected end of " + name);
                        }
                        if (line.size())
                            break;
                    }
                    if (line.compare(0, 11, "_atom_site."))
                        break;
                    _atom_site[Trim(line.substr(11))] = ++atom_site_pos;
                    buf << line << '\n';
                }

                if (_atom_site.count("group_PDB") *
                        _atom_site.count("Cartn_x") *
                        _atom_site.count("Cartn_y") *
                        _atom_site.count("Cartn_z") ==
                    0)
                {
                    buf << line << '\n';
                    cerr << "Warning! Missing one of the following _atom_site data items: group_PDB, Cartn_x, Cartn_y, Cartn_z" << endl;
                    continue;
                }

                while (1)
                {
                    line_vec.clear();
                    split(line, line_vec);
                    if (line_vec[_atom_site["group_PDB"]] != "ATOM" &&
                        line_vec[_atom_site["group_PDB"]] != "HETATM")
                        break;

                    x[0] = atof(line_vec[_atom_site["Cartn_x"]].c_str());
                    x[1] = atof(line_vec[_atom_site["Cartn_y"]].c_str());
                    x[2] = atof(line_vec[_atom_site["Cartn_z"]].c_str());
                    transform(t, u, x, x1);

                    for (atom_site_pos = 0; atom_site_pos < _atom_site.size();
                         atom_site_pos++)
                    {
                        if (atom_site_pos == _atom_site["Cartn_x"])
                            buf << setiosflags(ios::fixed) << setprecision(3)
                                << setw(8) << x1[0] << ' ';
                        else if (atom_site_pos == _atom_site["Cartn_y"])
                            buf << setiosflags(ios::fixed) << setprecision(3)
                                << setw(8) << x1[1] << ' ';
                        else if (atom_site_pos == _atom_site["Cartn_z"])
                            buf << setiosflags(ios::fixed) << setprecision(3)
                                << setw(8) << x1[2] << ' ';
                        else
                            buf << line_vec[atom_site_pos] << ' ';
                    }
                    buf << '\n';

                    if (compress_type && fin_gz.good())
                        getline(fin_gz, line);
                    else if (!compress_type && fin.good())
                        getline(fin, line);
                    else
                        break;
                }
                if (compress_type ? fin_gz.good() : fin.good())
                    buf << line << '\n';
            }
            else if (line.size())
                buf << line << '\n';
        }
        if (compress_type)
            fin_gz.close();
        else
            fin.close();

        ofstream fp;
        fp.open(filename.c_str());
        fp << buf.str();
        fp.close();
        buf.str(string()); // clear stream

        if (o_opt == 1)
            buf_pymol
                << "cmd.load(\"" << filename << "\",\"structure" << m << "\")\n"
                << "color " << color_list[m % color_list.size()] << ", structure" << m << "\n";
        else if (o_opt == 3)
            buf_pymol
                << "open \"" << filename << "\" name structure" << m << "\n"
                << "color #" << m + 1 << " " << color_list[m % color_list.size()] << "\n";
    }
    if (o_opt == 1)
        buf_pymol
            << "hide all\n"
            << "show cartoon\n"
            << "set ribbon_width, 6\n"
            << "set stick_radius, 0.3\n"
            << "set sphere_scale, 0.25\n"
            << "set ray_shadow, 0\n"
            << "bg_color white\n"
            << "set transparency=0.2\n"
            << endl;
    else if (o_opt == 3)
        buf_pymol
            << "set bgColor white\n"
            << endl;

    ofstream fp;
    if (o_opt == 1)
    {
        fp.open((fname_super + "_all_atm.pml").c_str());
        fp << buf_pymol.str();
        fp.close();
        fp.open((fname_super + "_all_atm_lig.pml").c_str());
        fp << buf_pymol.str()
           << "show stick, not polymer\n"
           << "show sphere, not polymer\n"
           << endl;
    }
    else if (o_opt == 3)
    {
        fp.open((fname_super + "_all_atm.cxc").c_str());
        fp << buf_pymol.str()
           << "hide ligand bonds\n"
           << "hide ligand atoms\n"
           << "hide solvent bonds\n"
           << "hide solvent atoms\n"
           << "hide ions bonds\n"
           << "hide ions atoms\n"
           << endl;
        fp.close();
        fp.open((fname_super + "_all_atm_lig.cxc").c_str());
        fp << buf_pymol.str() << endl;
    }

    fp.close();
    buf_pymol.str(string());
    vector<string>().swap(color_list);
}

void output_rasmol(const string xname, const string yname,
                   const string fname_super, double t[3], double u[3][3], const int ter_opt,
                   const int mm_opt, const int split_opt, const int mirror_opt,
                   const char *seqM, const char *seqxA, const char *seqyA,
                   const vector<string> &resi_vec1, const vector<string> &resi_vec2,
                   const string chainID1, const string chainID2,
                   const int xlen, const int ylen, const double d0A, const int n_ali8,
                   const double rmsd, const double TM1, const double Liden)
{
    stringstream buf;
    stringstream buf_all;
    stringstream buf_atm;
    stringstream buf_all_atm;
    stringstream buf_all_atm_lig;
    // stringstream buf_pdb;
    stringstream buf_tm;
    string line;
    double x[3];    // before transform
    double x1[3];   // after transform
    bool after_ter; // true if passed the "TER" line in PDB
    string asym_id; // chain ID

    buf_tm << "REMARK US-align"
           << "\nREMARK Structure 1:" << setw(11) << left << xname + chainID1 << " Size= " << xlen
           << "\nREMARK Structure 2:" << setw(11) << yname + chainID2 << right << " Size= " << ylen
           << " (TM-score is normalized by " << setw(4) << ylen << ", d0="
           << setiosflags(ios::fixed) << setprecision(2) << setw(6) << d0A << ")"
           << "\nREMARK Aligned length=" << setw(4) << n_ali8 << ", RMSD="
           << setw(6) << setiosflags(ios::fixed) << setprecision(2) << rmsd
           << ", TM-score=" << setw(7) << setiosflags(ios::fixed) << setprecision(5) << TM1
           << ", ID=" << setw(5) << setiosflags(ios::fixed) << setprecision(3)
           << ((n_ali8 > 0) ? Liden / n_ali8 : 0) << endl;
    string rasmol_CA_header = "load inline\nselect *A\nwireframe .45\nselect *B\nwireframe .20\nselect all\ncolor white\n";
    string rasmol_cartoon_header = "load inline\nselect all\ncartoon\nselect *A\ncolor blue\nselect *B\ncolor red\nselect ligand\nwireframe 0.25\nselect solvent\nspacefill 0.25\nselect all\nexit\n" + buf_tm.str();
    if (!mm_opt)
        buf << rasmol_CA_header;
    buf_all << rasmol_CA_header;
    if (!mm_opt)
        buf_atm << rasmol_cartoon_header;
    buf_all_atm << rasmol_cartoon_header;
    buf_all_atm_lig << rasmol_cartoon_header;

    /* selecting chains for -mol */
    string chain1_sele;
    string chain2_sele;
    int i;
    if (!mm_opt)
    {
        if (split_opt == 2 && ter_opt >= 1) // align one chain from model 1
        {
            chain1_sele = chainID1.substr(1);
            chain2_sele = chainID2.substr(1);
        }
        else if (split_opt == 2 && ter_opt == 0) // align one chain from each model
        {
            for (i = 1; i < chainID1.size(); i++)
                if (chainID1[i] == ',')
                    break;
            chain1_sele = chainID1.substr(i + 1);
            for (i = 1; i < chainID2.size(); i++)
                if (chainID2[i] == ',')
                    break;
            chain2_sele = chainID2.substr(i + 1);
        }
    }

    /* for PDBx/mmCIF only */
    map<string, int> _atom_site;
    int atom_site_pos;
    vector<string> line_vec;
    string atom;        // 4-character atom name
    string AA;          // 3-character residue name
    string resi;        // 4-character residue sequence number
    string inscode;     // 1-character insertion code
    string model_index; // model index
    bool is_mmcif = false;

    /* used for CONECT record of chain1 */
    int ca_idx1 = 0;  // all CA atoms
    int lig_idx1 = 0; // all atoms
    vector<int> idx_vec;

    /* used for CONECT record of chain2 */
    int ca_idx2 = 0;  // all CA atoms
    int lig_idx2 = 0; // all atoms

    /* extract aligned region */
    vector<string> resi_aln1;
    vector<string> resi_aln2;
    int i1 = -1;
    int i2 = -1;
    if (!mm_opt)
    {
        for (i = 0; i < strlen(seqM); i++)
        {
            i1 += (seqxA[i] != '-');
            i2 += (seqyA[i] != '-');
            if (seqM[i] == ' ')
                continue;
            resi_aln1.push_back(resi_vec1[i1].substr(0, 4));
            resi_aln2.push_back(resi_vec2[i2].substr(0, 4));
            if (seqM[i] != ':')
                continue;
            buf << "select " << resi_aln1.back() << ":A,"
                << resi_aln2.back() << ":B\ncolor red\n";
            buf_all << "select " << resi_aln1.back() << ":A,"
                    << resi_aln2.back() << ":B\ncolor red\n";
        }
        buf << "select all\nexit\n"
            << buf_tm.str();
    }
    buf_all << "select all\nexit\n"
            << buf_tm.str();

    ifstream fin;
    /* read first file */
    after_ter = false;
    asym_id = "";
    fin.open(xname.c_str());
    while (fin.good())
    {
        getline(fin, line);
        if (ter_opt >= 3 && line.compare(0, 3, "TER") == 0)
            after_ter = true;
        if (is_mmcif == false && line.size() >= 54 &&
            (line.compare(0, 6, "ATOM  ") == 0 ||
             line.compare(0, 6, "HETATM") == 0)) // PDB format
        {
            if (line[16] != 'A' && line[16] != ' ')
                continue;
            x[0] = atof(line.substr(30, 8).c_str());
            x[1] = atof(line.substr(38, 8).c_str());
            x[2] = atof(line.substr(46, 8).c_str());
            if (mirror_opt)
                x[2] = -x[2];
            transform(t, u, x, x1);
            // buf_pdb<<line.substr(0,30)<<setiosflags(ios::fixed)
            //<<setprecision(3)
            //<<setw(8)<<x1[0] <<setw(8)<<x1[1] <<setw(8)<<x1[2]
            //<<line.substr(54)<<'\n';

