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[gromacs.git] / src / gromacs / gmxana / gmx_helixorient.cpp

/*
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 * Copyright (c) 2013,2014,2015,2017,2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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#include "gmxpre.h"

#include <cmath>

#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/do_fit.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"

int gmx_helixorient(int argc, char* argv[])
{
    const char* desc[] = {
        "[THISMODULE] calculates the coordinates and direction of the average",
        "axis inside an alpha helix, and the direction/vectors of both the",
        "C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.[PAR]",
        "As input, you need to specify an index group with C[GRK]alpha[grk] atoms",
        "corresponding to an [GRK]alpha[grk]-helix of continuous residues. Sidechain",
        "directions require a second index group of the same size, containing",
        "the heavy atom in each residue that should represent the sidechain.[PAR]",
        "[BB]Note[bb] that this program does not do any fitting of structures.[PAR]",
        "We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix",
        "axis.[PAR]",
        "The tilt/rotation is calculated from Euler rotations, where we define",
        "the helix axis as the local [IT]x[it]-axis, the residues/C[GRK]alpha[grk] vector as ",
        "[IT]y[it], and the",
        "[IT]z[it]-axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
        "we first tilt the helix axis (1) around and (2) orthogonal to the residues",
        "vector, and finally apply the (3) rotation around it. For debugging or other",
        "purposes, we also write out the actual Euler rotation angles as [TT]theta[1-3].xvg[tt]"
    };

    t_topology*  top = nullptr;
    real         t;
    rvec*        x = nullptr;
    matrix       box;
    t_trxstatus* status;
    int          natoms;
    real         theta1, theta2, theta3;

    int   i, j, teller = 0;
    int   iCA, iSC;
    int*  ind_CA;
    int*  ind_SC;
    char* gn_CA;
    char* gn_SC;
    rvec  v1, v2;
    rvec *x_CA, *x_SC;
    rvec* r12;
    rvec* r23;
    rvec* r34;
    rvec* diff13;
    rvec* diff24;
    rvec* helixaxis;
    rvec* residuehelixaxis;
    rvec* residueorigin;
    rvec* residuevector;
    rvec* sidechainvector;

    rvec* residuehelixaxis_t0;
    rvec* residuevector_t0;
    rvec* axis3_t0;
    rvec* residuehelixaxis_tlast;
    rvec* residuevector_tlast;
    rvec* axis3_tlast;
    rvec  refaxes[3], newaxes[3];
    rvec  unitaxes[3];
    rvec  rot_refaxes[3], rot_newaxes[3];

    real  tilt, rotation;
    rvec* axis3;
    real *twist, *residuetwist;
    real *radius, *residueradius;
    real *rise, *residuerise;
    real* residuebending;

    real   tmp;
    real   weight[3];
    t_pbc  pbc;
    matrix A;

    FILE *  fpaxis, *fpcenter, *fptilt, *fprotation;
    FILE *  fpradius, *fprise, *fptwist;
    FILE *  fptheta1, *fptheta2, *fptheta3;
    FILE*   fpbending;
    PbcType pbcType;

    gmx_output_env_t* oenv;
    gmx_rmpbc_t       gpbc = nullptr;

    static gmx_bool bSC          = FALSE;
    static gmx_bool bIncremental = FALSE;

    static t_pargs pa[] = {
        { "-sidechain",
          FALSE,
          etBOOL,
          { &bSC },
          "Calculate sidechain directions relative to helix axis too." },
        { "-incremental",
          FALSE,
          etBOOL,
          { &bIncremental },
          "Calculate incremental rather than total rotation/tilt." },
    };
#define NPA asize(pa)

    t_filenm fnm[] = {
        { efTPR, nullptr, nullptr, ffREAD },        { efTRX, "-f", nullptr, ffREAD },
        { efNDX, nullptr, nullptr, ffOPTRD },       { efDAT, "-oaxis", "helixaxis", ffWRITE },
        { efDAT, "-ocenter", "center", ffWRITE },   { efXVG, "-orise", "rise", ffWRITE },
        { efXVG, "-oradius", "radius", ffWRITE },   { efXVG, "-otwist", "twist", ffWRITE },
        { efXVG, "-obending", "bending", ffWRITE }, { efXVG, "-otilt", "tilt", ffWRITE },
        { efXVG, "-orot", "rotation", ffWRITE }
    };
#define NFILE asize(fnm)

    if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
                           nullptr, &oenv))
    {
        return 0;
    }

    top = read_top(ftp2fn(efTPR, NFILE, fnm), &pbcType);

