Removed legacyheaders/typedefs.h

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

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015, 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
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
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#include "gmxpre.h"

#include <cmath>
#include <cstring>

#include <algorithm>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/strdb.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/princ.h"
#include "gromacs/gmxlib/conformation-utilities.h"
#include "gromacs/legacyheaders/txtdump.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"


real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
{
    real tmass;
    int  i;

    tmass = 0;
    for (i = 0; (i < atoms->nr); i++)
    {
        if (bGetMass)
        {
            gmx_atomprop_query(aps, epropMass,
                               *atoms->resinfo[atoms->atom[i].resind].name,
                               *atoms->atomname[i], &(atoms->atom[i].m));
        }
        tmass += atoms->atom[i].m;
    }

    return tmass;
}

real calc_geom(int isize, atom_id *index, rvec *x, rvec geom_center, rvec minval,
               rvec maxval, gmx_bool bDiam)
{
    real  diam2, d;
    int   ii, i, j;

    clear_rvec(geom_center);
    diam2 = 0;
    if (isize == 0)
    {
        clear_rvec(minval);
        clear_rvec(maxval);
    }
    else
    {
        if (index)
        {
            ii = index[0];
        }
        else
        {
            ii = 0;
        }
        for (j = 0; j < DIM; j++)
        {
            minval[j] = maxval[j] = x[ii][j];
        }
        for (i = 0; i < isize; i++)
        {
            if (index)
            {
                ii = index[i];
            }
            else
            {
                ii = i;
            }
            rvec_inc(geom_center, x[ii]);
            for (j = 0; j < DIM; j++)
            {
                if (x[ii][j] < minval[j])
                {
                    minval[j] = x[ii][j];
                }
                if (x[ii][j] > maxval[j])
                {
                    maxval[j] = x[ii][j];
                }
            }
            if (bDiam)
            {
                if (index)
                {
                    for (j = i + 1; j < isize; j++)
                    {
                        d     = distance2(x[ii], x[index[j]]);
                        diam2 = std::max(d, diam2);
                    }
                }
                else
                {
                    for (j = i + 1; j < isize; j++)
                    {
                        d     = distance2(x[i], x[j]);
                        diam2 = std::max(d, diam2);
                    }
                }
            }
        }
        svmul(1.0 / isize, geom_center, geom_center);
    }

    return std::sqrt(diam2);
}

void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
{
    int  i;
    rvec shift;

    rvec_sub(center, geom_cent, shift);

    printf("    shift       :%7.3f%7.3f%7.3f (nm)\n", shift[XX], shift[YY],
           shift[ZZ]);

    for (i = 0; (i < natom); i++)
    {
        rvec_inc(x[i], shift);
    }
}

void scale_conf(int natom, rvec x[], matrix box, rvec scale)
{
    int i, j;

    for (i = 0; i < natom; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            x[i][j] *= scale[j];
        }
    }
    for (i = 0; i < DIM; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            box[i][j] *= scale[j];
        }
    }
}

void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
{
    int    i;
    char **bfac_lines;

    *n_bfac = get_lines(fn, &bfac_lines);
    snew(*bfac_val, *n_bfac);
    snew(*bfac_nr, *n_bfac);
    fprintf(stderr, "Reading %d B-factors from %s\n", *n_bfac, fn);
    for (i = 0; (i < *n_bfac); i++)
    {
        /*fprintf(stderr, "Line %d: %s",i,bfac_lines[i]);*/
        sscanf(bfac_lines[i], "%d %lf", &(*bfac_nr)[i], &(*bfac_val)[i]);
        /*fprintf(stderr," nr %d val %g\n",(*bfac_nr)[i],(*bfac_val)[i]);*/
    }

}

void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
                       double *bfac, int *bfac_nr, gmx_bool peratom)
{
    real     bfac_min, bfac_max;
    int      i, n;
    gmx_bool found;

    bfac_max = -1e10;
    bfac_min = 1e10;
    for (i = 0; (i < n_bfac); i++)
    {
        if (bfac_nr[i] - 1 >= atoms->nres)
        {
            peratom = TRUE;
        }
        /*    if ((bfac_nr[i]-1<0) || (bfac_nr[i]-1>=atoms->nr))
           gmx_fatal(FARGS,"Index of B-Factor %d is out of range: %d (%g)",
           i+1,bfac_nr[i],bfac[i]); */
        if (bfac[i] > bfac_max)
        {
            bfac_max = bfac[i];
        }
        if (bfac[i] < bfac_min)
        {
            bfac_min = bfac[i];
        }
    }
    while ((bfac_max > 99.99) || (bfac_min < -99.99))
    {
        fprintf(stderr,
                "Range of values for B-factors too large (min %g, max %g) "
                "will scale down a factor 10\n", bfac_min, bfac_max);
        for (i = 0; (i < n_bfac); i++)
        {
            bfac[i] /= 10;
        }
        bfac_max /= 10;
        bfac_min /= 10;
    }
    while ((std::abs(bfac_max) < 0.5) && (std::abs(bfac_min) < 0.5))
    {
        fprintf(stderr,
                "Range of values for B-factors too small (min %g, max %g) "
                "will scale up a factor 10\n", bfac_min, bfac_max);
        for (i = 0; (i < n_bfac); i++)
        {
            bfac[i] *= 10;
        }
        bfac_max *= 10;
        bfac_min *= 10;
    }