            if (after_ter && line.compare(0, 6, "ATOM  ") == 0)
                continue;
            lig_idx1++;
            buf_all_atm_lig << line.substr(0, 6) << setw(5) << lig_idx1
                            << line.substr(11, 9) << " A" << line.substr(22, 8)
                            << setiosflags(ios::fixed) << setprecision(3)
                            << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2] << '\n';
            if (chain1_sele.size() && line[21] != chain1_sele[0])
                continue;
            if (after_ter || line.compare(0, 6, "ATOM  "))
                continue;
            if (ter_opt >= 2)
            {
                if (ca_idx1 && asym_id.size() && asym_id != line.substr(21, 1))
                {
                    after_ter = true;
                    continue;
                }
                asym_id = line[21];
            }
            buf_all_atm << "ATOM  " << setw(5) << lig_idx1
                        << line.substr(11, 9) << " A" << line.substr(22, 8)
                        << setiosflags(ios::fixed) << setprecision(3)
                        << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2] << '\n';
            if (!mm_opt && find(resi_aln1.begin(), resi_aln1.end(),
                                line.substr(22, 4)) != resi_aln1.end())
            {
                buf_atm << "ATOM  " << setw(5) << lig_idx1
                        << line.substr(11, 9) << " A" << line.substr(22, 8)
                        << setiosflags(ios::fixed) << setprecision(3)
                        << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2] << '\n';
            }
            if (line.substr(12, 4) != " CA " && line.substr(12, 4) != " C3'")
                continue;
            ca_idx1++;
            buf_all << "ATOM  " << setw(5) << ca_idx1 << ' '
                    << line.substr(12, 4) << ' ' << line.substr(17, 3) << " A" << line.substr(22, 8)
                    << setiosflags(ios::fixed) << setprecision(3)
                    << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2] << '\n';
            if (find(resi_aln1.begin(), resi_aln1.end(),
                     line.substr(22, 4)) == resi_aln1.end())
                continue;
            if (!mm_opt)
                buf << "ATOM  " << setw(5) << ca_idx1 << ' '
                    << line.substr(12, 4) << ' ' << line.substr(17, 3) << " A" << line.substr(22, 8)
                    << setiosflags(ios::fixed) << setprecision(3)
                    << setw(8) << x1[0] << setw(8) << x1[1] << setw(8) << x1[2] << '\n';
            idx_vec.push_back(ca_idx1);
        }
        else if (line.compare(0, 5, "loop_") == 0) // PDBx/mmCIF
        {
            while (1)
            {
                if (fin.good())
                    getline(fin, line);
                else
                    PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                if (line.size())
                    break;
            }
            if (line.compare(0, 11, "_atom_site."))
                continue;
            _atom_site.clear();
            atom_site_pos = 0;
            _atom_site[line.substr(11, line.size() - 12)] = atom_site_pos;
            while (1)
            {
                if (fin.good())
                    getline(fin, line);
                else
                    PrintErrorAndQuit("ERROR! Unexpected end of " + xname);
                if (line.size() == 0)
                    continue;
                if (line.compare(0, 11, "_atom_site."))
                    break;
                _atom_site[line.substr(11, line.size() - 12)] = ++atom_site_pos;
            }

            if (is_mmcif == false)
            {
                // buf_pdb.str(string());
                is_mmcif = true;
            }

            while (1)
            {
                line_vec.clear();
                split(line, line_vec);
                if (line_vec[_atom_site["group_PDB"]] != "ATOM" &&
                    line_vec[_atom_site["group_PDB"]] != "HETATM")
                    break;
                if (_atom_site.count("pdbx_PDB_model_num"))
                {
                    if (model_index.size() && model_index !=
                                                  line_vec[_atom_site["pdbx_PDB_model_num"]])
                        break;
                    model_index = line_vec[_atom_site["pdbx_PDB_model_num"]];
                }

                x[0] = atof(line_vec[_atom_site["Cartn_x"]].c_str());
                x[1] = atof(line_vec[_atom_site["Cartn_y"]].c_str());
                x[2] = atof(line_vec[_atom_site["Cartn_z"]].c_str());
                if (mirror_opt)
                    x[2] = -x[2];
                transform(t, u, x, x1);

                if (_atom_site.count("label_alt_id") == 0 ||
                    line_vec[_atom_site["label_alt_id"]] == "." ||
                    line_vec[_atom_site["label_alt_id"]] == "A")
                {
                    atom = line_vec[_atom_site["label_atom_id"]];
                    if (atom[0] == '"')
                        atom = atom.substr(1);
                    if (atom.size() && atom[atom.size() - 1] == '"')
                        atom = atom.substr(0, atom.size() - 1);
                    if (atom.size() == 0)
                        atom = "    ";
                    else if (atom.size() == 1)
                        atom = " " + atom + "  ";
                    else if (atom.size() == 2)
                        atom = " " + atom + " ";
                    else if (atom.size() == 3)
                        atom = " " + atom;
                    else if (atom.size() >= 5)
                        atom = atom.substr(0, 4);

                    AA = line_vec[_atom_site["label_comp_id"]]; // residue name
                    if (AA.size() == 1)
                        AA = "  " + AA;
                    else if (AA.size() == 2)
                        AA = " " + AA;
                    else if (AA.size() >= 4)
                        AA = AA.substr(0, 3);

                    if (_atom_site.count("auth_seq_id"))
                        resi = line_vec[_atom_site["auth_seq_id"]];
                    else
                        resi = line_vec[_atom_site["label_seq_id"]];
                    while (resi.size() < 4)
                        resi = ' ' + resi;
                    if (resi.size() > 4)
                        resi = resi.substr(0, 4);

                    inscode = ' ';
                    if (_atom_site.count("pdbx_PDB_ins_code") &&
                        line_vec[_atom_site["pdbx_PDB_ins_code"]] != "?")
                        inscode = line_vec[_atom_site["pdbx_PDB_ins_code"]][0];

                    if (_atom_site.count("auth_asym_id"))
                    {
                        if (chain1_sele.size())
                            after_ter = line_vec[_atom_site["auth_asym_id"]] != chain1_sele;
                        else if (ter_opt >= 2 && ca_idx1 && asym_id.size() &&
                                 asym_id != line_vec[_atom_site["auth_asym_id"]])
                            after_ter = true;
                        asym_id = line_vec[_atom_site["auth_asym_id"]];
                    }
                    else if (_atom_site.count("label_asym_id"))
                    {
                        if (chain1_sele.size())
                            after_ter = line_vec[_atom_site["label_asym_id"]] != chain1_sele;
                        if (ter_opt >= 2 && ca_idx1 && asym_id.size() &&
                            asym_id != line_vec[_atom_site["label_asym_id"]])
                            after_ter = true;
                        asym_id = line_vec[_atom_site["label_asym_id"]];
                    }
                    // buf_pdb<<left<<setw(6)
                    //<<line_vec[_atom_site["group_PDB"]]<<right
                    //<<setw(5)<<lig_idx1%100000<<' '<<atom<<' '
                    //<<AA<<" "<<asym_id[asym_id.size()-1]
                    //<<resi<<inscode<<"   "
                    //<<setiosflags(ios::fixed)<<setprecision(3)
                    //<<setw(8)<<x1[0]
                    //<<setw(8)<<x1[1]
                    //<<setw(8)<<x1[2]<<'\n';

                    if (after_ter == false ||
                        line_vec[_atom_site["group_pdb"]] == "HETATM")
                    {
                        lig_idx1++;
                        buf_all_atm_lig << left << setw(6)
                                        << line_vec[_atom_site["group_PDB"]] << right
                                        << setw(5) << lig_idx1 % 100000 << ' ' << atom << ' '
                                        << AA << " A" << resi << inscode << "   "
                                        << setiosflags(ios::fixed) << setprecision(3)
                                        << setw(8) << x1[0]
                                        << setw(8) << x1[1]
                                        << setw(8) << x1[2] << '\n';
                        if (after_ter == false &&
                            line_vec[_atom_site["group_PDB"]] == "ATOM")
                        {
                            buf_all_atm << "ATOM  " << setw(6)
                                        << setw(5) << lig_idx1 % 100000 << ' ' << atom << ' '
                                        << AA << " A" << resi << inscode << "   "
                                        << setiosflags(ios::fixed) << setprecision(3)
                                        << setw(8) << x1[0]
                                        << setw(8) << x1[1]
                                        << setw(8) << x1[2] << '\n';
                            if (!mm_opt && find(resi_aln1.begin(),
                                                resi_aln1.end(), resi) != resi_aln1.end())
                            {
                                buf_atm << "ATOM  " << setw(6)
                                        << setw(5) << lig_idx1 % 100000 << ' '
                                        << atom << ' ' << AA << " A" << resi << inscode << "   "
                                        << setiosflags(ios::fixed) << setprecision(3)
                                        << setw(8) << x1[0]
                                        << setw(8) << x1[1]
                                        << setw(8) << x1[2] << '\n';
                            }
                            if (atom == " CA " || atom == " C3'")
                            {
                                ca_idx1++;
                                // mm_opt, split_opt, mirror_opt, chainID1,chainID2);
                                buf_all << "ATOM  " << setw(6)
                                        << setw(5) << ca_idx1 % 100000 << ' ' << atom << ' '
                                        << AA << " A" << resi << inscode << "   "
                                        << setiosflags(ios::fixed) << setprecision(3)
                                        << setw(8) << x1[0]
                                        << setw(8) << x1[1]
                                        << setw(8) << x1[2] << '\n';
                                if (!mm_opt && find(resi_aln1.begin(),
                                                    resi_aln1.end(), resi) != resi_aln1.end())
                                {
                                    buf << "ATOM  " << setw(6)
                                        << setw(5) << ca_idx1 % 100000 << ' ' << atom << ' '
                                        << AA << " A" << resi << inscode << "   "
                                        << setiosflags(ios::fixed) << setprecision(3)
                                        << setw(8) << x1[0]
                                        << setw(8) << x1[1]
                                        << setw(8) << x1[2] << '\n';
                                    idx_vec.push_back(ca_idx1);
                                }
                            }
                        }
                    }
                }

                while (1)
                {
                    if (fin.good())
                        getline(fin, line);
                    else
                        break;
                    if (line.size())
                        break;
                }
            }
        }
        else if (line.size() && is_mmcif == false)
        {
            // buf_pdb<<line<<'\n';
            if (ter_opt >= 1 && line.compare(0, 3, "END") == 0)
                break;
        }
    }
    fin.close();
    if (!mm_opt)
        buf << "TER\n";
    buf_all << "TER\n";
    if (!mm_opt)
        buf_atm << "TER\n";
    buf_all_atm << "TER\n";
    buf_all_atm_lig << "TER\n";
    for (i = 1; i < ca_idx1; i++)
        buf_all << "CONECT"
                << setw(5) << i % 100000 << setw(5) << (i + 1) % 100000 << '\n';
    if (!mm_opt)
        for (i = 1; i < idx_vec.size(); i++)
            buf << "CONECT"
                << setw(5) << idx_vec[i - 1] % 100000 << setw(5) << idx_vec[i] % 100000 << '\n';
    idx_vec.clear();

