src/gromacs/gmxana/fitahx.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include "fitahx.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/math/do_fit.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 static void my_calc_xcm(int nbb, const int bbind[], rvec x[], rvec xcm)
  49 {
  50     int    i, m, ai;
  51
  52     clear_rvec(xcm);
  53     for (i = 0; (i < nbb); i++)
  54     {
  55         ai = bbind[i];
  56         rvec_inc(xcm, x[ai]);
  57     }
  58     for (m = 0; (m < DIM); m++)
  59     {
  60         xcm[m] /= (nbb);
  61     }
  62 }
  63
  64 static void my_sub_xcm(int nbb, const int bbind[], rvec x[], rvec xcm)
  65 {
  66     int i, ai;
  67
  68     for (i = 0; (i < nbb); i++)
  69     {
  70         ai = bbind[i];
  71         rvec_dec(x[ai], xcm);
  72     }
  73 }
  74
  75 real fit_ahx(int nres, t_bb bb[], int natoms, int nall, int allindex[],
  76              rvec x[], int nca,
  77              int caindex[], gmx_bool bFit)
  78 {
  79     static rvec *xref = nullptr;
  80     static real *mass = nullptr;
  81     const  real  d    = 0.15;  /* Rise per residue (nm)    */
  82     const  real  tw   = 1.745; /* Twist per residue (rad)  */
  83     const  real  rad  = 0.23;  /* Radius of the helix (nm) */
  84     real         phi0, trms, rms;
  85     rvec         dx, xcm;
  86     int          ai, i, nmass;
  87
  88     if (nca < 3)
  89     {
  90         gmx_fatal(FARGS, "Need at least 3 Calphas to fit to, (now %d)...\n", nca);
  91     }
  92
  93     if (xref == nullptr)
  94     {
  95         snew(xref, natoms);
  96         snew(mass, natoms);
  97     }
  98     phi0 = 0;
  99     for (i = 0; (i < nca); i++)
 100     {
 101         ai           = caindex[i];
 102         xref[ai][XX] = rad*std::cos(phi0);
 103         xref[ai][YY] = rad*std::sin(phi0);
 104         xref[ai][ZZ] = d*i;
 105
 106         /* Set the mass to select that this Calpha contributes to fitting */
 107         mass[ai] = 10.0;
 108 /*#define DEBUG*/
 109 #ifdef DEBUG
 110         fprintf(stderr, "%5d  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f\n", ai,
 111                 x[ai][XX], x[ai][YY], x[ai][ZZ],
 112                 xref[ai][XX], xref[ai][YY], xref[ai][ZZ]);
 113 #endif
 114         phi0 += tw;
 115     }
 116
 117     /* Center the referece around the origin */
 118     my_calc_xcm(nca, caindex, xref, xcm);
 119     my_sub_xcm(nca, caindex, xref, xcm);
 120
 121     if (bFit)
 122     {
 123         /* Now center the to-be-fitted coords around the origin */
 124         my_calc_xcm(nca, caindex, x, xcm);
 125         my_sub_xcm(nall, allindex, x, xcm);
 126     }
 127 #ifdef DEBUG
 128     dump_ahx(nres, bb, xref, box, 0);
 129 #endif
 130
 131     nmass = 0;
 132     for (i = 0; (i < natoms); i++)
 133     {
 134         if (mass[i] > 0)
 135         {
 136             nmass++;
 137         }
 138     }
 139     if (nmass != nca)
 140     {
 141         gmx_fatal(FARGS, "nmass=%d, nca=%d\n", nmass, nca);
 142     }
 143
 144     /* Now call the fitting routine */
 145     if (bFit)
 146     {
 147         do_fit(natoms, mass, xref, x);
 148     }
 149
 150     /* Reset masses and calc rms */
 151     trms = 0.0;
 152     for (i = 0; (i < nres); i++)
 153     {
 154         ai = bb[i].CA;
 155
 156         if (mass[ai] > 0.0)
 157         {
 158             rvec_sub(x[ai], xref[ai], dx);
 159             rms         = iprod(dx, dx);
 160             bb[i].rmsa += std::sqrt(rms);
 161             bb[i].nrms++;
 162             trms    += rms;
 163             mass[ai] = 0.0;
 164         }
 165     }
 166     return std::sqrt(trms/nca);
 167 }