    for (i = 0; (i < natoms); i++)
    {
        atoms->pdbinfo[i].bfac = 0;
    }

    if (!peratom)
    {
        fprintf(stderr, "Will attach %d B-factors to %d residues\n", n_bfac,
                nres);
        for (i = 0; (i < n_bfac); i++)
        {
            found = FALSE;
            for (n = 0; (n < natoms); n++)
            {
                if (bfac_nr[i] == atoms->resinfo[atoms->atom[n].resind].nr)
                {
                    atoms->pdbinfo[n].bfac = bfac[i];
                    found                  = TRUE;
                }
            }
            if (!found)
            {
                gmx_warning("Residue nr %d not found\n", bfac_nr[i]);
            }
        }
    }
    else
    {
        fprintf(stderr, "Will attach %d B-factors to %d atoms\n", n_bfac,
                natoms);
        for (i = 0; (i < n_bfac); i++)
        {
            atoms->pdbinfo[bfac_nr[i] - 1].bfac = bfac[i];
        }
    }
}

void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
{
    real bfac_min, bfac_max, xmin, ymin, zmin;
    int  i;
    int  space = ' ';

    bfac_max = -1e10;
    bfac_min = 1e10;
    xmin     = 1e10;
    ymin     = 1e10;
    zmin     = 1e10;
    for (i = 0; (i < natoms); i++)
    {
        xmin     = std::min(xmin, x[i][XX]);
        ymin     = std::min(ymin, x[i][YY]);
        zmin     = std::min(zmin, x[i][ZZ]);
        bfac_min = std::min(bfac_min, atoms->pdbinfo[i].bfac);
        bfac_max = std::max(bfac_max, atoms->pdbinfo[i].bfac);
    }
    fprintf(stderr, "B-factors range from %g to %g\n", bfac_min, bfac_max);
    for (i = 1; (i < 12); i++)
    {
        fprintf(out,
                "%-6s%5d  %-4.4s%3.3s %c%4d%c   %8.3f%8.3f%8.3f%6.2f%6.2f\n",
                "ATOM  ", natoms + 1 + i, "CA", "LEG", space, nres + 1, space,
                (xmin + (i * 0.12)) * 10, ymin * 10, zmin * 10, 1.0, bfac_min
                + ((i - 1.0) * (bfac_max - bfac_min) / 10));
    }
}

void visualize_images(const char *fn, int ePBC, matrix box)
{
    t_atoms atoms;
    rvec   *img;
    char   *c, *ala;
    int     nat, i;

    nat = NTRICIMG + 1;
    init_t_atoms(&atoms, nat, FALSE);
    atoms.nr = nat;
    snew(img, nat);
    /* FIXME: Constness should not be cast away */
    c   = (char *) "C";
    ala = (char *) "ALA";
    for (i = 0; i < nat; i++)
    {
        atoms.atomname[i]        = &c;
        atoms.atom[i].resind     = i;
        atoms.resinfo[i].name    = &ala;
        atoms.resinfo[i].nr      = i + 1;
        atoms.resinfo[i].chainid = 'A' + i / NCUCVERT;
    }
    calc_triclinic_images(box, img + 1);

    write_sto_conf(fn, "Images", &atoms, img, NULL, ePBC, box);

    done_atom(&atoms);
    sfree(img);
}

void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
{
    int  *edge;
    rvec *vert, shift;
    int   nx, ny, nz, nbox, nat;
    int   i, j, x, y, z;
    int   rectedge[24] =
    {
        0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6,
        4
    };

    a0++;
    r0++;

    nx   = static_cast<int>(gridsize[XX] + 0.5);
    ny   = static_cast<int>(gridsize[YY] + 0.5);
    nz   = static_cast<int>(gridsize[ZZ] + 0.5);
    nbox = nx * ny * nz;
    if (TRICLINIC(box))
    {
        nat = nbox * NCUCVERT;
        snew(vert, nat);
        calc_compact_unitcell_vertices(ecenterDEF, box, vert);
        j = 0;
        for (z = 0; z < nz; z++)
        {
            for (y = 0; y < ny; y++)
            {
                for (x = 0; x < nx; x++)
                {
                    for (i = 0; i < DIM; i++)
                    {
                        shift[i] = x * box[0][i] + y * box[1][i] + z
                            * box[2][i];
                    }
                    for (i = 0; i < NCUCVERT; i++)
                    {
                        rvec_add(vert[i], shift, vert[j]);
                        j++;
                    }
                }
            }
        }

        for (i = 0; i < nat; i++)
        {
            gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
                                     10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
        }

        edge = compact_unitcell_edges();
        for (j = 0; j < nbox; j++)
        {
            for (i = 0; i < NCUCEDGE; i++)
            {
                fprintf(out, "CONECT%5d%5d\n", a0 + j * NCUCVERT + edge[2 * i],
                        a0 + j * NCUCVERT + edge[2 * i + 1]);
            }
        }

        sfree(vert);
    }
    else
    {
        i = 0;
        for (z = 0; z <= 1; z++)
        {
            for (y = 0; y <= 1; y++)
            {
                for (x = 0; x <= 1; x++)
                {
                    gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
                                             x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
                    i++;
                }
            }
        }
        for (i = 0; i < 24; i += 2)
        {
            fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i + 1]);
        }
    }
}

void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
{
    rvec rotvec;
    real ux, uy, uz, costheta, sintheta;

    costheta = cos_angle(principal_axis, targetvec);
    sintheta = std::sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */

    /* Determine rotation from cross product with target vector */
    cprod(principal_axis, targetvec, rotvec);
    unitv(rotvec, rotvec);
    printf("Aligning %g %g %g to %g %g %g : xprod  %g %g %g\n",
           principal_axis[XX], principal_axis[YY], principal_axis[ZZ], targetvec[XX], targetvec[YY], targetvec[ZZ],
           rotvec[XX], rotvec[YY], rotvec[ZZ]);

    ux              = rotvec[XX];
    uy              = rotvec[YY];
    uz              = rotvec[ZZ];
    rotmatrix[0][0] = ux*ux + (1.0-ux*ux)*costheta;
    rotmatrix[0][1] = ux*uy*(1-costheta)-uz*sintheta;
    rotmatrix[0][2] = ux*uz*(1-costheta)+uy*sintheta;
    rotmatrix[1][0] = ux*uy*(1-costheta)+uz*sintheta;
    rotmatrix[1][1] = uy*uy + (1.0-uy*uy)*costheta;
    rotmatrix[1][2] = uy*uz*(1-costheta)-ux*sintheta;
    rotmatrix[2][0] = ux*uz*(1-costheta)-uy*sintheta;
    rotmatrix[2][1] = uy*uz*(1-costheta)+ux*sintheta;
    rotmatrix[2][2] = uz*uz + (1.0-uz*uz)*costheta;

    printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
           rotmatrix[0][0], rotmatrix[0][1], rotmatrix[0][2],
           rotmatrix[1][0], rotmatrix[1][1], rotmatrix[1][2],
           rotmatrix[2][0], rotmatrix[2][1], rotmatrix[2][2]);
}

static void renum_resnr(t_atoms *atoms, int isize, const int *index,
                        int resnr_start)
{
    int i, resind_prev, resind;

    resind_prev = -1;
    for (i = 0; i < isize; i++)
    {
        resind = atoms->atom[index == NULL ? i : index[i]].resind;
        if (resind != resind_prev)
        {
            atoms->resinfo[resind].nr = resnr_start;
            resnr_start++;
        }
        resind_prev = resind;
    }
}