    /* read second file */
    after_ter = false;
    asym_id = "";
    fin.open(yname.c_str());
    while (fin.good())
    {
        getline(fin, line);
        if (ter_opt >= 3 && line.compare(0, 3, "TER") == 0)
            after_ter = true;
        if (line.size() >= 54 && (line.compare(0, 6, "ATOM  ") == 0 ||
                                  line.compare(0, 6, "HETATM") == 0)) // PDB format
        {
            if (line[16] != 'A' && line[16] != ' ')
                continue;
            if (after_ter && line.compare(0, 6, "ATOM  ") == 0)
                continue;
            lig_idx2++;
            buf_all_atm_lig << line.substr(0, 6) << setw(5) << lig_idx1 + lig_idx2
                            << line.substr(11, 9) << " B" << line.substr(22, 32) << '\n';
            if (chain2_sele.size() && line[21] != chain2_sele[0])
                continue;
            if (after_ter || line.compare(0, 6, "ATOM  "))
                continue;
            if (ter_opt >= 2)
            {
                if (ca_idx2 && asym_id.size() && asym_id != line.substr(21, 1))
                {
                    after_ter = true;
                    continue;
                }
                asym_id = line[21];
            }
            buf_all_atm << "ATOM  " << setw(5) << lig_idx1 + lig_idx2
                        << line.substr(11, 9) << " B" << line.substr(22, 32) << '\n';
            if (!mm_opt && find(resi_aln2.begin(), resi_aln2.end(),
                                line.substr(22, 4)) != resi_aln2.end())
            {
                buf_atm << "ATOM  " << setw(5) << lig_idx1 + lig_idx2
                        << line.substr(11, 9) << " B" << line.substr(22, 32) << '\n';
            }
            if (line.substr(12, 4) != " CA " && line.substr(12, 4) != " C3'")
                continue;
            ca_idx2++;
            buf_all << "ATOM  " << setw(5) << ca_idx1 + ca_idx2 << ' ' << line.substr(12, 4)
                    << ' ' << line.substr(17, 3) << " B" << line.substr(22, 32) << '\n';
            if (find(resi_aln2.begin(), resi_aln2.end(), line.substr(22, 4)) == resi_aln2.end())
                continue;
            if (!mm_opt)
                buf << "ATOM  " << setw(5) << ca_idx1 + ca_idx2 << ' '
                    << line.substr(12, 4) << ' ' << line.substr(17, 3) << " B"
                    << line.substr(22, 32) << '\n';
            idx_vec.push_back(ca_idx1 + ca_idx2);
        }
        else if (line.compare(0, 5, "loop_") == 0) // PDBx/mmCIF
        {
            while (1)
            {
                if (fin.good())
                    getline(fin, line);
                else
                    PrintErrorAndQuit("ERROR! Unexpected end of " + yname);
                if (line.size())
                    break;
            }
            if (line.compare(0, 11, "_atom_site."))
                continue;
            _atom_site.clear();
            atom_site_pos = 0;
            _atom_site[line.substr(11, line.size() - 12)] = atom_site_pos;
            while (1)
            {
                if (fin.good())
                    getline(fin, line);
                else
                    PrintErrorAndQuit("ERROR! Unexpected end of " + yname);
                if (line.size() == 0)
                    continue;
                if (line.compare(0, 11, "_atom_site."))
                    break;
                _atom_site[line.substr(11, line.size() - 12)] = ++atom_site_pos;
            }

            while (1)
            {
                line_vec.clear();
                split(line, line_vec);
                if (line_vec[_atom_site["group_PDB"]] != "ATOM" &&
                    line_vec[_atom_site["group_PDB"]] != "HETATM")
                    break;
                if (_atom_site.count("pdbx_PDB_model_num"))
                {
                    if (model_index.size() && model_index !=
                                                  line_vec[_atom_site["pdbx_PDB_model_num"]])
                        break;
                    model_index = line_vec[_atom_site["pdbx_PDB_model_num"]];
                }

                if (_atom_site.count("label_alt_id") == 0 ||
                    line_vec[_atom_site["label_alt_id"]] == "." ||
                    line_vec[_atom_site["label_alt_id"]] == "A")
                {
                    atom = line_vec[_atom_site["label_atom_id"]];
                    if (atom[0] == '"')
                        atom = atom.substr(1);
                    if (atom.size() && atom[atom.size() - 1] == '"')
                        atom = atom.substr(0, atom.size() - 1);
                    if (atom.size() == 0)
                        atom = "    ";
                    else if (atom.size() == 1)
                        atom = " " + atom + "  ";
                    else if (atom.size() == 2)
                        atom = " " + atom + " ";
                    else if (atom.size() == 3)
                        atom = " " + atom;
                    else if (atom.size() >= 5)
                        atom = atom.substr(0, 4);

                    AA = line_vec[_atom_site["label_comp_id"]]; // residue name
                    if (AA.size() == 1)
                        AA = "  " + AA;
                    else if (AA.size() == 2)
                        AA = " " + AA;
                    else if (AA.size() >= 4)
                        AA = AA.substr(0, 3);

                    if (_atom_site.count("auth_seq_id"))
                        resi = line_vec[_atom_site["auth_seq_id"]];
                    else
                        resi = line_vec[_atom_site["label_seq_id"]];
                    while (resi.size() < 4)
                        resi = ' ' + resi;
                    if (resi.size() > 4)
                        resi = resi.substr(0, 4);

                    inscode = ' ';
                    if (_atom_site.count("pdbx_PDB_ins_code") &&
                        line_vec[_atom_site["pdbx_PDB_ins_code"]] != "?")
                        inscode = line_vec[_atom_site["pdbx_PDB_ins_code"]][0];

                    if (_atom_site.count("auth_asym_id"))
                    {
                        if (chain2_sele.size())
                            after_ter = line_vec[_atom_site["auth_asym_id"]] != chain2_sele;
                        if (ter_opt >= 2 && ca_idx2 && asym_id.size() &&
                            asym_id != line_vec[_atom_site["auth_asym_id"]])
                            after_ter = true;
                        asym_id = line_vec[_atom_site["auth_asym_id"]];
                    }
                    else if (_atom_site.count("label_asym_id"))
                    {
                        if (chain2_sele.size())
                            after_ter = line_vec[_atom_site["label_asym_id"]] != chain2_sele;
                        if (ter_opt >= 2 && ca_idx2 && asym_id.size() &&
                            asym_id != line_vec[_atom_site["label_asym_id"]])
                            after_ter = true;
                        asym_id = line_vec[_atom_site["label_asym_id"]];
                    }
                    if (after_ter == false ||
                        line_vec[_atom_site["group_PDB"]] == "HETATM")
                    {
                        lig_idx2++;
                        buf_all_atm_lig << left << setw(6)
                                        << line_vec[_atom_site["group_PDB"]] << right
                                        << setw(5) << (lig_idx1 + lig_idx2) % 100000 << ' '
                                        << atom << ' ' << AA << " B" << resi << inscode << "   "
                                        << setw(8) << line_vec[_atom_site["Cartn_x"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_y"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_z"]]
                                        << '\n';
                        if (after_ter == false &&
                            line_vec[_atom_site["group_PDB"]] == "ATOM")
                        {
                            buf_all_atm << "ATOM  " << setw(6)
                                        << setw(5) << (lig_idx1 + lig_idx2) % 100000 << ' '
                                        << atom << ' ' << AA << " B" << resi << inscode << "   "
                                        << setw(8) << line_vec[_atom_site["Cartn_x"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_y"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_z"]]
                                        << '\n';
                            if (!mm_opt && find(resi_aln2.begin(),
                                                resi_aln2.end(), resi) != resi_aln2.end())
                            {
                                buf_atm << "ATOM  " << setw(6)
                                        << setw(5) << (lig_idx1 + lig_idx2) % 100000 << ' '
                                        << atom << ' ' << AA << " B" << resi << inscode << "   "
                                        << setw(8) << line_vec[_atom_site["Cartn_x"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_y"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_z"]]
                                        << '\n';
                            }
                            if (atom == " CA " || atom == " C3'")
                            {
                                ca_idx2++;
                                buf_all << "ATOM  " << setw(6)
                                        << setw(5) << (ca_idx1 + ca_idx2) % 100000
                                        << ' ' << atom << ' ' << AA << " B" << resi << inscode << "   "
                                        << setw(8) << line_vec[_atom_site["Cartn_x"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_y"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_z"]]
                                        << '\n';
                                if (!mm_opt && find(resi_aln2.begin(),
                                                    resi_aln2.end(), resi) != resi_aln2.end())
                                {
                                    buf << "ATOM  " << setw(6)
                                        << setw(5) << (ca_idx1 + ca_idx2) % 100000
                                        << ' ' << atom << ' ' << AA << " B" << resi << inscode << "   "
                                        << setw(8) << line_vec[_atom_site["Cartn_x"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_y"]]
                                        << setw(8) << line_vec[_atom_site["Cartn_z"]]
                                        << '\n';
                                    idx_vec.push_back(ca_idx1 + ca_idx2);
                                }
                            }
                        }
                    }
                }

                if (fin.good())
                    getline(fin, line);
                else
                    break;
            }
        }
        else if (line.size())
        {
            if (ter_opt >= 1 && line.compare(0, 3, "END") == 0)
                break;
        }
    }
    fin.close();
    if (!mm_opt)
        buf << "TER\n";
    buf_all << "TER\n";
    if (!mm_opt)
        buf_atm << "TER\n";
    buf_all_atm << "TER\n";
    buf_all_atm_lig << "TER\n";
    for (i = ca_idx1 + 1; i < ca_idx1 + ca_idx2; i++)
        buf_all << "CONECT"
                << setw(5) << i % 100000 << setw(5) << (i + 1) % 100000 << '\n';
    for (i = 1; i < idx_vec.size(); i++)
        buf << "CONECT"
            << setw(5) << idx_vec[i - 1] % 100000 << setw(5) << idx_vec[i] % 100000 << '\n';
    idx_vec.clear();