    for (i = 0; i < 3; i++)
    {
        weight[i] = 1.0;
    }

    /* read index files */
    printf("Select a group of Calpha atoms corresponding to a single continuous helix:\n");
    get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &iCA, &ind_CA, &gn_CA);
    snew(x_CA, iCA);
    snew(x_SC, iCA); /* sic! */

    snew(r12, iCA - 3);
    snew(r23, iCA - 3);
    snew(r34, iCA - 3);
    snew(diff13, iCA - 3);
    snew(diff24, iCA - 3);
    snew(helixaxis, iCA - 3);
    snew(twist, iCA);
    snew(residuetwist, iCA);
    snew(radius, iCA);
    snew(residueradius, iCA);
    snew(rise, iCA);
    snew(residuerise, iCA);
    snew(residueorigin, iCA);
    snew(residuehelixaxis, iCA);
    snew(residuevector, iCA);
    snew(sidechainvector, iCA);
    snew(residuebending, iCA);
    snew(residuehelixaxis_t0, iCA);
    snew(residuevector_t0, iCA);
    snew(axis3_t0, iCA);
    snew(residuehelixaxis_tlast, iCA);
    snew(residuevector_tlast, iCA);
    snew(axis3_tlast, iCA);
    snew(axis3, iCA);

    if (bSC)
    {
        printf("Select a group of atoms defining the sidechain direction (1/residue):\n");
        get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &iSC, &ind_SC, &gn_SC);
        if (iSC != iCA)
        {
            gmx_fatal(FARGS, "Number of sidechain atoms (%d) != number of CA atoms (%d)", iSC, iCA);
        }
    }

    natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);

    fpaxis    = gmx_ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
    fpcenter  = gmx_ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
    fprise    = gmx_ffopen(opt2fn("-orise", NFILE, fnm), "w");
    fpradius  = gmx_ffopen(opt2fn("-oradius", NFILE, fnm), "w");
    fptwist   = gmx_ffopen(opt2fn("-otwist", NFILE, fnm), "w");
    fpbending = gmx_ffopen(opt2fn("-obending", NFILE, fnm), "w");

    fptheta1 = gmx_ffopen("theta1.xvg", "w");
    fptheta2 = gmx_ffopen("theta2.xvg", "w");
    fptheta3 = gmx_ffopen("theta3.xvg", "w");

    if (bIncremental)
    {
        fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm), "Incremental local helix tilt", "Time(ps)",
                          "Tilt (degrees)", oenv);
        fprotation = xvgropen(opt2fn("-orot", NFILE, fnm), "Incremental local helix rotation",
                              "Time(ps)", "Rotation (degrees)", oenv);
    }
    else
    {
        fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm), "Cumulative local helix tilt", "Time(ps)",
                          "Tilt (degrees)", oenv);
        fprotation = xvgropen(opt2fn("-orot", NFILE, fnm), "Cumulative local helix rotation",
                              "Time(ps)", "Rotation (degrees)", oenv);
    }

    clear_rvecs(3, unitaxes);
    unitaxes[0][0] = 1;
    unitaxes[1][1] = 1;
    unitaxes[2][2] = 1;

    gpbc = gmx_rmpbc_init(&top->idef, pbcType, natoms);

    do
    {
        /* initialisation for correct distance calculations */
        set_pbc(&pbc, pbcType, box);
        /* make molecules whole again */
        gmx_rmpbc(gpbc, natoms, box, x);

        /* copy coords to our smaller arrays */
        for (i = 0; i < iCA; i++)
        {
            copy_rvec(x[ind_CA[i]], x_CA[i]);
            if (bSC)
            {
                copy_rvec(x[ind_SC[i]], x_SC[i]);
            }
        }

        for (i = 0; i < iCA - 3; i++)
        {
            rvec_sub(x_CA[i + 1], x_CA[i], r12[i]);
            rvec_sub(x_CA[i + 2], x_CA[i + 1], r23[i]);
            rvec_sub(x_CA[i + 3], x_CA[i + 2], r34[i]);
            rvec_sub(r12[i], r23[i], diff13[i]);
            rvec_sub(r23[i], r34[i], diff24[i]);
            /* calculate helix axis */
            cprod(diff13[i], diff24[i], helixaxis[i]);
            svmul(1.0 / norm(helixaxis[i]), helixaxis[i], helixaxis[i]);