int gmx_editconf(int argc, char *argv[])
{
    const char     *desc[] =
    {
        "[THISMODULE] converts generic structure format to [REF].gro[ref], [TT].g96[tt]",
        "or [REF].pdb[ref].",
        "[PAR]",
        "The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
        "[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
        "will center the system in the box, unless [TT]-noc[tt] is used.",
        "[PAR]",
        "Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
        "triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
        "[TT]dodecahedron[tt] represents a rhombic dodecahedron and",
        "[TT]octahedron[tt] is a truncated octahedron.",
        "The last two are special cases of a triclinic box.",
        "The length of the three box vectors of the truncated octahedron is the",
        "shortest distance between two opposite hexagons.",
        "Relative to a cubic box with some periodic image distance, the volume of a ",
        "dodecahedron with this same periodic distance is 0.71 times that of the cube, ",
        "and that of a truncated octahedron is 0.77 times.",
        "[PAR]",
        "Option [TT]-box[tt] requires only",
        "one value for a cubic, rhombic dodecahedral, or truncated octahedral box.",
        "[PAR]",
        "With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the [IT]x[it]-, [IT]y[it]-,",
        "and [IT]z[it]-directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
        "[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
        "to the diameter of the system (largest distance between atoms) plus twice",
        "the specified distance.",
        "[PAR]",
        "Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
        "a triclinic box and cannot be used with option [TT]-d[tt].",
        "[PAR]",
        "When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
        "can be selected for calculating the size and the geometric center,",
        "otherwise the whole system is used.",
        "[PAR]",
        "[TT]-rotate[tt] rotates the coordinates and velocities.",
        "[PAR]",
        "[TT]-princ[tt] aligns the principal axes of the system along the",
        "coordinate axes, with the longest axis aligned with the [IT]x[it]-axis. ",
        "This may allow you to decrease the box volume,",
        "but beware that molecules can rotate significantly in a nanosecond.",
        "[PAR]",
        "Scaling is applied before any of the other operations are",
        "performed. Boxes and coordinates can be scaled to give a certain density (option",
        "[TT]-density[tt]). Note that this may be inaccurate in case a [REF].gro[ref]",
        "file is given as input. A special feature of the scaling option is that when the",
        "factor -1 is given in one dimension, one obtains a mirror image,",
        "mirrored in one of the planes. When one uses -1 in three dimensions, ",
        "a point-mirror image is obtained.[PAR]",
        "Groups are selected after all operations have been applied.[PAR]",
        "Periodicity can be removed in a crude manner.",
        "It is important that the box vectors at the bottom of your input file",
        "are correct when the periodicity is to be removed.",
        "[PAR]",
        "When writing [REF].pdb[ref] files, B-factors can be",
        "added with the [TT]-bf[tt] option. B-factors are read",
        "from a file with with following format: first line states number of",
        "entries in the file, next lines state an index",
        "followed by a B-factor. The B-factors will be attached per residue",
        "unless an index is larger than the number of residues or unless the",
        "[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
        "be added instead of B-factors. [TT]-legend[tt] will produce",
        "a row of CA atoms with B-factors ranging from the minimum to the",
        "maximum value found, effectively making a legend for viewing.",
        "[PAR]",
        "With the option [TT]-mead[tt] a special [REF].pdb[ref] ([REF].pqr[ref])",
        "file for the MEAD electrostatics",
        "program (Poisson-Boltzmann solver) can be made. A further prerequisite",
        "is that the input file is a run input file.",
        "The B-factor field is then filled with the Van der Waals radius",
        "of the atoms while the occupancy field will hold the charge.",
        "[PAR]",
        "The option [TT]-grasp[tt] is similar, but it puts the charges in the B-factor",
        "and the radius in the occupancy.",
        "[PAR]",
        "Option [TT]-align[tt] allows alignment",
        "of the principal axis of a specified group against the given vector, ",
        "with an optional center of rotation specified by [TT]-aligncenter[tt].",
        "[PAR]",
        "Finally, with option [TT]-label[tt], [TT]editconf[tt] can add a chain identifier",
        "to a [REF].pdb[ref] file, which can be useful for analysis with e.g. Rasmol.",
        "[PAR]",
        "To convert a truncated octrahedron file produced by a package which uses",
        "a cubic box with the corners cut off (such as GROMOS), use::",
        "",
        "  gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out",
        "",
        "where [TT]veclen[tt] is the size of the cubic box times [SQRT]3[sqrt]/2."
    };
    const char     *bugs[] =
    {
        "For complex molecules, the periodicity removal routine may break down, "
        "in that case you can use [gmx-trjconv]."
    };
    static real     dist    = 0.0;
    static gmx_bool bNDEF   = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
        FALSE, bCONECT      = FALSE;
    static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead =
        FALSE, bGrasp       = FALSE, bSig56 = FALSE;
    static rvec     scale   =
    { 1, 1, 1 }, newbox     =
    { 0, 0, 0 }, newang     =
    { 90, 90, 90 };
    static real rho          = 1000.0, rvdw = 0.12;
    static rvec center       =
    { 0, 0, 0 }, translation =
    { 0, 0, 0 }, rotangles   =
    { 0, 0, 0 }, aligncenter =
    { 0, 0, 0 }, targetvec   =
    { 0, 0, 0 };
    static const char *btype[] =
    { NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
    *label             = "A";
    static rvec visbox =
    { 0, 0, 0 };
    static int  resnr_start = -1;
    t_pargs
                pa[] =
    {
        { "-ndef", FALSE, etBOOL,
          { &bNDEF }, "Choose output from default index groups" },
        { "-visbox", FALSE, etRVEC,
          { visbox },
          "HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
        { "-bt", FALSE, etENUM,
          { btype }, "Box type for [TT]-box[tt] and [TT]-d[tt]" },
        { "-box", FALSE, etRVEC,
          { newbox }, "Box vector lengths (a,b,c)" },
        { "-angles", FALSE, etRVEC,
          { newang }, "Angles between the box vectors (bc,ac,ab)" },
        { "-d", FALSE, etREAL,
          { &dist }, "Distance between the solute and the box" },
        { "-c", FALSE, etBOOL,
          { &bCenter },
          "Center molecule in box (implied by [TT]-box[tt] and [TT]-d[tt])" },
        { "-center", FALSE, etRVEC,
          { center }, "Coordinates of geometrical center" },
        { "-aligncenter", FALSE, etRVEC,
          { aligncenter }, "Center of rotation for alignment" },
        { "-align", FALSE, etRVEC,
          { targetvec },
          "Align to target vector" },
        { "-translate", FALSE, etRVEC,
          { translation }, "Translation" },
        { "-rotate", FALSE, etRVEC,
          { rotangles },
          "Rotation around the X, Y and Z axes in degrees" },
        { "-princ", FALSE, etBOOL,
          { &bOrient },
          "Orient molecule(s) along their principal axes" },
        { "-scale", FALSE, etRVEC,
          { scale }, "Scaling factor" },
        { "-density", FALSE, etREAL,
          { &rho },
          "Density (g/L) of the output box achieved by scaling" },
        { "-pbc", FALSE, etBOOL,
          { &bRMPBC },
          "Remove the periodicity (make molecule whole again)" },
        { "-resnr", FALSE, etINT,
          { &resnr_start },
          " Renumber residues starting from resnr" },
        { "-grasp", FALSE, etBOOL,
          { &bGrasp },
          "Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
        {
            "-rvdw", FALSE, etREAL,
            { &rvdw },
            "Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file"
        },
        { "-sig56", FALSE, etBOOL,
          { &bSig56 },
          "Use rmin/2 (minimum in the Van der Waals potential) rather than [GRK]sigma[grk]/2 " },
        {
            "-vdwread", FALSE, etBOOL,
            { &bReadVDW },
            "Read the Van der Waals radii from the file [TT]vdwradii.dat[tt] rather than computing the radii based on the force field"
        },
        { "-atom", FALSE, etBOOL,
          { &peratom }, "Force B-factor attachment per atom" },
        { "-legend", FALSE, etBOOL,
          { &bLegend }, "Make B-factor legend" },
        { "-label", FALSE, etSTR,
          { &label }, "Add chain label for all residues" },
        {
            "-conect", FALSE, etBOOL,
            { &bCONECT },
            "Add CONECT records to a [REF].pdb[ref] file when written. Can only be done when a topology is present"
        }
    };
#define NPA asize(pa)