    /* write pymol script */
    ofstream fp;
    /*
    stringstream buf_pymol;
    vector<string> pml_list;
    pml_list.push_back(fname_super+"");
    pml_list.push_back(fname_super+"_atm");
    pml_list.push_back(fname_super+"_all");
    pml_list.push_back(fname_super+"_all_atm");
    pml_list.push_back(fname_super+"_all_atm_lig");
    for (i=0;i<pml_list.size();i++)
    {
        buf_pymol<<"#!/usr/bin/env pymol\n"
            <<"load "<<pml_list[i]<<"\n"
            <<"hide all\n"
            <<((i==0 || i==2)?("show stick\n"):("show cartoon\n"))
            <<"color blue, chain A\n"
            <<"color red, chain B\n"
            <<"set ray_shadow, 0\n"
            <<"set stick_radius, 0.3\n"
            <<"set sphere_scale, 0.25\n"
            <<"show stick, not polymer\n"
            <<"show sphere, not polymer\n"
            <<"bg_color white\n"
            <<"set transparency=0.2\n"
            <<"zoom polymer\n"
            <<endl;
        fp.open((pml_list[i]+".pml").c_str());
        fp<<buf_pymol.str();
        fp.close();
        buf_pymol.str(string());
        pml_list[i].clear();
    }
    pml_list.clear();
    */

    /* write rasmol script */
    if (!mm_opt)
    {
        fp.open((fname_super+".spt").c_str());
        fp << buf.str();
        fp.close();
    }
    fp.open((fname_super + "_all.spt").c_str());
    fp << buf_all.str();
    fp.close();
    if (!mm_opt)
    {
        fp.open((fname_super + "_atm.spt").c_str());
        fp << buf_atm.str();
        fp.close();
    }
    fp.open((fname_super + "_all_atm.spt").c_str());
    fp << buf_all_atm.str();
    fp.close();
    fp.open((fname_super + "_all_atm_lig.spt").c_str());
    fp << buf_all_atm_lig.str();
    fp.close();
    // fp.open((fname_super+".pdb").c_str());
    // fp<<buf_pdb.str();
    // fp.close();

    /* clear stream */
    buf.str(string());
    buf_all.str(string());
    buf_atm.str(string());
    buf_all_atm.str(string());
    buf_all_atm_lig.str(string());
    // buf_pdb.str(string());
    buf_tm.str(string());
    resi_aln1.clear();
    resi_aln2.clear();
    asym_id.clear();
    line_vec.clear();
    atom.clear();
    AA.clear();
    resi.clear();
    inscode.clear();
    model_index.clear();
}

/* extract rotation matrix based on TMscore8 */
void output_rotation_matrix(const char *fname_matrix,
                            const double t[3], const double u[3][3])
{
    stringstream ss;
    ss << "------ The rotation matrix to rotate Structure_1 to Structure_2 ------\n";
    char dest[1000];
    sprintf(dest, "m %18s %14s %14s %14s\n", "t[m]", "u[m][0]", "u[m][1]", "u[m][2]");
    ss << string(dest);
    for (int k = 0; k < 3; k++)
    {
        sprintf(dest, "%d %18.10f %14.10f %14.10f %14.10f\n", k, t[k], u[k][0], u[k][1], u[k][2]);
        ss << string(dest);
    }
    ss << "\nCode for rotating Structure 1 from (x,y,z) to (X,Y,Z):\n"
          "for(i=0; i<L; i++)\n"
          "{\n"
          "   X[i] = t[0] + u[0][0]*x[i] + u[0][1]*y[i] + u[0][2]*z[i];\n"
          "   Y[i] = t[1] + u[1][0]*x[i] + u[1][1]*y[i] + u[1][2]*z[i];\n"
          "   Z[i] = t[2] + u[2][0]*x[i] + u[2][1]*y[i] + u[2][2]*z[i];\n"
          "}\n";
    if (strcmp(fname_matrix, (char *)("-")) == 0)
        cout << ss.str();
    else
    {
        fstream fout;
        fout.open(fname_matrix, ios::out | ios::trunc);
        if (fout)
        {
            fout << ss.str();
            fout.close();
        }
        else
            cout << "Open file to output rotation matrix fail.\n";
    }
    ss.str(string());
}

// output the final results
void output_results(const string xname, const string yname,
                    const string chainID1, const string chainID2,
                    const int xlen, const int ylen, double t[3], double u[3][3],
                    const double TM1, const double TM2,
                    const double TM3, const double TM4, const double TM5,
                    const double rmsd, const double d0_out, const char *seqM,
                    const char *seqxA, const char *seqyA, const double Liden,
                    const int n_ali8, const int L_ali, const double TM_ali,
                    const double rmsd_ali, const double TM_0, const double d0_0,
                    const double d0A, const double d0B, const double Lnorm_ass,
                    const double d0_scale, const double d0a, const double d0u,
                    const char *fname_matrix, const int outfmt_opt, const int ter_opt,
                    const int mm_opt, const int split_opt, const int o_opt,
                    const string fname_super, const int i_opt, const int a_opt,
                    const bool u_opt, const bool d_opt, const int mirror_opt,
                    const vector<string> &resi_vec1, const vector<string> &resi_vec2)
{
    if (outfmt_opt <= 0)
    {
        printf("\nName of Structure_1: %s%s (to be superimposed onto Structure_2)\n",
               xname.c_str(), chainID1.c_str());
        printf("Name of Structure_2: %s%s\n", yname.c_str(), chainID2.c_str());
        printf("Length of Structure_1: %d residues\n", xlen);
        printf("Length of Structure_2: %d residues\n\n", ylen);

        if (i_opt)
            printf("User-specified initial alignment: TM/Lali/rmsd = %7.5lf, %4d, %6.3lf\n", TM_ali, L_ali, rmsd_ali);

        printf("Aligned length= %d, RMSD= %6.2f, Seq_ID=n_identical/n_aligned= %4.3f\n", n_ali8, rmsd, (n_ali8 > 0) ? Liden / n_ali8 : 0);
        printf("TM-score= %6.5f (normalized by length of Structure_1: L=%d, d0=%.2f)\n", TM2, xlen, d0B);
        printf("TM-score= %6.5f (normalized by length of Structure_2: L=%d, d0=%.2f)\n", TM1, ylen, d0A);

        if (a_opt == 1)
            printf("TM-score= %6.5f (if normalized by average length of two structures: L=%.1f, d0=%.2f)\n", TM3, (xlen + ylen) * 0.5, d0a);
        if (u_opt)
            printf("TM-score= %6.5f (normalized by user-specified L=%.2f and d0=%.2f)\n", TM4, Lnorm_ass, d0u);
        if (d_opt)
            printf("TM-score= %6.5f (scaled by user-specified d0=%.2f, and L=%d)\n", TM5, d0_scale, ylen);
        printf("(You should use TM-score normalized by length of the reference structure)\n");

        // output alignment
        printf("\n(\":\" denotes residue pairs of d <%4.1f Angstrom, ", d0_out);
        printf("\".\" denotes other aligned residues)\n");
        printf("%s\n", seqxA);
        printf("%s\n", seqM);
        printf("%s\n", seqyA);
    }
    else if (outfmt_opt == 1)
    {
        printf(">%s%s\tL=%d\td0=%.2f\tseqID=%.3f\tTM-score=%.5f\n",
               xname.c_str(), chainID1.c_str(), xlen, d0B, Liden / xlen, TM2);
        printf("%s\n", seqxA);
        printf(">%s%s\tL=%d\td0=%.2f\tseqID=%.3f\tTM-score=%.5f\n",
               yname.c_str(), chainID2.c_str(), ylen, d0A, Liden / ylen, TM1);
        printf("%s\n", seqyA);

        printf("# Lali=%d\tRMSD=%.2f\tseqID_ali=%.3f\n",
               n_ali8, rmsd, (n_ali8 > 0) ? Liden / n_ali8 : 0);

        if (i_opt)
            printf("# User-specified initial alignment: TM=%.5lf\tLali=%4d\trmsd=%.3lf\n", TM_ali, L_ali, rmsd_ali);

        if (a_opt)
            printf("# TM-score=%.5f (normalized by average length of two structures: L=%.1f\td0=%.2f)\n", TM3, (xlen + ylen) * 0.5, d0a);

        if (u_opt)
            printf("# TM-score=%.5f (normalized by user-specified L=%.2f\td0=%.2f)\n", TM4, Lnorm_ass, d0u);

        if (d_opt)
            printf("# TM-score=%.5f (scaled by user-specified d0=%.2f\tL=%d)\n", TM5, d0_scale, ylen);

        printf("$$$$\n");
    }
    else if (outfmt_opt == 2)
    {
        printf("%s%s\t%s%s\t%.4f\t%.4f\t%.2f\t%4.3f\t%4.3f\t%4.3f\t%d\t%d\t%d",
               xname.c_str(), chainID1.c_str(), yname.c_str(), chainID2.c_str(),
               TM2, TM1, rmsd, Liden / xlen, Liden / ylen, (n_ali8 > 0) ? Liden / n_ali8 : 0,
               xlen, ylen, n_ali8);
    }
    if (outfmt_opt < 5)
        cout << endl;

    if (strlen(fname_matrix))
        output_rotation_matrix(fname_matrix, t, u);

    if (o_opt == 1 || o_opt == 3)
        output_pymol(xname, yname, fname_super, t, u, ter_opt,
                     mm_opt, split_opt, mirror_opt, seqM, seqxA, seqyA,
                     resi_vec1, resi_vec2, chainID1, chainID2, o_opt);
    else if (o_opt == 2)
        output_rasmol(xname, yname, fname_super, t, u, ter_opt,
                      mm_opt, split_opt, mirror_opt, seqM, seqxA, seqyA,
                      resi_vec1, resi_vec2, chainID1, chainID2,
                      xlen, ylen, d0A, n_ali8, rmsd, TM1, Liden);
}

