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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  30  * For more info, check our website at http://www.gromacs.org
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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 #include <ctype.h>
  42 #include "pdbio.h"
  43 #include "confio.h"
  44 #include "symtab.h"
  45 #include "smalloc.h"
  46 #include "symtab.h"
  47 #include "macros.h"
  48 #include "smalloc.h"
  49 #include "copyrite.h"
  50 #include "statutil.h"
  51 #include "string2.h"
  52 #include "strdb.h"
  53 #include "index.h"
  54 #include "vec.h"
  55 #include "typedefs.h"
  56 #include "gbutil.h"
  57 #include "strdb.h"
  58 #include "physics.h"
  59 #include "atomprop.h"
  60
  61 void copy_atom(t_symtab *tab,t_atoms *a1,int i1,t_atoms *a2,int i2,
  62                rvec xin[],rvec xout[],rvec vin[],rvec vout[])
  63 {
  64   a2->atom[i2]     = a1->atom[i1];
  65   a2->atomname[i2] = put_symtab(tab,*a1->atomname[i1]);
  66   a2->resname[a2->atom[i2].resnr] =
  67     put_symtab(tab,*a1->resname[a1->atom[i1].resnr]);
  68   copy_rvec(xin[i1],xout[i2]);
  69   copy_rvec(vin[i1],vout[i2]);
  70 }
  71
  72 static void rotate_x(int natom,rvec xin[],real angle,rvec xout[],
  73                      bool bZ,bool bUpsideDown,real dz)
  74 {
  75   int i;
  76   matrix mat;
  77
  78   angle *= DEG2RAD;
  79   clear_mat(mat);
  80   if (bZ) {
  81     mat[XX][XX] = cos(angle);
  82     mat[XX][YY] = sin(angle);
  83     mat[YY][XX] = -sin(angle);
  84     mat[YY][YY] = cos(angle);
  85     mat[ZZ][ZZ] = 1;
  86   }
  87   else {
  88     mat[XX][XX] = 1;
  89     mat[YY][YY] = cos(angle);
  90     mat[YY][ZZ] = sin(angle);
  91     mat[ZZ][YY] = -sin(angle);
  92     mat[ZZ][ZZ] = cos(angle);
  93   }
  94
  95   for(i=0; (i<natom); i++) {
  96     mvmul(mat,xin[i],xout[i]);
  97     if (bUpsideDown)
  98       xout[i][ZZ] *= -1;
  99     xout[i][ZZ] += dz;
 100   }
 101 }
 102
 103 static void prep_x(int natom,rvec x[],real rDist,real rAngleZ,real rAngleX)
 104 {
 105   int  i;
 106   rvec xcm;
 107   rvec *xx;
 108
 109   /* Center on Z-axis */
 110   clear_rvec(xcm);
 111   for(i=0; (i<natom); i++) {
 112     xcm[XX] += x[i][XX];
 113     xcm[YY] += x[i][YY];
 114     xcm[ZZ] += x[i][ZZ];
 115   }
 116   xcm[XX] /= natom;
 117   xcm[YY] /= natom;
 118   xcm[ZZ] /= natom;
 119   for(i=0; (i<natom); i++) {
 120     x[i][XX] -= xcm[XX];
 121     x[i][YY] -= xcm[YY];
 122     x[i][ZZ] -= xcm[ZZ];
 123   }
 124   if (rAngleZ != 0) {
 125     snew(xx,natom);
 126     rotate_x(natom,x,rAngleZ,xx,TRUE,FALSE,0);
 127     for(i=0; (i<natom); i++)
 128       copy_rvec(xx[i],x[i]);
 129     sfree(xx);
 130   }
 131   if (rAngleX != 0) {
 132     snew(xx,natom);
 133     rotate_x(natom,x,rAngleX,xx,FALSE,FALSE,0);
 134     for(i=0; (i<natom); i++)
 135       copy_rvec(xx[i],x[i]);
 136     sfree(xx);
 137   }
 138   if (rDist > 0) {
 139     for(i=0; (i<natom); i++)
 140       x[i][XX] += rDist;
 141   }
 142 }
 143
 144 int main(int argc, char *argv[])
 145 {
 146   t_symtab tab;
 147   static char *desc[] = {
 148     "hexamer takes a single input coordinate file and makes five symmetry",
 149     "related copies."
 150   };
 151 #define NPA asize(pa)
 152   t_filenm fnm[] = {
 153     { efSTX, "-f", NULL, ffREAD },
 154     { efPDB, "-o", NULL, ffWRITE }
 155   };
 156 #define NFILE asize(fnm)
 157   bool bCenter    = FALSE;
 158   bool bTrimer    = FALSE;
 159   bool bAlternate = FALSE;
 160   real rDist = 0,rAngleZ = 0,rAngleX = 0, alterz = 0;
 161   t_pargs pa[] = {
 162     { "-center",   FALSE, etBOOL,  {&bCenter},
 163       "Center molecule on Z-axis first" },
 164     { "-trimer",   FALSE, etBOOL,  {&bTrimer},
 165       "Make trimer rather than hexamer" },
 166     { "-alternate",FALSE, etBOOL,  {&bAlternate},
 167       "Turn every other molecule upside down" },
 168     { "-alterz",   FALSE, etREAL,  {&alterz},
 169       "Add this amount to Z-coordinate in every other molecule" },
 170     { "-radius",   FALSE, etREAL,  {&rDist},
 171       "Distance of protein axis from Z-axis (implies -center)" },
 172     { "-anglez",   FALSE, etREAL,  {&rAngleZ},
 173       "Initial angle of rotation around Z-axis of protein" },
 174     { "-anglex",   FALSE, etREAL,  {&rAngleX},
 175       "Initial angle of rotation around X-axis of protein" }
 176   };
 177 #define NPA asize(pa)
 178   FILE    *fp;
 179   int     i,iout,now,natom;
 180   rvec    *xin,*vin,*xout;
 181   matrix  box;
 182   t_atoms atoms,aout;
 183   char    *infile,*outfile,title[256],buf[32];
 184
 185   CopyRight(stderr,argv[0]);
 186   parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
 187                     asize(desc),desc,0,NULL);
 188   bCenter = bCenter || (rDist > 0) || bAlternate;
 189
 190   infile  = ftp2fn(efSTX,NFILE,fnm);
 191   outfile = ftp2fn(efPDB,NFILE,fnm);
 192
 193   get_stx_coordnum(infile,&natom);
 194   init_t_atoms(&atoms,natom,TRUE);
 195   snew(xin,natom);
 196   snew(xout,natom);
 197   snew(vin,natom);
 198   read_stx_conf(infile,title,&atoms,xin,vin,box);
 199   printf("Read %d atoms\n",atoms.nr);
 200
 201   if (bCenter)
 202     prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
 203
 204   fp = ffopen(outfile,"w");
 205   for(i=0; (i<(bTrimer ? 3 : 6)); i++) {
 206     rotate_x(atoms.nr,xin,i*(bTrimer ? 120.0 : 60.0),xout,TRUE,
 207              bAlternate && ((i % 2) != 0),alterz*(((i % 2) == 0) ? 0 : 1));
 208     sprintf(buf,"Rotated %d degrees",i*(bTrimer ? 120 : 60));
 209     write_pdbfile(fp,buf,&atoms,xout,box,'A'+i,1+i);
 210   }
 211   ffclose(fp);
 212
 213   thanx(stderr);
 214
 215   return 0;
 216 }