void gmx_espresso_read_conf(const char *infile,
t_topology *top, rvec x[], rvec *v, matrix box)
{
t_atoms *atoms = &top->atoms;
FILE *fp;
char word[STRLEN], buf[STRLEN];
int level, r, nprop, p, i, m, molnr;
int prop[32];
double d;
gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
// TODO: The code does not understand titles it writes...
top->name = put_symtab(&top->symtab, "");
clear_mat(box);
fp = gmx_fio_fopen(infile, "r");
bFoundParticles = FALSE;
bFoundVariable = FALSE;
bMol = FALSE;
level = 0;
while ((r = get_espresso_word(fp, word)))
{
if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
{
bFoundParticles = TRUE;
level += check_open_parenthesis(fp, r, infile, "particles");
nprop = 0;
while (level == 2 && (r = get_espresso_word(fp, word)))
{
bFoundProp = FALSE;
for (p = 0; p < espNR; p++)
{
if (strcmp(word, esp_prop[p]) == 0)
{
bFoundProp = TRUE;
prop[nprop++] = p;
/* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
}
}
if (!bFoundProp && word[0] != '}')
{
gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
}
if (bFoundProp && p == espMOLECULE)
{
bMol = TRUE;
}
if (r == 3)
{
level--;
}
}
i = 0;
while (level > 0 && (r = get_espresso_word(fp, word)))
{
if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
if (level == 2)
{
for (p = 0; p < nprop; p++)
{
switch (prop[p])
{
case espID:
r = get_espresso_word(fp, word);
/* Not used */
break;
case espPOS:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
x[i][m] = d;
}
break;
case espTYPE:
r = get_espresso_word(fp, word);
atoms->atom[i].type = std::strtol(word, NULL, 10);
break;
case espQ:
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
atoms->atom[i].q = d;
break;
case espV:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
v[i][m] = d;
}
break;
case espF:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
/* not used */
}
break;
case espMOLECULE:
r = get_espresso_word(fp, word);
molnr = std::strtol(word, NULL, 10);
if (i == 0 ||
atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
{
atoms->atom[i].resind =
(i == 0 ? 0 : atoms->atom[i-1].resind+1);
atoms->resinfo[atoms->atom[i].resind].nr = molnr;
atoms->resinfo[atoms->atom[i].resind].ic = ' ';
atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
}
else
{
atoms->atom[i].resind = atoms->atom[i-1].resind;
}
break;
}
}
/* Generate an atom name from the particle type */
sprintf(buf, "T%u", atoms->atom[i].type);
atoms->atomname[i] = put_symtab(&top->symtab, buf);
if (bMol)
{
if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
{
atoms->resinfo[atoms->atom[i].resind].name =
put_symtab(&top->symtab, "MOL");
}
}
else
{
/* Residue number is the atom number */
atoms->atom[i].resind = i;
/* Generate an residue name from the particle type */
if (atoms->atom[i].type < 26)
{
sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
}
else
{
sprintf(buf, "T%c%c",
'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
}
t_atoms_set_resinfo(atoms, i, &top->symtab, buf, i, ' ', 0, ' ');
}
if (r == 3)
{
level--;
}
i++;
}
}
atoms->nres = atoms->nr;
if (i != atoms->nr)
{
gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
}
}
else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
{
bFoundVariable = TRUE;
level += check_open_parenthesis(fp, r, infile, "variable");
while (level == 2 && (r = get_espresso_word(fp, word)))
{
if (level == 2 && std::strcmp(word, "box_l") == 0)
{
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
box[m][m] = d;
}
level += check_close_parenthesis(fp, r, infile, "box_l");
}
}
}
else if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
}
if (!bFoundParticles)
{
fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
infile);
}
gmx_fio_fclose(fp);
}
void connelly_plot(const char *fn,int ndots,real dots[],rvec x[],t_atoms *atoms,
t_symtab *symtab,int ePBC,matrix box,gmx_bool bSave)
{
static const char *atomnm="DOT";
static const char *resnm ="DOT";
static const char *title ="Connely Dot Surface Generated by g_sas";
int i,i0,r0,ii0,k;
rvec *xnew;
t_atoms aaa;
if (bSave) {
i0 = atoms->nr;
r0 = atoms->nres;
srenew(atoms->atom,atoms->nr+ndots);
srenew(atoms->atomname,atoms->nr+ndots);
srenew(atoms->resinfo,r0+1);
atoms->atom[i0].resind = r0;
t_atoms_set_resinfo(atoms,i0,symtab,resnm,r0+1,' ',0,' ');
srenew(atoms->pdbinfo,atoms->nr+ndots);
snew(xnew,atoms->nr+ndots);
for(i=0; (i<atoms->nr); i++)
copy_rvec(x[i],xnew[i]);
for(i=k=0; (i<ndots); i++) {
ii0 = i0+i;
atoms->atomname[ii0] = put_symtab(symtab,atomnm);
atoms->pdbinfo[ii0].type = epdbATOM;
atoms->pdbinfo[ii0].atomnr= ii0;
atoms->atom[ii0].resind = r0;
xnew[ii0][XX] = dots[k++];