void output_mTMalign_results(const string xname, const string yname,
                             const string chainID1, const string chainID2,
                             const int xlen, const int ylen, double t[3], double u[3][3],
                             const double TM1, const double TM2,
                             const double TM3, const double TM4, const double TM5,
                             const double rmsd, const double d0_out, const char *seqM,
                             const char *seqxA, const char *seqyA, const double Liden,
                             const int n_ali8, const int L_ali, const double TM_ali,
                             const double rmsd_ali, const double TM_0, const double d0_0,
                             const double d0A, const double d0B, const double Lnorm_ass,
                             const double d0_scale, const double d0a, const double d0u,
                             const char *fname_matrix, const int outfmt_opt, const int ter_opt,
                             const int mm_opt, const int split_opt, const int o_opt,
                             const string fname_super, const int i_opt, const int a_opt,
                             const bool u_opt, const bool d_opt, const int mirror_opt,
                             const vector<string> &resi_vec1, const vector<string> &resi_vec2)
{
    if (outfmt_opt <= 0)
    {
        printf("Average aligned length= %d, RMSD= %6.2f, Seq_ID=n_identical/n_aligned= %4.3f\n", n_ali8, rmsd, (n_ali8 > 0) ? Liden / n_ali8 : 0);
        printf("Average TM-score= %6.5f (normalized by length of shorter structure: L=%d, d0=%.2f)\n", TM2, xlen, d0B);
        printf("Average TM-score= %6.5f (normalized by length of longer structure: L=%d, d0=%.2f)\n", TM1, ylen, d0A);

        if (a_opt == 1)
            printf("Average TM-score= %6.5f (if normalized by average length of two structures: L=%.1f, d0=%.2f)\n", TM3, (xlen + ylen) * 0.5, d0a);
        if (u_opt)
            printf("Average TM-score= %6.5f (normalized by average L=%.2f and d0=%.2f)\n", TM4, Lnorm_ass, d0u);
        if (d_opt)
            printf("Average TM-score= %6.5f (scaled by user-specified d0=%.2f, and L=%d)\n", TM5, d0_scale, ylen);

        // output alignment
        printf("In the following, seqID=n_identical/L.\n\n%s\n", seqM);
    }
    else if (outfmt_opt == 1)
    {
        printf("%s\n", seqM);

        printf("# Lali=%d\tRMSD=%.2f\tseqID_ali=%.3f\n",
               n_ali8, rmsd, (n_ali8 > 0) ? Liden / n_ali8 : 0);

        if (i_opt)
            printf("# User-specified initial alignment: TM=%.5lf\tLali=%4d\trmsd=%.3lf\n", TM_ali, L_ali, rmsd_ali);

        if (a_opt)
            printf("# TM-score=%.5f (normalized by average length of two structures: L=%.1f\td0=%.2f)\n", TM3, (xlen + ylen) * 0.5, d0a);

        if (u_opt)
            printf("# TM-score=%.5f (normalized by average L=%.2f\td0=%.2f)\n", TM4, Lnorm_ass, d0u);

        if (d_opt)
            printf("# TM-score=%.5f (scaled by user-specified d0=%.2f\tL=%d)\n", TM5, d0_scale, ylen);

        printf("$$$$\n");
    }
    else if (outfmt_opt == 2)
    {
        printf("%s%s\t%s%s\t%.4f\t%.4f\t%.2f\t%4.3f\t%4.3f\t%4.3f\t%d\t%d\t%d",
               xname.c_str(), chainID1.c_str(), yname.c_str(), chainID2.c_str(),
               TM2, TM1, rmsd, Liden / xlen, Liden / ylen, (n_ali8 > 0) ? Liden / n_ali8 : 0,
               xlen, ylen, n_ali8);
    }
    cout << endl;

    if (strlen(fname_matrix))
        output_rotation_matrix(fname_matrix, t, u);

    if (o_opt == 1 || o_opt == 3)
        output_pymol(xname, yname, fname_super, t, u, ter_opt,
                     mm_opt, split_opt, mirror_opt, seqM, seqxA, seqyA,
                     resi_vec1, resi_vec2, chainID1, chainID2, o_opt);
    else if (o_opt == 2)
        output_rasmol(xname, yname, fname_super, t, u, ter_opt,
                      mm_opt, split_opt, mirror_opt, seqM, seqxA, seqyA,
                      resi_vec1, resi_vec2, chainID1, chainID2,
                      xlen, ylen, d0A, n_ali8, rmsd, TM1, Liden);
}

double standard_TMscore(double **r1, double **r2, double **xtm, double **ytm,
                        double **xt, double **x, double **y, int xlen, int ylen, int invmap[],
                        int &L_ali, double &RMSD, double D0_MIN, double Lnorm, double d0,
                        double d0_search, double score_d8, double t[3], double u[3][3],
                        const int mol_type)
{
    D0_MIN = 0.5;
    Lnorm = ylen;
    if (mol_type > 0) // RNA
    {
        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);
    }
    else
    {
        if (Lnorm > 21)
            d0 = (1.24 * pow((Lnorm * 1.0 - 15), 1.0 / 3) - 1.8);
        else
            d0 = D0_MIN;
        if (d0 < D0_MIN)
            d0 = D0_MIN;
    }
    double d0_input = d0; // Scaled by seq_min

    double tmscore; // collected alined residues from invmap
    int n_al = 0;
    int i;
    for (int j = 0; j < ylen; j++)
    {
        i = invmap[j];
        if (i >= 0)
        {
            xtm[n_al][0] = x[i][0];
            xtm[n_al][1] = x[i][1];
            xtm[n_al][2] = x[i][2];

            ytm[n_al][0] = y[j][0];
            ytm[n_al][1] = y[j][1];
            ytm[n_al][2] = y[j][2];

            r1[n_al][0] = x[i][0];
            r1[n_al][1] = x[i][1];
            r1[n_al][2] = x[i][2];

            r2[n_al][0] = y[j][0];
            r2[n_al][1] = y[j][1];
            r2[n_al][2] = y[j][2];

            n_al++;
        }
        else if (i != -1)
            PrintErrorAndQuit("Wrong map!\n");
    }
    L_ali = n_al;

    Kabsch(r1, r2, n_al, 0, &RMSD, t, u);
    RMSD = sqrt(RMSD / (1.0 * n_al));

    int temp_simplify_step = 1;
    int temp_score_sum_method = 0;
    d0_search = d0_input;
    double rms = 0.0;
    tmscore = TMscore8_search_standard(r1, r2, xtm, ytm, xt, n_al, t, u,
                                       temp_simplify_step, temp_score_sum_method, &rms, d0_input,
                                       score_d8, d0);
    tmscore = tmscore * n_al / (1.0 * Lnorm);

    return tmscore;
}

/* copy the value of t and u into t0,u0 */
void copy_t_u(double t[3], double u[3][3], double t0[3], double u0[3][3])
{
    int i, j;
    for (i = 0; i < 3; i++)
    {
        t0[i] = t[i];
        for (j = 0; j < 3; j++)
            u0[i][j] = u[i][j];
    }
}

/* calculate approximate TM-score given rotation matrix */
double approx_TM(const int xlen, const int ylen, const int a_opt,
                 double **xa, double **ya, double t[3], double u[3][3],
                 const int invmap0[], const int mol_type)
{
    double Lnorm_0 = ylen; // normalized by the second protein
    if (a_opt == -2 && xlen > ylen)
        Lnorm_0 = xlen; // longer
    else if (a_opt == -1 && xlen < ylen)
        Lnorm_0 = xlen; // shorter
    else if (a_opt == 1)
        Lnorm_0 = (xlen + ylen) / 2.; // average

    double D0_MIN;
    double Lnorm;
    double d0;
    double d0_search;
    parameter_set4final(Lnorm_0, D0_MIN, Lnorm, d0, d0_search, mol_type);
    double TMtmp = 0;
    double d;
    double xtmp[3] = {0, 0, 0};

    for (int i = 0, j = 0; j < ylen; j++)
    {
        i = invmap0[j];
        if (i >= 0) // aligned
        {
            transform(t, u, &xa[i][0], &xtmp[0]);
            d = sqrt(dist(&xtmp[0], &ya[j][0]));
            TMtmp += 1 / (1 + (d / d0) * (d / d0));
            // if (d <= score_d8) TMtmp+=1/(1+(d/d0)*(d/d0));
        }
    }
    TMtmp /= Lnorm_0;
    return TMtmp;
}

void clean_up_after_approx_TM(int *invmap0, int *invmap,
                              double **score, bool **path, double **val, double **xtm, double **ytm,
                              double **xt, double **r1, double **r2, const int xlen, const int minlen)
{
    delete[] invmap0;
    delete[] invmap;
    DeleteArray(&score, xlen + 1);
    DeleteArray(&path, xlen + 1);
    DeleteArray(&val, xlen + 1);
    DeleteArray(&xtm, minlen);
    DeleteArray(&ytm, minlen);
    DeleteArray(&xt, xlen);
    DeleteArray(&r1, minlen);
    DeleteArray(&r2, minlen);
    return;
}

/* Entry function for TM-align. Return TM-score calculation status:
 * 0   - full TM-score calculation
 * 1   - terminated due to exception
 * 2-7 - pre-terminated due to low TM-score */
int TMalign_main(double **xa, double **ya,
                 const char *seqx, const char *seqy, const char *secx, const char *secy,
                 double t0[3], double u0[3][3],
                 double &TM1, double &TM2, double &TM3, double &TM4, double &TM5,
                 double &d0_0, double &TM_0,
                 double &d0A, double &d0B, double &d0u, double &d0a, double &d0_out,
                 string &seqM, string &seqxA, string &seqyA, vector<double> &do_vec,
                 double &rmsd0, int &L_ali, double &Liden,
                 double &TM_ali, double &rmsd_ali, int &n_ali, int &n_ali8,
                 const int xlen, const int ylen,
                 const vector<string> sequence, const double Lnorm_ass,
                 const double d0_scale, const int i_opt, const int a_opt,
                 const bool u_opt, const bool d_opt, const bool fast_opt,
                 const int mol_type, const double TMcut, const int ss_opt)
{
    double D0_MIN;                        // for d0
    double Lnorm;                         // normalization length
    double score_d8, d0, d0_search, dcu0; // for TMscore search
    double t[3], u[3][3];                 // Kabsch translation vector and rotation matrix
    double **score;                       // Input score table for dynamic programming
    bool **path;                          // for dynamic programming
    double **val;                         // for dynamic programming
    double **xtm, **ytm;                  // for TMscore search engine
    double **xt;                          // for saving the superposed version of r_1 or xtm
    double **r1, **r2;                    // for Kabsch rotation