    FILE             *out;
    const char       *infile, *outfile;
    int               outftp, inftp, natom, i, j, n_bfac, itype, ntype;
    double           *bfac    = NULL, c6, c12;
    int              *bfac_nr = NULL;
    t_topology       *top     = NULL;
    char             *grpname, *sgrpname, *agrpname;
    int               isize, ssize, asize;
    atom_id          *index, *sindex, *aindex;
    rvec             *x, *v, gc, rmin, rmax, size;
    int               ePBC;
    matrix            box, rotmatrix, trans;
    rvec              princd, tmpvec;
    gmx_bool          bIndex, bSetSize, bSetAng, bDist, bSetCenter, bAlign;
    gmx_bool          bHaveV, bScale, bRho, bTranslate, bRotate, bCalcGeom, bCalcDiam;
    real              diam = 0, mass = 0, d, vdw;
    gmx_atomprop_t    aps;
    gmx_conect        conect;
    gmx_output_env_t *oenv;
    t_filenm          fnm[] =
    {
        { efSTX, "-f", NULL, ffREAD },
        { efNDX, "-n", NULL, ffOPTRD },
        { efSTO, NULL, NULL, ffOPTWR },
        { efPQR, "-mead", "mead", ffOPTWR },
        { efDAT, "-bf", "bfact", ffOPTRD }
    };
#define NFILE asize(fnm)

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

    bIndex     = opt2bSet("-n", NFILE, fnm) || bNDEF;
    bMead      = opt2bSet("-mead", NFILE, fnm);
    bSetSize   = opt2parg_bSet("-box", NPA, pa);
    bSetAng    = opt2parg_bSet("-angles", NPA, pa);
    bSetCenter = opt2parg_bSet("-center", NPA, pa);
    bDist      = opt2parg_bSet("-d", NPA, pa);
    bAlign     = opt2parg_bSet("-align", NPA, pa);
    /* Only automatically turn on centering without -noc */
    if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c", NPA, pa))
    {
        bCenter = TRUE;
    }
    bScale     = opt2parg_bSet("-scale", NPA, pa);
    bRho       = opt2parg_bSet("-density", NPA, pa);
    bTranslate = opt2parg_bSet("-translate", NPA, pa);
    bRotate    = opt2parg_bSet("-rotate", NPA, pa);
    if (bScale && bRho)
    {
        fprintf(stderr, "WARNING: setting -density overrides -scale\n");
    }
    bScale    = bScale || bRho;
    bCalcGeom = bCenter || bRotate || bOrient || bScale;

    GMX_RELEASE_ASSERT(btype[0] != NULL, "Option setting inconsistency; btype[0] is NULL");

    bCalcDiam = (btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o');

    infile = ftp2fn(efSTX, NFILE, fnm);
    if (bMead)
    {
        outfile = ftp2fn(efPQR, NFILE, fnm);
    }
    else
    {
        outfile = ftp2fn(efSTO, NFILE, fnm);
    }
    outftp = fn2ftp(outfile);
    inftp  = fn2ftp(infile);

    aps = gmx_atomprop_init();

    if (bMead && bGrasp)
    {
        printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
        bGrasp = FALSE;
    }
    if (bGrasp && (outftp != efPDB))
    {
        gmx_fatal(FARGS, "Output file should be a .pdb file"
                  " when using the -grasp option\n");
    }
    if ((bMead || bGrasp) && (fn2ftp(infile) != efTPR))
    {
        gmx_fatal(FARGS, "Input file should be a .tpr file"
                  " when using the -mead option\n");
    }

    t_topology *top_tmp;
    snew(top_tmp, 1);
    read_tps_conf(infile, top_tmp, &ePBC, &x, &v, box, FALSE);
    t_atoms  &atoms = top_tmp->atoms;
    natom = atoms.nr;
    if (atoms.pdbinfo == NULL)
    {
        snew(atoms.pdbinfo, atoms.nr);
    }
    if (fn2ftp(infile) == efPDB)
    {
        get_pdb_atomnumber(&atoms, aps);
    }
    printf("Read %d atoms\n", atoms.nr);

