int main()
{
char coordinate_input[BUFSIZ];
char ammp_output[BUFSIZ];
char dictionary[BUFSIZ];
char work[1000],keep[1000];
char atype[20],aname[20];
char *fgets();
float sigma,emin;
int ifile,i,imreading,ii,myres;
FILE *in1,*dict,*output,*fopen();
printf(" atom definition file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
/* now read in the atoms */
dict = fopen( dictionary, "r");
if( dict == NULL)
{ fprintf(stderr," sorry i can't open %s\n",dictionary); exit(0);}
inkinds = 0;
while ( fgets( work,256, dict) != NULL)
{
sscanf( work,"%s %f %f %f %f %f %f %f %f %f %f %f %f %f \n",
&kinds[inkinds].type[0],
&kinds[inkinds].r ,
&kinds[inkinds].theta ,
&sigma ,
&emin ,
&kinds[inkinds].Z ,
&kinds[inkinds].angle_inc,
&kinds[inkinds].X ,
&kinds[inkinds].jaa ,
&kinds[inkinds].mass ,
&kinds[inkinds].charge ,
&kinds[inkinds].V, &kinds[inkinds].U ,
&kinds[inkinds].hybrid
);
/* kinds[inkinds].theta *= 3.14159265/180.;
*/
sigma = sigma*sigma;
sigma = sigma*sigma*sigma;
/* kinds[inkinds].b = sqrt( 4.*emin*sigma*sigma);
kinds[inkinds].a = sqrt( 4.*emin*sigma);
*/
kinds[inkinds].b = sqrt( emin*sigma*sigma);
kinds[inkinds].a = sqrt( 2*emin*sigma);
inkinds ++;
if( inkinds > MAX_ATOM)
{ fprintf( stderr," too many kinds of atoms in dictionary\n");
exit(0); }
}
fclose( dict);
printf(" Residue dictionary directory:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
ifile = ifile -i ;
if( ifile == 0 ){ dictionary[ifile++] = '.';
dictionary[ifile] = '\0'; }
if( dictionary[ifile-1] != '/')
{ ifile++; dictionary[ifile-1] = '/'; dictionary[ifile] = '\0';}
printf(" atom input coordinate file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
coordinate_input[ifile -i ] = work[ifile];
coordinate_input[ifile -i +1 ] = '\0';
}
printf(" AMMP file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
ammp_output[ifile -i ] = work[ifile];
ammp_output[ifile -i +1 ] = '\0';
}
in1 = fopen( coordinate_input, "r");
output = fopen( ammp_output, "w");
if (in1 == NULL) goto NO_IN1_FILE;
/* read in the first residue
* stuff is read into work when the residue number changes then
* work is copied into keep, so the first atom of any residue is
* going to be in the keep buffer. to initialize we read the
* first atom into keep
*/
keep[0] = '\0';
while( !(keep[0] == 'A' && keep[1] == 'T' && keep[2] == 'O' && keep[3] == 'M')
&& !(keep[0] == 'H'&& keep[1] == 'E'
&& keep[1] == 'T'&& keep[1] == 'A'&& keep[1] == 'T' ) )
{ if( fgets(keep,90,in1) == NULL) {
fprintf(stderr," no atoms in input file ? \n") ;
NO_IN1_FILE:
printf(" enter the dictionary name >\n");
fgets( keep, 90, stdin);
i=0; while( (keep[i] == ' ' || keep[i] == '\t') && keep[i] != '\0') i++;
for( imreading = 0; imreading < 3; imreading++)
{ aname[imreading] = toupper( keep[i + imreading] ); }
aname[3] = '\0';
goto NO_ATOMS;
}
}
imreading = 0;
while( imreading == 0)
{/* begining of imreading loop */
inres = 0;
for(i=0; i< MAX_RES; i++)
{ mykind[i] = -1;
defined[i] = -1;
name[i][0] = '\0';
x[i] = 0.;
y[i] = 0.;
z[i] = 0.;
}
sscanf( &keep[22],"%d",&myres);
