Fixing missing references in web documentation
[gromacs.git] / src / contrib / hexamer.c
blobbd477eb91b52e89ae0e954da4e6acd82facfa5ab
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.
15 * This program is free software; you can redistribute it and/or
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33 * Groningen Machine for Chemical Simulation
35 #ifdef HAVE_CONFIG_H
36 #include <config.h>
37 #endif
39 #include <math.h>
40 #include <string.h>
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"
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[])
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]);
65 static void rotate_x(int natom,rvec xin[],real angle,rvec xout[],
66 gmx_bool bZ,gmx_bool bUpsideDown,real dz)
68 int i;
69 matrix mat;
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;
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);
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;
96 static void prep_x(int natom,rvec x[],real rDist,real rAngleZ,real rAngleX)
98 int i;
99 rvec xcm;
100 rvec *xx;
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];
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];
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);
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);
131 if (rDist > 0) {
132 for(i=0; (i<natom); i++)
133 x[i][XX] += rDist;
137 int main(int argc, char *argv[])
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."
144 #define NPA asize(pa)
145 t_filenm fnm[] = {
146 { efSTX, "-f", NULL, ffREAD },
147 { efPDB, "-o", NULL, ffWRITE }
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" }
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];
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;
183 infile = ftp2fn(efSTX,NFILE,fnm);
184 outfile = ftp2fn(efPDB,NFILE,fnm);
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);
194 if (bCenter)
195 prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
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);
204 gmx_ffclose(fp);
206 gmx_thanx(stderr);
208 return 0;