src/contrib/hexamer.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.3.99_development_20071104
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2006, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
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  18  * of the License, or (at your option) any later version.
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  20  * If you want to redistribute modifications, please consider that
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40 #include <string.h>
  41
  42 #include "gromacs/fileio/pdbio.h"
  43 #include "gromacs/fileio/confio.h"
  44 #include "gromacs/utility/smalloc.h"
  45 #include "gromacs/topology/symtab.h"
  46 #include "macros.h"
  47 #include "copyrite.h"
  48 #include "gromacs/commandline/pargs.h"
  49 #include "gromacs/math/vec.h"
  50 #include "typedefs.h"
  51 #include "gbutil.h"
  52 #include "gromacs/math/units.h"
  53
  54 void copy_atom(t_symtab *tab,t_atoms *a1,int i1,t_atoms *a2,int i2,
  55                rvec xin[],rvec xout[],rvec vin[],rvec vout[])
  56 {
  57   a2->atom[i2]     = a1->atom[i1];
  58   a2->atomname[i2] = put_symtab(tab,*a1->atomname[i1]);
  59   a2->resname[a2->atom[i2].resnr] =
  60     put_symtab(tab,*a1->resname[a1->atom[i1].resnr]);
  61   copy_rvec(xin[i1],xout[i2]);
  62   copy_rvec(vin[i1],vout[i2]);
  63 }
  64
  65 static void rotate_x(int natom,rvec xin[],real angle,rvec xout[],
  66                      gmx_bool bZ,gmx_bool bUpsideDown,real dz)
  67 {
  68   int i;
  69   matrix mat;
  70
  71   angle *= DEG2RAD;
  72   clear_mat(mat);
  73   if (bZ) {
  74     mat[XX][XX] = cos(angle);
  75     mat[XX][YY] = sin(angle);
  76     mat[YY][XX] = -sin(angle);
  77     mat[YY][YY] = cos(angle);
  78     mat[ZZ][ZZ] = 1;
  79   }
  80   else {
  81     mat[XX][XX] = 1;
  82     mat[YY][YY] = cos(angle);
  83     mat[YY][ZZ] = sin(angle);
  84     mat[ZZ][YY] = -sin(angle);
  85     mat[ZZ][ZZ] = cos(angle);
  86   }
  87
  88   for(i=0; (i<natom); i++) {
  89     mvmul(mat,xin[i],xout[i]);
  90     if (bUpsideDown)
  91       xout[i][ZZ] *= -1;
  92     xout[i][ZZ] += dz;
  93   }
  94 }
  95
  96 static void prep_x(int natom,rvec x[],real rDist,real rAngleZ,real rAngleX)
  97 {
  98   int  i;
  99   rvec xcm;
 100   rvec *xx;
 101
 102   /* Center on Z-axis */
 103   clear_rvec(xcm);
 104   for(i=0; (i<natom); i++) {
 105     xcm[XX] += x[i][XX];
 106     xcm[YY] += x[i][YY];
 107     xcm[ZZ] += x[i][ZZ];
 108   }
 109   xcm[XX] /= natom;
 110   xcm[YY] /= natom;
 111   xcm[ZZ] /= natom;
 112   for(i=0; (i<natom); i++) {
 113     x[i][XX] -= xcm[XX];
 114     x[i][YY] -= xcm[YY];
 115     x[i][ZZ] -= xcm[ZZ];
 116   }
 117   if (rAngleZ != 0) {
 118     snew(xx,natom);
 119     rotate_x(natom,x,rAngleZ,xx,TRUE,FALSE,0);
 120     for(i=0; (i<natom); i++)
 121       copy_rvec(xx[i],x[i]);
 122     sfree(xx);
 123   }
 124   if (rAngleX != 0) {
 125     snew(xx,natom);
 126     rotate_x(natom,x,rAngleX,xx,FALSE,FALSE,0);
 127     for(i=0; (i<natom); i++)
 128       copy_rvec(xx[i],x[i]);
 129     sfree(xx);
 130   }
 131   if (rDist > 0) {
 132     for(i=0; (i<natom); i++)
 133       x[i][XX] += rDist;
 134   }
 135 }
 136
 137 int main(int argc, char *argv[])
 138 {
 139   t_symtab tab;
 140   static char *desc[] = {
 141     "[TT]hexamer[tt] takes a single input coordinate file and makes five symmetry",
 142     "related copies."
 143   };
 144 #define NPA asize(pa)
 145   t_filenm fnm[] = {
 146     { efSTX, "-f", NULL, ffREAD },
 147     { efPDB, "-o", NULL, ffWRITE }
 148   };
 149 #define NFILE asize(fnm)
 150   gmx_bool bCenter    = FALSE;
 151   gmx_bool bTrimer    = FALSE;
 152   gmx_bool bAlternate = FALSE;
 153   real rDist = 0,rAngleZ = 0,rAngleX = 0, alterz = 0;
 154   t_pargs pa[] = {
 155     { "-center",   FALSE, etBOOL,  {&bCenter},
 156       "Center molecule on Z-axis first" },
 157     { "-trimer",   FALSE, etBOOL,  {&bTrimer},
 158       "Make trimer rather than hexamer" },
 159     { "-alternate",FALSE, etBOOL,  {&bAlternate},
 160       "Turn every other molecule upside down" },
 161     { "-alterz",   FALSE, etREAL,  {&alterz},
 162       "Add this amount to Z-coordinate in every other molecule" },
 163     { "-radius",   FALSE, etREAL,  {&rDist},
 164       "Distance of protein axis from Z-axis (implies [TT]-center[tt])" },
 165     { "-anglez",   FALSE, etREAL,  {&rAngleZ},
 166       "Initial angle of rotation around Z-axis of protein" },
 167     { "-anglex",   FALSE, etREAL,  {&rAngleX},
 168       "Initial angle of rotation around X-axis of protein" }
 169   };
 170 #define NPA asize(pa)
 171   FILE    *fp;
 172   int     i,iout,now,natom;
 173   rvec    *xin,*vin,*xout;
 174   matrix  box;
 175   t_atoms atoms,aout;
 176   char    *infile,*outfile,title[256],buf[32];
 177
 178   CopyRight(stderr,argv[0]);
 179   parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
 180                     asize(desc),desc,0,NULL);
 181   bCenter = bCenter || (rDist > 0) || bAlternate;
 182
 183   infile  = ftp2fn(efSTX,NFILE,fnm);
 184   outfile = ftp2fn(efPDB,NFILE,fnm);
 185
 186   get_stx_coordnum(infile,&natom);
 187   init_t_atoms(&atoms,natom,TRUE);
 188   snew(xin,natom);
 189   snew(xout,natom);
 190   snew(vin,natom);
 191   read_stx_conf(infile,title,&atoms,xin,vin,box);
 192   printf("Read %d atoms\n",atoms.nr);
 193
 194   if (bCenter)
 195     prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
 196
 197   fp = gmx_ffopen(outfile,"w");
 198   for(i=0; (i<(bTrimer ? 3 : 6)); i++) {
 199     rotate_x(atoms.nr,xin,i*(bTrimer ? 120.0 : 60.0),xout,TRUE,
 200              bAlternate && ((i % 2) != 0),alterz*(((i % 2) == 0) ? 0 : 1));
 201     sprintf(buf,"Rotated %d degrees",i*(bTrimer ? 120 : 60));
 202     write_pdbfile(fp,buf,&atoms,xout,box,'A'+i,1+i);
 203   }
 204   gmx_ffclose(fp);
 205
 206   gmx_thanx(stderr);
 207
 208   return 0;
 209 }