sscanf(&keep[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&keep[11],"%s",&atype[0]);
sscanf(&keep[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
for( inres = 1; inres < MAX_RES; inres ++)
{ /* start of reading an atom loop */
if( fgets( work,90,in1) == NULL) {
imreading = 1; break; }
if( work[0] != 'A' && work[0] != 'H') {
imreading = 1; break; }
/*
printf("%s\n",work);
printf("%d\n",inres);
*/
sscanf( &work[22],"%d",&ii);
if( ii != myres )
{ii = 0; while( work[ii] != '\0'){ keep[ii] = work[ii] ; ii++;}
/* inres += 1; */
break;
}
sscanf(&work[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&work[11],"%s",&atype[0]);
sscanf(&work[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
}/* end of reading an atom loop */
/*
for( i=0; i< inres; i++)
printf(">%s<\n",&name[i][0]);
*/
/* if here then all of the atoms in the residue are read in */
/* now we have to open and read the dictionary file
* there could be atoms in either the residue or dictionary which
* are not there i.e. oxt for a residue or a missing H */
/* prepare the filename */
NO_ATOMS:
i = 0;
while(dictionary[i] != '\0') { work[i] = dictionary[i]; i++;}
ii = 0;
while(aname[ii] != '\0') {work[i] = aname[ii]; i++; ii++;}
work[i++] = '\0';
dict = fopen(work,"r");
if( dict == NULL ){
fprintf(stderr," dictionary %s not found \n", work);
write_atoms(output);
goto DONE;
}
/* read the number of atoms */
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&natoms);
read_atoms( dict,natoms );
write_atoms(output);
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&nbond);
do_bonds( dict,nbond,output);
inbondlist = nbond;
nangle = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nangle);
do_angle(dict,nangle,output);
nhybrid = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nhybrid);
do_hybrid(dict,nhybrid,output);
ntorsion = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&ntorsion);
do_torsion(dict,ntorsion,output);
DONE:
fclose( dict );
}/* end of imreading loop */
}/* end of module main */
void calc_angles(void)
{
cell *p, *q,* r, *s;
int i1, i2, i3, j1, j2, j3;
int k1, k2, k3, l1, l2, l3;
int a1, a2, a3, b1, b2, b3, c1, c2, c3;
vektor pbc_q, pbc_r, pbc_s;
/* for each cell p */
for (i1 = 0; i1 < cell_dim.x; ++i1)
for (i2 = 0; i2 < cell_dim.y; ++i2)
for (i3 = 0; i3 < cell_dim.z; ++i3)
/* For half of the neighbours q of this cell */
for (j1 = 0; j1 <= 1; ++j1)
for (j2 = -j1; j2 <= 1; ++j2)
for (j3= (j1 == 0 ? -j2 : -j1); j3 <= 1; ++j3)
/* For the neighbours r of cell p */
for (k1 = -1; k1 <= 1; ++k1)
for (k2 = -1; k2 <= 1; ++k2)
for (k3 = -1; k3 <= 1; ++k3)
/* for the neighbours s of cell q */
for (l1 = -1; l1 <= 1; ++l1)
for (l2 = -1; l2 <= 1; ++l2)
for (l3 = -1; l3 <= 1; ++l3)
{
/* Given cell */
p = PTR_3D_V(cell_array,i1,i2,i3,cell_dim);
/* Calculate Indices of Neighbour */
a1 = i1 + j1;
pbc_q.x = 0;
a2 = i2 + j2;
pbc_q.y = 0;
a3 = i3 + j3;
pbc_q.z = 0;
/* deal with periodic boundary conditions if necessary */
if (a1 < 0) {
if (pbc_dirs.x == 1) {
a1 = cell_dim.x-1;
pbc_q.x -= box_x.x;