    /* Get the element numbers if available in a pdb file */
    if (fn2ftp(infile) == efPDB)
    {
        get_pdb_atomnumber(&atoms, aps);
    }

    if (ePBC != epbcNONE)
    {
        real vol = det(box);
        printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
               vol, 100*(static_cast<int>(vol*4.5)));
    }

    if (bMead || bGrasp || bCONECT)
    {
        top = read_top(infile, NULL);
    }

    if (bMead || bGrasp)
    {
        if (atoms.nr != top->atoms.nr)
        {
            gmx_fatal(FARGS, "Atom numbers don't match (%d vs. %d)", atoms.nr, top->atoms.nr);
        }
        snew(atoms.pdbinfo, top->atoms.nr);
        ntype = top->idef.atnr;
        for (i = 0; (i < atoms.nr); i++)
        {
            /* Determine the Van der Waals radius from the force field */
            if (bReadVDW)
            {
                if (!gmx_atomprop_query(aps, epropVDW,
                                        *top->atoms.resinfo[top->atoms.atom[i].resind].name,
                                        *top->atoms.atomname[i], &vdw))
                {
                    vdw = rvdw;
                }
            }
            else
            {
                itype = top->atoms.atom[i].type;
                c12   = top->idef.iparams[itype*ntype+itype].lj.c12;
                c6    = top->idef.iparams[itype*ntype+itype].lj.c6;
                if ((c6 != 0) && (c12 != 0))
                {
                    real sig6;
                    if (bSig56)
                    {
                        sig6 = 2*c12/c6;
                    }
                    else
                    {
                        sig6 = c12/c6;
                    }
                    vdw   = 0.5*std::pow(sig6, static_cast<real>(1.0/6.0));
                }
                else
                {
                    vdw = rvdw;
                }
            }
            /* Factor of 10 for nm -> Angstroms */
            vdw *= 10;

            if (bMead)
            {
                atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
                atoms.pdbinfo[i].bfac  = vdw;
            }
            else
            {
                atoms.pdbinfo[i].occup = vdw;
                atoms.pdbinfo[i].bfac  = top->atoms.atom[i].q;
            }
        }
    }
    bHaveV = FALSE;
    for (i = 0; (i < natom) && !bHaveV; i++)
    {
        for (j = 0; (j < DIM) && !bHaveV; j++)
        {
            bHaveV = bHaveV || (v[i][j] != 0);
        }
    }
    printf("%selocities found\n", bHaveV ? "V" : "No v");

    if (visbox[0] > 0)
    {
        if (bIndex)
        {
            gmx_fatal(FARGS, "Sorry, can not visualize box with index groups");
        }
        if (outftp != efPDB)
        {
            gmx_fatal(FARGS, "Sorry, can only visualize box with a pdb file");
        }
    }
    else if (visbox[0] == -1)
    {
        visualize_images("images.pdb", ePBC, box);
    }

    /* remove pbc */
    if (bRMPBC)
    {
        rm_gropbc(&atoms, x, box);
    }

    if (bCalcGeom)
    {
        if (bIndex)
        {
            fprintf(stderr, "\nSelect a group for determining the system size:\n");
            get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
                      1, &ssize, &sindex, &sgrpname);
        }
        else
        {
            ssize  = atoms.nr;
            sindex = NULL;
        }
        diam = calc_geom(ssize, sindex, x, gc, rmin, rmax, bCalcDiam);
        rvec_sub(rmax, rmin, size);
        printf("    system size :%7.3f%7.3f%7.3f (nm)\n",
               size[XX], size[YY], size[ZZ]);
        if (bCalcDiam)
        {
            printf("    diameter    :%7.3f               (nm)\n", diam);
        }
        printf("    center      :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
        printf("    box vectors :%7.3f%7.3f%7.3f (nm)\n",
               norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
        printf("    box angles  :%7.2f%7.2f%7.2f (degrees)\n",
               norm2(box[ZZ]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[YY], box[ZZ])),
               norm2(box[ZZ]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[ZZ])),
               norm2(box[YY]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[YY])));
        printf("    box volume  :%7.2f               (nm^3)\n", det(box));
    }

    if (bRho || bOrient || bAlign)
    {
        mass = calc_mass(&atoms, !fn2bTPX(infile), aps);
    }

    if (bOrient)
    {
        atom_id *index;
        char    *grpnames;

        /* Get a group for principal component analysis */
        fprintf(stderr, "\nSelect group for the determining the orientation\n");
        get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);

        /* Orient the principal axes along the coordinate axes */
        orient_princ(&atoms, isize, index, natom, x, bHaveV ? v : NULL, NULL);
        sfree(index);
        sfree(grpnames);
    }

    if (bScale)
    {
        /* scale coordinates and box */
        if (bRho)
        {
            /* Compute scaling constant */
            real vol, dens;

            vol  = det(box);
            dens = (mass*AMU)/(vol*NANO*NANO*NANO);
            fprintf(stderr, "Volume  of input %g (nm^3)\n", vol);
            fprintf(stderr, "Mass    of input %g (a.m.u.)\n", mass);
            fprintf(stderr, "Density of input %g (g/l)\n", dens);
            if (vol == 0 || mass == 0)
            {
                gmx_fatal(FARGS, "Cannot scale density with "
                          "zero mass (%g) or volume (%g)\n", mass, vol);
            }

            scale[XX] = scale[YY] = scale[ZZ] = std::pow(dens/rho, static_cast<real>(1.0/3.0));
            fprintf(stderr, "Scaling all box vectors by %g\n", scale[XX]);
        }
        scale_conf(atoms.nr, x, box, scale);
    }