    /***********************/
    /* allocate memory     */
    /***********************/
    int minlen = min(xlen, ylen);
    NewArray(&score, xlen + 1, ylen + 1);
    NewArray(&path, xlen + 1, ylen + 1);
    NewArray(&val, xlen + 1, ylen + 1);
    NewArray(&xtm, minlen, 3);
    NewArray(&ytm, minlen, 3);
    NewArray(&xt, xlen, 3);
    NewArray(&r1, minlen, 3);
    NewArray(&r2, minlen, 3);

    /***********************/
    /* parameter set    */
    /***********************/
    parameter_set4search(xlen, ylen, D0_MIN, Lnorm,
                         score_d8, d0, d0_search, dcu0);
    int simplify_step = 40;   // for simplified search engine
    int score_sum_method = 8; // for scoring method, whether only sum over pairs with dis<score_d8

    int i;
    int *invmap0 = new int[ylen + 1];
    int *invmap = new int[ylen + 1];
    double TM, TMmax = -1;
    for (i = 0; i < ylen; i++)
        invmap0[i] = -1;

    double ddcc = 0.4;
    if (Lnorm <= 40)
        ddcc = 0.1; // Lnorm was setted in parameter_set4search
    double local_d0_search = d0_search;

    //************************************************//
    //    get initial alignment from user's input:    //
    //    Stick to the initial alignment              //
    //************************************************//
    if (i_opt == 3) // if input has set parameter for "-I"
    {
        // In the original code, this loop starts from 1, which is
        // incorrect. Fortran starts from 1 but C++ should starts from 0.
        for (int j = 0; j < ylen; j++) // Set aligned position to be "-1"
            invmap[j] = -1;

        int i1 = -1; // in C version, index starts from zero, not from one
        int i2 = -1;
        int L1 = sequence[0].size();
        int L2 = sequence[1].size();
        int L = min(L1, L2); // Get positions for aligned residues
        for (int kk1 = 0; kk1 < L; kk1++)
        {
            if (sequence[0][kk1] != '-')
                i1++;
            if (sequence[1][kk1] != '-')
            {
                i2++;
                if (i2 >= ylen || i1 >= xlen)
                    kk1 = L;
                else if (sequence[0][kk1] != '-')
                    invmap[i2] = i1;
            }
        }

        //--------------- 2. Align proteins from original alignment
        double prevD0_MIN = D0_MIN; // stored for later use
        int prevLnorm = Lnorm;
        double prevd0 = d0;
        TM_ali = standard_TMscore(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen,
                                  invmap, L_ali, rmsd_ali, D0_MIN, Lnorm, d0, d0_search, score_d8,
                                  t, u, mol_type);
        D0_MIN = prevD0_MIN;
        Lnorm = prevLnorm;
        d0 = prevd0;
        TM = detailed_search_standard(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen,
                                      invmap, t, u, 40, 8, local_d0_search, true, Lnorm, score_d8, d0);
        if (TM > TMmax)
        {
            TMmax = TM;
            for (i = 0; i < ylen; i++)
                invmap0[i] = invmap[i];
        }
    }

    /******************************************************/
    /* get initial alignment with gapless threading    */
    /******************************************************/
    if (i_opt <= 1)
    {
        get_initial(r1, r2, xtm, ytm, xa, ya, xlen, ylen, invmap0, d0,
                    d0_search, fast_opt, t, u);
        TM = detailed_search(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen, invmap0,
                             t, u, simplify_step, score_sum_method, local_d0_search, Lnorm,
                             score_d8, d0);
        if (TM > TMmax)
            TMmax = TM;
        if (TMcut > 0)
            copy_t_u(t, u, t0, u0);
        // run dynamic programing iteratively to find the best alignment
        TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya, xlen, ylen,
                     t, u, invmap, 0, 2, (fast_opt) ? 2 : 30, local_d0_search,
                     D0_MIN, Lnorm, d0, score_d8);
        if (TM > TMmax)
        {
            TMmax = TM;
            for (int i = 0; i < ylen; i++)
                invmap0[i] = invmap[i];
            if (TMcut > 0)
                copy_t_u(t, u, t0, u0);
        }

        if (TMcut > 0) // pre-terminate if TM-score is too low
        {
            double TMtmp = approx_TM(xlen, ylen, a_opt,
                                     xa, ya, t0, u0, invmap0, mol_type);

            if (TMtmp < 0.5 * TMcut)
            {
                TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
                clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                         xtm, ytm, xt, r1, r2, xlen, minlen);
                return 2;
            }
        }

        /************************************************************/
        /* get initial alignment based on secondary structure    */
        /************************************************************/
        if (ss_opt != 1)
        {
            get_initial_ss(path, val, secx, secy, xlen, ylen, invmap);
            TM = detailed_search(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen, invmap,
                                 t, u, simplify_step, score_sum_method, local_d0_search, Lnorm,
                                 score_d8, d0);
            if (TM > TMmax)
            {
                TMmax = TM;
                for (int i = 0; i < ylen; i++)
                    invmap0[i] = invmap[i];
                if (TMcut > 0)
                    copy_t_u(t, u, t0, u0);
            }
            if (TM > TMmax * 0.2)
            {
                TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya,
                             xlen, ylen, t, u, invmap, 0, 2, (fast_opt) ? 2 : 30,
                             local_d0_search, D0_MIN, Lnorm, d0, score_d8);
                if (TM > TMmax)
                {
                    TMmax = TM;
                    for (int i = 0; i < ylen; i++)
                        invmap0[i] = invmap[i];
                    if (TMcut > 0)
                        copy_t_u(t, u, t0, u0);
                }
            }

            if (TMcut > 0) // pre-terminate if TM-score is too low
            {
                double TMtmp = approx_TM(xlen, ylen, a_opt,
                                         xa, ya, t0, u0, invmap0, mol_type);

                if (TMtmp < 0.52 * TMcut)
                {
                    TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
                    clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                             xtm, ytm, xt, r1, r2, xlen, minlen);
                    return 3;
                }
            }
        }

        /************************************************************/
        /* get initial alignment based on local superposition    */
        /************************************************************/
        //=initial5 in original TM-align
        if (ss_opt != 1)
        {
            if (get_initial5(r1, r2, xtm, ytm, path, val, xa, ya,
                             xlen, ylen, invmap, d0, d0_search, fast_opt, D0_MIN))
            {
                TM = detailed_search(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen,
                                     invmap, t, u, simplify_step, score_sum_method,
                                     local_d0_search, Lnorm, score_d8, d0);
                if (TM > TMmax)
                {
                    TMmax = TM;
                    for (int i = 0; i < ylen; i++)
                        invmap0[i] = invmap[i];
                    if (TMcut > 0)
                        copy_t_u(t, u, t0, u0);
                }
                if (TM > TMmax * ddcc)
                {
                    TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya,
                                 xlen, ylen, t, u, invmap, 0, 2, 2, local_d0_search,
                                 D0_MIN, Lnorm, d0, score_d8);
                    if (TM > TMmax)
                    {
                        TMmax = TM;
                        for (int i = 0; i < ylen; i++)
                            invmap0[i] = invmap[i];
                        if (TMcut > 0)
                            copy_t_u(t, u, t0, u0);
                    }
                }
            }
            else
                cerr << "\n\nWarning: initial alignment from local superposition fail!\n\n"
                     << endl;
        }

        if (TMcut > 0) // pre-terminate if TM-score is too low
        {
            double TMtmp = approx_TM(xlen, ylen, a_opt,
                                     xa, ya, t0, u0, invmap0, mol_type);

            if (TMtmp < 0.54 * TMcut)
            {
                TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
                clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                         xtm, ytm, xt, r1, r2, xlen, minlen);
                return 4;
            }
        }

        /********************************************************************/
        /* get initial alignment by local superposition+secondary structure */
        /********************************************************************/
        //=initial3 in original TM-align
        if (ss_opt != 1)
        {
            get_initial_ssplus(r1, r2, score, path, val, secx, secy, xa, ya,
                               xlen, ylen, invmap0, invmap, D0_MIN, d0);
            TM = detailed_search(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen, invmap,
                                 t, u, simplify_step, score_sum_method, local_d0_search, Lnorm,
                                 score_d8, d0);
            if (TM > TMmax)
            {
                TMmax = TM;
                for (i = 0; i < ylen; i++)
                    invmap0[i] = invmap[i];
                if (TMcut > 0)
                    copy_t_u(t, u, t0, u0);
            }
            if (TM > TMmax * ddcc)
            {
                TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya,
                             xlen, ylen, t, u, invmap, 0, 2, (fast_opt) ? 2 : 30,
                             local_d0_search, D0_MIN, Lnorm, d0, score_d8);
                if (TM > TMmax)
                {
                    TMmax = TM;
                    for (i = 0; i < ylen; i++)
                        invmap0[i] = invmap[i];
                    if (TMcut > 0)
                        copy_t_u(t, u, t0, u0);
                }
            }

            if (TMcut > 0) // pre-terminate if TM-score is too low
            {
                double TMtmp = approx_TM(xlen, ylen, a_opt,
                                         xa, ya, t0, u0, invmap0, mol_type);

                if (TMtmp < 0.56 * TMcut)
                {
                    TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
                    clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                             xtm, ytm, xt, r1, r2, xlen, minlen);
                    return 5;
                }
            }
        }