pbc_q.y -= box_x.y;
pbc_q.z -= box_x.z;
} else continue;
}
if (a2 < 0) {
if (pbc_dirs.y == 1) {
a2 = cell_dim.y-1;
pbc_q.x -= box_y.x;
pbc_q.y -= box_y.y;
pbc_q.z -= box_y.z;
} else continue;
}
if (a3 < 0) {
if (pbc_dirs.z == 1) {
a3 = cell_dim.z-1;
pbc_q.x -= box_z.x;
pbc_q.y -= box_z.y;
pbc_q.z -= box_z.z;
} else continue;
}
if (a1 > cell_dim.x-1) {
if (pbc_dirs.x == 1) {
a1 = 0;
pbc_q.x += box_x.x;
pbc_q.y += box_x.y;
pbc_q.z += box_x.z;
} else continue;
}
if (a2 > cell_dim.y-1) {
if (pbc_dirs.y == 1) {
a2 = 0;
pbc_q.x += box_y.x;
pbc_q.y += box_y.y;
pbc_q.z += box_y.z;
} else continue;
}
if (a3 > cell_dim.z-1) {
if (pbc_dirs.z == 1) {
a3 = 0;
pbc_q.x += box_z.x;
pbc_q.y += box_z.y;
pbc_q.z += box_z.z;
} else continue;
}
/* Neighbour cell q (note that p==q ist possible) */
q = PTR_3D_V(cell_array,a1,a2,a3,cell_dim);
/* Calculate Indices of neighbour r of p */
b1 = i1 + k1;
pbc_r.x = 0;
b2 = i2 + k2;
pbc_r.y = 0;
b3 = i3 + k3;
pbc_r.z = 0;
/* deal with periodic boundary conditions if necessary */
if (b1 < 0) {
if (pbc_dirs.x == 1) {
b1 = cell_dim.x-1;
pbc_r.x -= box_x.x;
pbc_r.y -= box_x.y;
pbc_r.z -= box_x.z;
} else continue;
}
if (b2 < 0) {
if (pbc_dirs.y == 1) {
b2 = cell_dim.y-1;
pbc_r.x -= box_y.x;
pbc_r.y -= box_y.y;
pbc_r.z -= box_y.z;
} else continue;
}
if (b3 < 0) {
if (pbc_dirs.z == 1) {
b3 = cell_dim.z-1;
pbc_r.x -= box_z.x;
pbc_r.y -= box_z.y;
pbc_r.z -= box_z.z;
} else continue;
}
if (b1 > cell_dim.x-1) {
if (pbc_dirs.x == 1) {
b1 = 0;
pbc_r.x += box_x.x;
pbc_r.y += box_x.y;
pbc_r.z += box_x.z;
} else continue;
}
if (b2 > cell_dim.y-1) {
if (pbc_dirs.y == 1) {
b2 = 0;
pbc_r.x += box_y.x;
pbc_r.y += box_y.y;
pbc_r.z += box_y.z;
} else continue;
}
if (b3 > cell_dim.z-1) {
if (pbc_dirs.z == 1) {
b3 = 0;
pbc_r.x += box_z.x;
pbc_r.y += box_z.y;
pbc_r.z += box_z.z;
} else continue;
}
/* Neighbour cell r */
r = PTR_3D_V(cell_array, b1, b2, b3, cell_dim);
/* Calculate Indices of neighbour s of q */
c1 = j1 + l1;
pbc_s.x = 0;
c2 = j2 + l2;
pbc_s.y = 0;
c3 = j3 + l3;
pbc_s.z = 0;
/* deal with periodic boundary conditions if necessary */
if (c1 < 0) {
if (pbc_dirs.x == 1) {
c1 = cell_dim.x-1;
pbc_s.x -= box_x.x;
pbc_s.y -= box_x.y;
pbc_s.z -= box_x.z;
} else continue;
}
if (c2 < 0) {
if (pbc_dirs.y == 1) {
c2 = cell_dim.y-1;
pbc_s.x -= box_y.x;
pbc_s.y -= box_y.y;
pbc_s.z -= box_y.z;
} else continue;
}
if (c3 < 0) {
if (pbc_dirs.z == 1) {
c3 = cell_dim.z-1;
pbc_s.x -= box_z.x;
pbc_s.y -= box_z.y;
pbc_s.z -= box_z.z;
} else continue;
}
if (c1 > cell_dim.x-1) {
if (pbc_dirs.x == 1) {
c1 = 0;
pbc_s.x += box_x.x;
pbc_s.y += box_x.y;
pbc_s.z += box_x.z;
} else continue;
}
if (c2 > cell_dim.y-1) {
if (pbc_dirs.y == 1) {
c2 = 0;
pbc_s.x += box_y.x;
pbc_s.y += box_y.y;
pbc_s.z += box_y.z;
} else continue;
}
if (c3 > cell_dim.z-1) {
if (pbc_dirs.z == 1) {
c3 = 0;
pbc_s.x += box_z.x;
pbc_s.y += box_z.y;
pbc_s.z += box_z.z;
} else continue;
}
/* Neighbour cell s */
s = PTR_3D_V(cell_array, c1, c2, c3, cell_dim);
/* Do the work */
do_angle(p,q,r,s,pbc_q,pbc_r,pbc_s);
}
}
