3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
9 * VERSION 3.3.99_development_20071104
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * Groningen Machine for Chemical Simulation
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[])
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]);
72 static void rotate_x(int natom,rvec xin[],real angle,rvec xout[],
73 gmx_bool bZ,gmx_bool bUpsideDown,real dz)
81 mat[XX][XX] = cos(angle);
82 mat[XX][YY] = sin(angle);
83 mat[YY][XX] = -sin(angle);
84 mat[YY][YY] = cos(angle);
89 mat[YY][YY] = cos(angle);
90 mat[YY][ZZ] = sin(angle);
91 mat[ZZ][YY] = -sin(angle);
92 mat[ZZ][ZZ] = cos(angle);
95 for(i=0; (i<natom); i++) {
96 mvmul(mat,xin[i],xout[i]);
103 static void prep_x(int natom,rvec x[],real rDist,real rAngleZ,real rAngleX)
109 /* Center on Z-axis */
111 for(i=0; (i<natom); i++) {
119 for(i=0; (i<natom); i++) {
126 rotate_x(natom,x,rAngleZ,xx,TRUE,FALSE,0);
127 for(i=0; (i<natom); i++)
128 copy_rvec(xx[i],x[i]);
133 rotate_x(natom,x,rAngleX,xx,FALSE,FALSE,0);
134 for(i=0; (i<natom); i++)
135 copy_rvec(xx[i],x[i]);
139 for(i=0; (i<natom); i++)
144 int main(int argc, char *argv[])
147 static char *desc[] = {
148 "[TT]hexamer[tt] takes a single input coordinate file and makes five symmetry",
151 #define NPA asize(pa)
153 { efSTX, "-f", NULL, ffREAD },
154 { efPDB, "-o", NULL, ffWRITE }
156 #define NFILE asize(fnm)
157 gmx_bool bCenter = FALSE;
158 gmx_bool bTrimer = FALSE;
159 gmx_bool bAlternate = FALSE;
160 real rDist = 0,rAngleZ = 0,rAngleX = 0, alterz = 0;
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 [TT]-center[tt])" },
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" }
177 #define NPA asize(pa)
179 int i,iout,now,natom;
180 rvec *xin,*vin,*xout;
183 char *infile,*outfile,title[256],buf[32];
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;
190 infile = ftp2fn(efSTX,NFILE,fnm);
191 outfile = ftp2fn(efPDB,NFILE,fnm);
193 get_stx_coordnum(infile,&natom);
194 init_t_atoms(&atoms,natom,TRUE);
198 read_stx_conf(infile,title,&atoms,xin,vin,box);
199 printf("Read %d atoms\n",atoms.nr);
202 prep_x(atoms.nr,xin,rDist,rAngleZ,rAngleX);
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);