        /*******************************************************************/
        /* get initial alignment based on fragment gapless threading    */
        /*******************************************************************/
        //=initial4 in original TM-align
        get_initial_fgt(r1, r2, xtm, ytm, xa, ya, xlen, ylen,
                        invmap, d0, d0_search, dcu0, fast_opt, t, u);
        TM = detailed_search(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen, invmap,
                             t, u, simplify_step, score_sum_method, local_d0_search, Lnorm,
                             score_d8, d0);
        if (TM > TMmax)
        {
            TMmax = TM;
            for (i = 0; i < ylen; i++)
                invmap0[i] = invmap[i];
            if (TMcut > 0)
                copy_t_u(t, u, t0, u0);
        }
        if (TM > TMmax * ddcc)
        {
            TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya,
                         xlen, ylen, t, u, invmap, 1, 2, 2, local_d0_search, D0_MIN,
                         Lnorm, d0, score_d8);
            if (TM > TMmax)
            {
                TMmax = TM;
                for (i = 0; i < ylen; i++)
                    invmap0[i] = invmap[i];
                if (TMcut > 0)
                    copy_t_u(t, u, t0, u0);
            }
        }

        if (TMcut > 0) // pre-terminate if TM-score is too low
        {
            double TMtmp = approx_TM(xlen, ylen, a_opt,
                                     xa, ya, t0, u0, invmap0, mol_type);

            if (TMtmp < 0.58 * TMcut)
            {
                TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
                clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                         xtm, ytm, xt, r1, r2, xlen, minlen);
                return 6;
            }
        }
    }

    //************************************************//
    //    get initial alignment from user's input:    //
    //************************************************//
    if (i_opt >= 1 && i_opt <= 2) // if input has set parameter for "-i"
    {
        for (int j = 0; j < ylen; j++) // Set aligned position to be "-1"
            invmap[j] = -1;

        int i1 = -1; // in C version, index starts from zero, not from one
        int i2 = -1;
        int L1 = sequence[0].size();
        int L2 = sequence[1].size();
        int L = min(L1, L2); // Get positions for aligned residues
        for (int kk1 = 0; kk1 < L; kk1++)
        {
            if (sequence[0][kk1] != '-')
                i1++;
            if (sequence[1][kk1] != '-')
            {
                i2++;
                if (i2 >= ylen || i1 >= xlen)
                    kk1 = L;
                else if (sequence[0][kk1] != '-')
                    invmap[i2] = i1;
            }
        }

        //--------------- 2. Align proteins from original alignment
        double prevD0_MIN = D0_MIN; // stored for later use
        int prevLnorm = Lnorm;
        double prevd0 = d0;
        TM_ali = standard_TMscore(r1, r2, xtm, ytm, xt, xa, ya,
                                  xlen, ylen, invmap, L_ali, rmsd_ali, D0_MIN, Lnorm, d0,
                                  d0_search, score_d8, t, u, mol_type);
        D0_MIN = prevD0_MIN;
        Lnorm = prevLnorm;
        d0 = prevd0;

        TM = detailed_search_standard(r1, r2, xtm, ytm, xt, xa, ya,
                                      xlen, ylen, invmap, t, u, 40, 8, local_d0_search, true, Lnorm,
                                      score_d8, d0);
        if (TM > TMmax)
        {
            TMmax = TM;
            for (i = 0; i < ylen; i++)
                invmap0[i] = invmap[i];
        }
        // Different from get_initial, get_initial_ss and get_initial_ssplus
        TM = DP_iter(r1, r2, xtm, ytm, xt, path, val, xa, ya,
                     xlen, ylen, t, u, invmap, 0, 2, (fast_opt) ? 2 : 30,
                     local_d0_search, D0_MIN, Lnorm, d0, score_d8);
        if (TM > TMmax)
        {
            TMmax = TM;
            for (i = 0; i < ylen; i++)
                invmap0[i] = invmap[i];
        }
    }

    //*******************************************************************//
    //    The alignment will not be changed any more in the following    //
    //*******************************************************************//
    // check if the initial alignment is generated appropriately
    bool flag = false;
    for (i = 0; i < ylen; i++)
    {
        if (invmap0[i] >= 0)
        {
            flag = true;
            break;
        }
    }
    if (!flag)
    {
        cout << "There is no alignment between the two structures! "
             << "Program stop with no result!" << endl;
        TM1 = TM2 = TM3 = TM4 = TM5 = 0;
        return 1;
    }

    /* last TM-score pre-termination */
    if (TMcut > 0)
    {
        double TMtmp = approx_TM(xlen, ylen, a_opt,
                                 xa, ya, t0, u0, invmap0, mol_type);

        if (TMtmp < 0.6 * TMcut)
        {
            TM1 = TM2 = TM3 = TM4 = TM5 = TMtmp;
            clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                                     xtm, ytm, xt, r1, r2, xlen, minlen);
            return 7;
        }
    }

    //********************************************************************//
    //    Detailed TMscore search engine --> prepare for final TMscore    //
    //********************************************************************//
    // run detailed TMscore search engine for the best alignment, and
    // extract the best rotation matrix (t, u) for the best alignment
    simplify_step = 1;
    if (fast_opt)
        simplify_step = 40;
    score_sum_method = 8;
    TM = detailed_search_standard(r1, r2, xtm, ytm, xt, xa, ya, xlen, ylen,
                                  invmap0, t, u, simplify_step, score_sum_method, local_d0_search,
                                  false, Lnorm, score_d8, d0);

    // select pairs with dis<d8 for final TMscore computation and output alignment
    int k = 0;
    int *m1, *m2;
    double d;
    m1 = new int[xlen]; // alignd index in x
    m2 = new int[ylen]; // alignd index in y
    do_rotation(xa, xt, xlen, t, u);
    k = 0;
    for (int j = 0; j < ylen; j++)
    {
        i = invmap0[j];
        if (i >= 0) // aligned
        {
            n_ali++;
            d = sqrt(dist(&xt[i][0], &ya[j][0]));
            if (d <= score_d8 || (i_opt == 3))
            {
                m1[k] = i;
                m2[k] = j;

                xtm[k][0] = xa[i][0];
                xtm[k][1] = xa[i][1];
                xtm[k][2] = xa[i][2];

                ytm[k][0] = ya[j][0];
                ytm[k][1] = ya[j][1];
                ytm[k][2] = ya[j][2];

                r1[k][0] = xt[i][0];
                r1[k][1] = xt[i][1];
                r1[k][2] = xt[i][2];
                r2[k][0] = ya[j][0];
                r2[k][1] = ya[j][1];
                r2[k][2] = ya[j][2];

                k++;
            }
        }
    }
    n_ali8 = k;

    Kabsch(r1, r2, n_ali8, 0, &rmsd0, t, u); // rmsd0 is used for final output, only recalculate rmsd0, not t & u
    rmsd0 = sqrt(rmsd0 / n_ali8);

    //****************************************//
    //              Final TMscore             //
    //    Please set parameters for output    //
    //****************************************//
    double rmsd;
    simplify_step = 1;
    score_sum_method = 0;
    double Lnorm_0 = ylen;

    // normalized by length of structure A
    parameter_set4final(Lnorm_0, D0_MIN, Lnorm, d0, d0_search, mol_type);
    d0A = d0;
    d0_0 = d0A;
    local_d0_search = d0_search;
    TM1 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0, simplify_step,
                          score_sum_method, &rmsd, local_d0_search, Lnorm, score_d8, d0);
    TM_0 = TM1;

    // normalized by length of structure B
    parameter_set4final(xlen + 0.0, D0_MIN, Lnorm, d0, d0_search, mol_type);
    d0B = d0;
    local_d0_search = d0_search;
    TM2 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t, u, simplify_step,
                          score_sum_method, &rmsd, local_d0_search, Lnorm, score_d8, d0);

    double Lnorm_d0;
    if (a_opt > 0)
    {
        // normalized by average length of structures A, B
        Lnorm_0 = (xlen + ylen) * 0.5;
        parameter_set4final(Lnorm_0, D0_MIN, Lnorm, d0, d0_search, mol_type);
        d0a = d0;
        d0_0 = d0a;
        local_d0_search = d0_search;

        TM3 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0,
                              simplify_step, score_sum_method, &rmsd, local_d0_search, Lnorm,
                              score_d8, d0);
        TM_0 = TM3;
    }
    if (u_opt)
    {
        // normalized by user assigned length
        parameter_set4final(Lnorm_ass, D0_MIN, Lnorm,
                            d0, d0_search, mol_type);
        d0u = d0;
        d0_0 = d0u;
        Lnorm_0 = Lnorm_ass;
        local_d0_search = d0_search;
        TM4 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0,
                              simplify_step, score_sum_method, &rmsd, local_d0_search, Lnorm,
                              score_d8, d0);
        TM_0 = TM4;
    }
    if (d_opt)
    {
        // scaled by user assigned d0
        parameter_set4scale(ylen, d0_scale, Lnorm, d0, d0_search);
        d0_out = d0_scale;
        d0_0 = d0_scale;
        // Lnorm_0=ylen;
        Lnorm_d0 = Lnorm_0;
        local_d0_search = d0_search;
        TM5 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0,
                              simplify_step, score_sum_method, &rmsd, local_d0_search, Lnorm,
                              score_d8, d0);
        TM_0 = TM5;
    }

    /* derive alignment from superposition */
    int ali_len = xlen + ylen; // maximum length of alignment
    seqxA.assign(ali_len, '-');
    seqM.assign(ali_len, ' ');
    seqyA.assign(ali_len, '-');
    do_vec.clear();
    do_vec.assign(ali_len, 0);

    // do_rotation(xa, xt, xlen, t, u);
    do_rotation(xa, xt, xlen, t0, u0);

    int kk = 0, i_old = 0, j_old = 0;
    d = 0;
    Liden = 0;
    // double SO=0;
    for (int k = 0; k < n_ali8; k++)
    {
        for (int i = i_old; i < m1[k]; i++)
        {
            // align x to gap
            seqxA[kk] = seqx[i];
            seqyA[kk] = '-';
            seqM[kk] = ' ';
            kk++;
        }

        for (int j = j_old; j < m2[k]; j++)
        {
            // align y to gap
            seqxA[kk] = '-';
            seqyA[kk] = seqy[j];
            seqM[kk] = ' ';
            kk++;
        }

        seqxA[kk] = seqx[m1[k]];
        seqyA[kk] = seqy[m2[k]];
        Liden += (seqxA[kk] == seqyA[kk]);
        d = sqrt(dist(&xt[m1[k]][0], &ya[m2[k]][0]));
        if (d < d0_out)
            seqM[kk] = ':';
        else
            seqM[kk] = '.';
        do_vec[kk] = d;
        // SO+=(d<3.5);
        kk++;
        i_old = m1[k] + 1;
        j_old = m2[k] + 1;
    }
    // SO/=getmin(xlen,ylen);
    // cout<<n_ali8<<'\t'
    //<<rmsd0<<'\t'
    //<<100.*SO<<endl;