            tmp       = cos_angle(diff13[i], diff24[i]);
            twist[i]  = 180.0 / M_PI * std::acos(tmp);
            radius[i] = std::sqrt(norm(diff13[i]) * norm(diff24[i])) / (2.0 * (1.0 - tmp));
            rise[i]   = std::abs(iprod(r23[i], helixaxis[i]));

            svmul(radius[i] / norm(diff13[i]), diff13[i], v1);
            svmul(radius[i] / norm(diff24[i]), diff24[i], v2);

            rvec_sub(x_CA[i + 1], v1, residueorigin[i + 1]);
            rvec_sub(x_CA[i + 2], v2, residueorigin[i + 2]);
        }
        residueradius[0] = residuetwist[0] = residuerise[0] = 0;

        residueradius[1] = radius[0];
        residuetwist[1]  = twist[0];
        residuerise[1]   = rise[0];

        residuebending[0] = residuebending[1] = 0;
        for (i = 2; i < iCA - 2; i++)
        {
            residueradius[i] = 0.5 * (radius[i - 2] + radius[i - 1]);
            residuetwist[i]  = 0.5 * (twist[i - 2] + twist[i - 1]);
            residuerise[i]   = 0.5 * (rise[i - 2] + rise[i - 1]);
            residuebending[i] = 180.0 / M_PI * std::acos(cos_angle(helixaxis[i - 2], helixaxis[i - 1]));
        }
        residueradius[iCA - 2] = radius[iCA - 4];
        residuetwist[iCA - 2]  = twist[iCA - 4];
        residuerise[iCA - 2]   = rise[iCA - 4];
        residueradius[iCA - 1] = residuetwist[iCA - 1] = residuerise[iCA - 1] = 0;
        residuebending[iCA - 2] = residuebending[iCA - 1] = 0;

        clear_rvec(residueorigin[0]);
        clear_rvec(residueorigin[iCA - 1]);

        /* average helix axes to define them on the residues.
         * Just extrapolate second first/list atom.
         */
        copy_rvec(helixaxis[0], residuehelixaxis[0]);
        copy_rvec(helixaxis[0], residuehelixaxis[1]);

        for (i = 2; i < iCA - 2; i++)
        {
            rvec_add(helixaxis[i - 2], helixaxis[i - 1], residuehelixaxis[i]);
            svmul(0.5, residuehelixaxis[i], residuehelixaxis[i]);
        }
        copy_rvec(helixaxis[iCA - 4], residuehelixaxis[iCA - 2]);
        copy_rvec(helixaxis[iCA - 4], residuehelixaxis[iCA - 1]);

        /* Normalize the axis */
        for (i = 0; i < iCA; i++)
        {
            svmul(1.0 / norm(residuehelixaxis[i]), residuehelixaxis[i], residuehelixaxis[i]);
        }

        /* calculate vector from origin to residue CA */
        fprintf(fpaxis, "%15.12g  ", t);
        fprintf(fpcenter, "%15.12g  ", t);
        fprintf(fprise, "%15.12g  ", t);
        fprintf(fpradius, "%15.12g  ", t);
        fprintf(fptwist, "%15.12g  ", t);
        fprintf(fpbending, "%15.12g  ", t);

        for (i = 0; i < iCA; i++)
        {
            if (i == 0 || i == iCA - 1)
            {
                fprintf(fpaxis, "%15.12g %15.12g %15.12g       ", 0.0, 0.0, 0.0);
                fprintf(fpcenter, "%15.12g %15.12g %15.12g       ", 0.0, 0.0, 0.0);
                fprintf(fprise, "%15.12g  ", 0.0);
                fprintf(fpradius, "%15.12g  ", 0.0);
                fprintf(fptwist, "%15.12g  ", 0.0);
                fprintf(fpbending, "%15.12g  ", 0.0);
            }
            else
            {
                rvec_sub(bSC ? x_SC[i] : x_CA[i], residueorigin[i], residuevector[i]);
                svmul(1.0 / norm(residuevector[i]), residuevector[i], residuevector[i]);
                cprod(residuehelixaxis[i], residuevector[i], axis3[i]);
                fprintf(fpaxis, "%15.12g %15.12g %15.12g       ", residuehelixaxis[i][0],
                        residuehelixaxis[i][1], residuehelixaxis[i][2]);
                fprintf(fpcenter, "%15.12g %15.12g %15.12g       ", residueorigin[i][0],
                        residueorigin[i][1], residueorigin[i][2]);