    if (bAlign)
    {
        if (bIndex)
        {
            fprintf(stderr, "\nSelect a group that you want to align:\n");
            get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
                      1, &asize, &aindex, &agrpname);
        }
        else
        {
            asize = atoms.nr;
            snew(aindex, asize);
            for (i = 0; i < asize; i++)
            {
                aindex[i] = i;
            }
        }
        printf("Aligning %d atoms (out of %d) to %g %g %g, center of rotation %g %g %g\n", asize, natom,
               targetvec[XX], targetvec[YY], targetvec[ZZ],
               aligncenter[XX], aligncenter[YY], aligncenter[ZZ]);
        /*subtract out pivot point*/
        for (i = 0; i < asize; i++)
        {
            rvec_dec(x[aindex[i]], aligncenter);
        }
        /*now determine transform and rotate*/
        /*will this work?*/
        principal_comp(asize, aindex, atoms.atom, x, trans, princd);

        unitv(targetvec, targetvec);
        printf("Using %g %g %g as principal axis\n", trans[0][2], trans[1][2], trans[2][2]);
        tmpvec[XX] = trans[0][2]; tmpvec[YY] = trans[1][2]; tmpvec[ZZ] = trans[2][2];
        calc_rotmatrix(tmpvec, targetvec, rotmatrix);
        /* rotmatrix finished */

        for (i = 0; i < asize; ++i)
        {
            mvmul(rotmatrix, x[aindex[i]], tmpvec);
            copy_rvec(tmpvec, x[aindex[i]]);
        }

        /*add pivot point back*/
        for (i = 0; i < asize; i++)
        {
            rvec_inc(x[aindex[i]], aligncenter);
        }
        if (!bIndex)
        {
            sfree(aindex);
        }
    }

    if (bTranslate)
    {
        if (bIndex)
        {
            fprintf(stderr, "\nSelect a group that you want to translate:\n");
            get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm),
                      1, &ssize, &sindex, &sgrpname);
        }
        else
        {
            ssize  = atoms.nr;
            sindex = NULL;
        }
        printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom,
               translation[XX], translation[YY], translation[ZZ]);
        if (sindex)
        {
            for (i = 0; i < ssize; i++)
            {
                rvec_inc(x[sindex[i]], translation);
            }
        }
        else
        {
            for (i = 0; i < natom; i++)
            {
                rvec_inc(x[i], translation);
            }
        }
    }
    if (bRotate)
    {
        /* Rotate */
        printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n", rotangles[XX], rotangles[YY], rotangles[ZZ]);
        for (i = 0; i < DIM; i++)
        {
            rotangles[i] *= DEG2RAD;
        }
        rotate_conf(natom, x, v, rotangles[XX], rotangles[YY], rotangles[ZZ]);
    }

    if (bCalcGeom)
    {
        /* recalc geometrical center and max and min coordinates and size */
        calc_geom(ssize, sindex, x, gc, rmin, rmax, FALSE);
        rvec_sub(rmax, rmin, size);
        if (bScale || bOrient || bRotate)
        {
            printf("new system size : %6.3f %6.3f %6.3f\n",
                   size[XX], size[YY], size[ZZ]);
        }
    }

    if ((btype[0] != NULL) && (bSetSize || bDist || (btype[0][0] == 't' && bSetAng)))
    {
        ePBC = epbcXYZ;
        if (!(bSetSize || bDist))
        {
            for (i = 0; i < DIM; i++)
            {
                newbox[i] = norm(box[i]);
            }
        }
        clear_mat(box);
        /* calculate new boxsize */
        switch (btype[0][0])
        {
            case 't':
                if (bDist)
                {
                    for (i = 0; i < DIM; i++)
                    {
                        newbox[i] = size[i]+2*dist;
                    }
                }
                if (!bSetAng)
                {
                    box[XX][XX] = newbox[XX];
                    box[YY][YY] = newbox[YY];
                    box[ZZ][ZZ] = newbox[ZZ];
                }
                else
                {
                    matrix_convert(box, newbox, newang);
                }
                break;
            case 'c':
            case 'd':
            case 'o':
                if (bSetSize)
                {
                    d = newbox[0];
                }
                else
                {
                    d = diam+2*dist;
                }
                if (btype[0][0] == 'c')
                {
                    for (i = 0; i < DIM; i++)
                    {
                        box[i][i] = d;
                    }
                }
                else if (btype[0][0] == 'd')
                {
                    box[XX][XX] = d;
                    box[YY][YY] = d;
                    box[ZZ][XX] = d/2;
                    box[ZZ][YY] = d/2;
                    box[ZZ][ZZ] = d*std::sqrt(2.0)/2.0;
                }
                else
                {
                    box[XX][XX] = d;
                    box[YY][XX] = d/3;
                    box[YY][YY] = d*std::sqrt(2.0)*2.0/3.0;
                    box[ZZ][XX] = -d/3;
                    box[ZZ][YY] = d*std::sqrt(2.0)/3.0;
                    box[ZZ][ZZ] = d*std::sqrt(6.0)/3.0;
                }
                break;
        }
    }