    // tail
    for (int i = i_old; i < xlen; i++)
    {
        // align x to gap
        seqxA[kk] = seqx[i];
        seqyA[kk] = '-';
        seqM[kk] = ' ';
        kk++;
    }
    for (int j = j_old; j < ylen; j++)
    {
        // align y to gap
        seqxA[kk] = '-';
        seqyA[kk] = seqy[j];
        seqM[kk] = ' ';
        kk++;
    }
    seqxA = seqxA.substr(0, kk);
    seqyA = seqyA.substr(0, kk);
    seqM = seqM.substr(0, kk);

    /* free memory */
    clean_up_after_approx_TM(invmap0, invmap, score, path, val,
                             xtm, ytm, xt, r1, r2, xlen, minlen);
    delete[] m1;
    delete[] m2;
    return 0; // zero for no exception
}
/* entry function for TM-align with circular permutation
 * i_opt, a_opt, u_opt, d_opt, TMcut are not implemented yet */
int CPalign_main(double **xa, double **ya,
                 const char *seqx, const char *seqy, const char *secx, const char *secy,
                 double t0[3], double u0[3][3],
                 double &TM1, double &TM2, double &TM3, double &TM4, double &TM5,
                 double &d0_0, double &TM_0,
                 double &d0A, double &d0B, double &d0u, double &d0a, double &d0_out,
                 string &seqM, string &seqxA, string &seqyA, vector<double> &do_vec,
                 double &rmsd0, int &L_ali, double &Liden,
                 double &TM_ali, double &rmsd_ali, int &n_ali, int &n_ali8,
                 const int xlen, const int ylen,
                 const vector<string> sequence, const double Lnorm_ass,
                 const double d0_scale, const int i_opt, const int a_opt,
                 const bool u_opt, const bool d_opt, const bool fast_opt,
                 const int mol_type, const double TMcut = -1)
{
    char *seqx_cp;             // for the protein sequence
    char *secx_cp;             // for the secondary structure
    double **xa_cp;            // coordinates
    string seqxA_cp, seqyA_cp; // alignment
    int i, r;
    int cp_point = 0;    // position of circular permutation
    int cp_aln_best = 0; // amount of aligned residue in sliding window
    int cp_aln_current;  // amount of aligned residue in sliding window

    /* duplicate structure */
    NewArray(&xa_cp, xlen * 2, 3);
    seqx_cp = new char[xlen * 2 + 1];
    secx_cp = new char[xlen * 2 + 1];
    for (r = 0; r < xlen; r++)
    {
        xa_cp[r + xlen][0] = xa_cp[r][0] = xa[r][0];
        xa_cp[r + xlen][1] = xa_cp[r][1] = xa[r][1];
        xa_cp[r + xlen][2] = xa_cp[r][2] = xa[r][2];
        seqx_cp[r + xlen] = seqx_cp[r] = seqx[r];
        secx_cp[r + xlen] = secx_cp[r] = secx[r];
    }
    seqx_cp[2 * xlen] = 0;
    secx_cp[2 * xlen] = 0;

    /* fTM-align alignment */
    double TM1_cp, TM2_cp, TM4_cp;
    const double Lnorm_tmp = getmin(xlen, ylen);
    TMalign_main(xa_cp, ya, seqx_cp, seqy, secx_cp, secy,
                 t0, u0, TM1_cp, TM2_cp, TM3, TM4_cp, TM5,
                 d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA_cp, seqyA_cp,
                 do_vec, rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
                 xlen * 2, ylen, sequence, Lnorm_tmp, d0_scale,
                 0, false, true, false, true, mol_type, -1, 0);

    /* delete gap in seqxA_cp */
    r = 0;
    seqxA = seqxA_cp;
    seqyA = seqyA_cp;
    for (i = 0; i < seqxA_cp.size(); i++)
    {
        if (seqxA_cp[i] != '-')
        {
            seqxA[r] = seqxA_cp[i];
            seqyA[r] = seqyA_cp[i];
            r++;
        }
    }
    seqxA = seqxA.substr(0, r);
    seqyA = seqyA.substr(0, r);

    /* count the number of aligned residues in each window
     * r - residue index in the original unaligned sequence
     * i - position in the alignment */
    for (r = 0; r < xlen - 1; r++)
    {
        cp_aln_current = 0;
        for (i = r; i < r + xlen; i++)
            cp_aln_current += (seqyA[i] != '-');

        if (cp_aln_current > cp_aln_best)
        {
            cp_aln_best = cp_aln_current;
            cp_point = r;
        }
    }
    seqM.clear();
    seqxA.clear();
    seqyA.clear();
    seqxA_cp.clear();
    seqyA_cp.clear();
    rmsd0 = Liden = n_ali = n_ali8 = 0;

    /* fTM-align alignment */
    TMalign_main(xa, ya, seqx, seqy, secx, secy,
                 t0, u0, TM1, TM2, TM3, TM4, TM5,
                 d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
                 do_vec, rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
                 xlen, ylen, sequence, Lnorm_tmp, d0_scale,
                 0, false, true, false, true, mol_type, -1, 0);

    /* do not use circular permutation of number of aligned residues is not
     * larger than sequence-order dependent alignment */
    // cout<<"cp: aln="<<cp_aln_best<<"\tTM="<<TM4_cp<<endl;
    // cout<<"TM: aln="<<n_ali8<<"\tTM="<<TM4<<endl;
    if (n_ali8 >= cp_aln_best || TM4 >= TM4_cp)
        cp_point = 0;

    /* prepare structure for final alignment */
    seqM.clear();
    seqxA.clear();
    seqyA.clear();
    rmsd0 = Liden = n_ali = n_ali8 = 0;
    if (cp_point != 0)
    {
        for (r = 0; r < xlen; r++)
        {
            xa_cp[r][0] = xa_cp[r + cp_point][0];
            xa_cp[r][1] = xa_cp[r + cp_point][1];
            xa_cp[r][2] = xa_cp[r + cp_point][2];
            seqx_cp[r] = seqx_cp[r + cp_point];
            secx_cp[r] = secx_cp[r + cp_point];
        }
    }
    seqx_cp[xlen] = 0;
    secx_cp[xlen] = 0;

    /* test another round of alignment as concatenated alignment can
     * inflate the number of aligned residues and TM-score. e.g. 1yadA 2duaA */
    if (cp_point != 0)
    {
        TMalign_main(xa_cp, ya, seqx_cp, seqy, secx_cp, secy,
                     t0, u0, TM1_cp, TM2_cp, TM3, TM4_cp, TM5,
                     d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA_cp, seqyA_cp,
                     do_vec, rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, cp_aln_best,
                     xlen, ylen, sequence, Lnorm_tmp, d0_scale,
                     0, false, true, false, true, mol_type, -1, 0);
        // cout<<"cp: aln="<<cp_aln_best<<"\tTM="<<TM4_cp<<endl;
        if (n_ali8 >= cp_aln_best || TM4 >= TM4_cp)
        {
            cp_point = 0;
            for (r = 0; r < xlen; r++)
            {
                xa_cp[r][0] = xa[r][0];
                xa_cp[r][1] = xa[r][1];
                xa_cp[r][2] = xa[r][2];
                seqx_cp[r] = seqx[r];
                secx_cp[r] = secx[r];
            }
        }
    }

    /* full TM-align */
    TMalign_main(xa_cp, ya, seqx_cp, seqy, secx_cp, secy,
                 t0, u0, TM1, TM2, TM3, TM4, TM5,
                 d0_0, TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA_cp, seqyA_cp,
                 do_vec, rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
                 xlen, ylen, sequence, Lnorm_ass, d0_scale,
                 i_opt, a_opt, u_opt, d_opt, fast_opt, mol_type, TMcut, 0);

    /* correct alignment
     * r - residue index in the original unaligned sequence
     * i - position in the alignment */
    if (cp_point > 0)
    {
        r = 0;
        for (i = 0; i < seqxA_cp.size(); i++)
        {
            r += (seqxA_cp[i] != '-');
            if (r >= (xlen - cp_point))
            {
                i++;
                break;
            }
        }
        seqxA = seqxA_cp.substr(0, i) + '*' + seqxA_cp.substr(i);
        seqM = seqM.substr(0, i) + ' ' + seqM.substr(i);
        seqyA = seqyA_cp.substr(0, i) + '-' + seqyA_cp.substr(i);
    }
    else
    {
        seqxA = seqxA_cp;
        seqyA = seqyA_cp;
    }

    /* clean up */
    delete[] seqx_cp;
    delete[] secx_cp;
    DeleteArray(&xa_cp, xlen * 2);
    seqxA_cp.clear();
    seqyA_cp.clear();
    return cp_point;
}

bool output_cp(const string &xname, const string &yname,
               const string &seqxA, const string &seqyA, const int outfmt_opt,
               int &left_num, int &right_num, int &left_aln_num, int &right_aln_num)
{
    int r;
    bool after_cp = false;
    for (r = 0; r < seqxA.size(); r++)
    {
        if (seqxA[r] == '*')
            after_cp = true;
        else
        {
            if (after_cp)
            {
                right_aln_num++;
                right_num += (seqxA[r] != '-');
            }
            else
            {
                left_aln_num++;
                left_num += (seqxA[r] != '-');
            }
        }
    }
    if (after_cp == false)
    {
        if (outfmt_opt <= 0)
            cout << "No CP" << endl;
        else if (outfmt_opt == 1)
            cout << "#No CP" << endl;
        else if (outfmt_opt == 2)
            cout << "@" << xname << '\t' << yname << '\t' << "No CP" << endl;
    }
    else
    {
        if (outfmt_opt <= 0)
            cout << "CP point in structure_1 alignment: " << left_aln_num << '/' << right_aln_num << '\n'
                 << "CP point in structure_1: " << left_num << '/' << right_num << endl;
        else if (outfmt_opt == 1)
            cout << "#CP_in_aln=" << left_aln_num << '/' << right_aln_num
                 << "\tCP_in_seq=" << left_num << '/' << right_num << endl;
        else if (outfmt_opt == 2)
            cout << "@" << xname << '\t' << yname << '\t' << left_aln_num
                 << '/' << right_aln_num << '\t' << left_num << '/' << right_num << endl;
    }
    return after_cp;
}
#endif