                fprintf(fprise, "%15.12g  ", residuerise[i]);
                fprintf(fpradius, "%15.12g  ", residueradius[i]);
                fprintf(fptwist, "%15.12g  ", residuetwist[i]);
                fprintf(fpbending, "%15.12g  ", residuebending[i]);
            }
        }
        fprintf(fprise, "\n");
        fprintf(fpradius, "\n");
        fprintf(fpaxis, "\n");
        fprintf(fpcenter, "\n");
        fprintf(fptwist, "\n");
        fprintf(fpbending, "\n");

        if (teller == 0)
        {
            for (i = 0; i < iCA; i++)
            {
                copy_rvec(residuehelixaxis[i], residuehelixaxis_t0[i]);
                copy_rvec(residuevector[i], residuevector_t0[i]);
                copy_rvec(axis3[i], axis3_t0[i]);
            }
        }
        else
        {
            fprintf(fptilt, "%15.12g       ", t);
            fprintf(fprotation, "%15.12g       ", t);
            fprintf(fptheta1, "%15.12g      ", t);
            fprintf(fptheta2, "%15.12g      ", t);
            fprintf(fptheta3, "%15.12g      ", t);

            for (i = 0; i < iCA; i++)
            {
                if (i == 0 || i == iCA - 1)
                {
                    tilt = rotation = 0;
                }
                else
                {
                    if (!bIncremental)
                    {
                        /* Total rotation & tilt */
                        copy_rvec(residuehelixaxis_t0[i], refaxes[0]);
                        copy_rvec(residuevector_t0[i], refaxes[1]);
                        copy_rvec(axis3_t0[i], refaxes[2]);
                    }
                    else
                    {
                        /* Rotation/tilt since last step */
                        copy_rvec(residuehelixaxis_tlast[i], refaxes[0]);
                        copy_rvec(residuevector_tlast[i], refaxes[1]);
                        copy_rvec(axis3_tlast[i], refaxes[2]);
                    }
                    copy_rvec(residuehelixaxis[i], newaxes[0]);
                    copy_rvec(residuevector[i], newaxes[1]);
                    copy_rvec(axis3[i], newaxes[2]);

                    /* rotate reference frame onto unit axes */
                    calc_fit_R(3, 3, weight, unitaxes, refaxes, A);
                    for (j = 0; j < 3; j++)
                    {
                        mvmul(A, refaxes[j], rot_refaxes[j]);
                        mvmul(A, newaxes[j], rot_newaxes[j]);
                    }

                    /* Determine local rotation matrix A */
                    calc_fit_R(3, 3, weight, rot_newaxes, rot_refaxes, A);
                    /* Calculate euler angles, from rotation order y-z-x, where
                     * x is helixaxis, y residuevector, and z axis3.
                     *
                     * A contains rotation column vectors.
                     */

                    theta1 = 180.0 / M_PI * std::atan2(A[0][2], A[0][0]);
                    theta2 = 180.0 / M_PI * std::asin(-A[0][1]);
                    theta3 = 180.0 / M_PI * std::atan2(A[2][1], A[1][1]);

                    tilt     = std::sqrt(theta1 * theta1 + theta2 * theta2);
                    rotation = theta3;
                    fprintf(fptheta1, "%15.12g  ", theta1);
                    fprintf(fptheta2, "%15.12g  ", theta2);
                    fprintf(fptheta3, "%15.12g  ", theta3);
                }
                fprintf(fptilt, "%15.12g  ", tilt);
                fprintf(fprotation, "%15.12g  ", rotation);
            }
            fprintf(fptilt, "\n");
            fprintf(fprotation, "\n");
            fprintf(fptheta1, "\n");
            fprintf(fptheta2, "\n");
            fprintf(fptheta3, "\n");
        }

        for (i = 0; i < iCA; i++)
        {
            copy_rvec(residuehelixaxis[i], residuehelixaxis_tlast[i]);
            copy_rvec(residuevector[i], residuevector_tlast[i]);
            copy_rvec(axis3[i], axis3_tlast[i]);
        }

        teller++;
    } while (read_next_x(oenv, status, &t, x, box));

    gmx_rmpbc_done(gpbc);

    gmx_ffclose(fpaxis);
    gmx_ffclose(fpcenter);
    xvgrclose(fptilt);
    xvgrclose(fprotation);
    gmx_ffclose(fprise);
    gmx_ffclose(fpradius);
    gmx_ffclose(fptwist);
    gmx_ffclose(fpbending);
    gmx_ffclose(fptheta1);
    gmx_ffclose(fptheta2);
    gmx_ffclose(fptheta3);

    close_trx(status);

    return 0;
}