    /* calculate new coords for geometrical center */
    if (!bSetCenter)
    {
        calc_box_center(ecenterDEF, box, center);
    }

    /* center molecule on 'center' */
    if (bCenter)
    {
        center_conf(natom, x, center, gc);
    }

    /* print some */
    if (bCalcGeom)
    {
        calc_geom(ssize, sindex, x, gc, rmin, rmax, FALSE);
        printf("new center      :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
    }
    if (bOrient || bScale || bDist || bSetSize)
    {
        printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
               norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
        printf("new box angles  :%7.2f%7.2f%7.2f (degrees)\n",
               norm2(box[ZZ]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[YY], box[ZZ])),
               norm2(box[ZZ]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[ZZ])),
               norm2(box[YY]) == 0 ? 0 :
               RAD2DEG*std::acos(cos_angle_no_table(box[XX], box[YY])));
        printf("new box volume  :%7.2f               (nm^3)\n", det(box));
    }

    if (check_box(epbcXYZ, box))
    {
        printf("\nWARNING: %s\n"
               "See the GROMACS manual for a description of the requirements that\n"
               "must be satisfied by descriptions of simulation cells.\n",
               check_box(epbcXYZ, box));
    }

    if (bDist && btype[0][0] == 't')
    {
        if (TRICLINIC(box))
        {
            printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
                   "distance from the solute to a box surface along the corresponding normal\n"
                   "vector might be somewhat smaller than your specified value %f.\n"
                   "You can check the actual value with g_mindist -pi\n", dist);
        }
        else if (!opt2parg_bSet("-bt", NPA, pa))
        {
            printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
                   "If the molecule rotates the actual distance will be smaller. You might want\n"
                   "to use a cubic box instead, or why not try a dodecahedron today?\n");
        }
    }
    if (bCONECT && (outftp == efPDB) && (inftp == efTPR))
    {
        conect = gmx_conect_generate(top);
    }
    else
    {
        conect = NULL;
    }

    if (bIndex)
    {
        fprintf(stderr, "\nSelect a group for output:\n");
        get_index(&atoms, opt2fn_null("-n", NFILE, fnm),
                  1, &isize, &index, &grpname);

        if (resnr_start >= 0)
        {
            renum_resnr(&atoms, isize, index, resnr_start);
        }

        if (opt2parg_bSet("-label", NPA, pa))
        {
            for (i = 0; (i < atoms.nr); i++)
            {
                atoms.resinfo[atoms.atom[i].resind].chainid = label[0];
            }
        }

        if (opt2bSet("-bf", NFILE, fnm) || bLegend)
        {
            gmx_fatal(FARGS, "Sorry, cannot do bfactors with an index group.");
        }

        if (outftp == efPDB)
        {
            out = gmx_ffopen(outfile, "w");
            write_pdbfile_indexed(out, *top_tmp->name, &atoms, x, ePBC, box, ' ', 1, isize, index, conect, TRUE);
            gmx_ffclose(out);
        }
        else
        {
            write_sto_conf_indexed(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : NULL, ePBC, box, isize, index);
        }
    }
    else
    {
        if (resnr_start >= 0)
        {
            renum_resnr(&atoms, atoms.nr, NULL, resnr_start);
        }

        if ((outftp == efPDB) || (outftp == efPQR))
        {
            out = gmx_ffopen(outfile, "w");
            if (bMead)
            {
                fprintf(out, "REMARK    "
                        "The B-factors in this file hold atomic radii\n");
                fprintf(out, "REMARK    "
                        "The occupancy in this file hold atomic charges\n");
            }
            else if (bGrasp)
            {
                fprintf(out, "GRASP PDB FILE\nFORMAT NUMBER=1\n");
                fprintf(out, "REMARK    "
                        "The B-factors in this file hold atomic charges\n");
                fprintf(out, "REMARK    "
                        "The occupancy in this file hold atomic radii\n");
            }
            else if (opt2bSet("-bf", NFILE, fnm))
            {
                read_bfac(opt2fn("-bf", NFILE, fnm), &n_bfac, &bfac, &bfac_nr);
                set_pdb_conf_bfac(atoms.nr, atoms.nres, &atoms,
                                  n_bfac, bfac, bfac_nr, peratom);
            }
            if (opt2parg_bSet("-label", NPA, pa))
            {
                for (i = 0; (i < atoms.nr); i++)
                {
                    atoms.resinfo[atoms.atom[i].resind].chainid = label[0];
                }
            }
            write_pdbfile(out, *top_tmp->name, &atoms, x, ePBC, box, ' ', -1, conect, TRUE);
            if (bLegend)
            {
                pdb_legend(out, atoms.nr, atoms.nres, &atoms, x);
            }
            if (visbox[0] > 0)
            {
                visualize_box(out, bLegend ? atoms.nr+12 : atoms.nr,
                              bLegend ? atoms.nres = 12 : atoms.nres, box, visbox);
            }
            gmx_ffclose(out);
        }
        else
        {
            write_sto_conf(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : NULL, ePBC, box);
        }
    }
    gmx_atomprop_destroy(aps);

    do_view(oenv, outfile, NULL);

    return 0;
}