xnew[ii0][YY] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
atoms->pdbinfo[ii0].bfac = 0.0;
atoms->pdbinfo[ii0].occup = 0.0;
}
atoms->nr = i0+ndots;
atoms->nres = r0+1;
write_sto_conf(fn,title,atoms,xnew,NULL,ePBC,box);
atoms->nres = r0;
atoms->nr = i0;
}
else {
init_t_atoms(&aaa,ndots,TRUE);
aaa.atom[0].resind = 0;
t_atoms_set_resinfo(&aaa,0,symtab,resnm,1,' ',0,' ');
snew(xnew,ndots);
for(i=k=0; (i<ndots); i++) {
ii0 = i;
aaa.atomname[ii0] = put_symtab(symtab,atomnm);
aaa.pdbinfo[ii0].type = epdbATOM;
aaa.pdbinfo[ii0].atomnr= ii0;
aaa.atom[ii0].resind = 0;
xnew[ii0][XX] = dots[k++];
xnew[ii0][YY] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
aaa.pdbinfo[ii0].bfac = 0.0;
aaa.pdbinfo[ii0].occup = 0.0;
}
aaa.nr = ndots;
write_sto_conf(fn,title,&aaa,xnew,NULL,ePBC,box);
do_conect(fn,ndots,xnew);
free_t_atoms(&aaa,FALSE);
}
sfree(xnew);
}
static gmx_bool get_w_conf(FILE *in, const char *infile, char *title,
t_symtab *symtab, t_atoms *atoms, int *ndec,
rvec x[], rvec *v, matrix box)
{
char name[6];
char line[STRLEN+1], *ptr;
char buf[256];
double x1, y1, z1, x2, y2, z2;
rvec xmin, xmax;
int natoms, i, m, resnr, newres, oldres, ddist, c;
gmx_bool bFirst, bVel;
char *p1, *p2, *p3;
newres = -1;
oldres = NOTSET; /* Unlikely number for the first residue! */
ddist = 0;
/* Read the title and number of atoms */
get_coordnum_fp(in, title, &natoms);
if (natoms > atoms->nr)
{
gmx_fatal(FARGS, "gro file contains more atoms (%d) than expected (%d)",
natoms, atoms->nr);
}
else if (natoms < atoms->nr)
{
fprintf(stderr, "Warning: gro file contains less atoms (%d) than expected"
" (%d)\n", natoms, atoms->nr);
}
bFirst = TRUE;
bVel = FALSE;
/* just pray the arrays are big enough */
for (i = 0; (i < natoms); i++)
{
if ((fgets2 (line, STRLEN, in)) == NULL)
{
gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d",
infile, i+2);
}
if (strlen(line) < 39)
{
gmx_fatal(FARGS, "Invalid line in %s for atom %d:\n%s", infile, i+1, line);
}
/* determine read precision from distance between periods
(decimal points) */
if (bFirst)
{
bFirst = FALSE;
p1 = strchr(line, '.');
if (p1 == NULL)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
p2 = strchr(&p1[1], '.');
if (p2 == NULL)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
ddist = p2 - p1;
*ndec = ddist - 5;
p3 = strchr(&p2[1], '.');
if (p3 == NULL)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
if (p3 - p2 != ddist)
{
gmx_fatal(FARGS, "The spacing of the decimal points in file %s is not consistent for x, y and z", infile);
}
}
/* residue number*/
memcpy(name, line, 5);
name[5] = '\0';
sscanf(name, "%d", &resnr);
memcpy(name, line+5, 5);
name[5] = '\0';
if (resnr != oldres)
{
oldres = resnr;
newres++;
if (newres >= natoms)
{
gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
infile, natoms);
}
atoms->atom[i].resind = newres;
t_atoms_set_resinfo(atoms, i, symtab, name, resnr, ' ', 0, ' ');
}
else
{
atoms->atom[i].resind = newres;
}
/* atomname */
memcpy(name, line+10, 5);
atoms->atomname[i] = put_symtab(symtab, name);
/* eventueel controle atomnumber met i+1 */
/* coordinates (start after residue data) */
ptr = line + 20;
/* Read fixed format */
for (m = 0; m < DIM; m++)
{
for (c = 0; (c < ddist && ptr[0]); c++)
{
buf[c] = ptr[0];
ptr++;
}
buf[c] = '\0';
if (sscanf (buf, "%lf %lf", &x1, &x2) != 1)
{
gmx_fatal(FARGS, "Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)", infile);
}
else
{
x[i][m] = x1;
}
}
/* velocities (start after residues and coordinates) */
if (v)
{
/* Read fixed format */
for (m = 0; m < DIM; m++)
{
for (c = 0; (c < ddist && ptr[0]); c++)
{
buf[c] = ptr[0];
ptr++;
}
buf[c] = '\0';
if (sscanf (buf, "%lf", &x1) != 1)
{
v[i][m] = 0;
}
else
{
v[i][m] = x1;
bVel = TRUE;
}
}
}
}
atoms->nres = newres + 1;
/* box */
fgets2 (line, STRLEN, in);
if (sscanf (line, "%lf%lf%lf", &x1, &y1, &z1) != 3)
{
gmx_warning("Bad box in file %s", infile);
/* Generate a cubic box */
for (m = 0; (m < DIM); m++)
{
xmin[m] = xmax[m] = x[0][m];
}
for (i = 1; (i < atoms->nr); i++)
{
for (m = 0; (m < DIM); m++)
{
xmin[m] = min(xmin[m], x[i][m]);
xmax[m] = max(xmax[m], x[i][m]);
}
}
for (i = 0; i < DIM; i++)
{
for (m = 0; m < DIM; m++)
{
box[i][m] = 0.0;
}
}
for (m = 0; (m < DIM); m++)
{
box[m][m] = (xmax[m]-xmin[m]);
}
fprintf(stderr, "Generated a cubic box %8.3f x %8.3f x %8.3f\n",
box[XX][XX], box[YY][YY], box[ZZ][ZZ]);
}
else
{
/* We found the first three values, the diagonal elements */
box[XX][XX] = x1;
box[YY][YY] = y1;
box[ZZ][ZZ] = z1;
if (sscanf (line, "%*f%*f%*f%lf%lf%lf%lf%lf%lf",
&x1, &y1, &z1, &x2, &y2, &z2) != 6)
{
x1 = y1 = z1 = x2 = y2 = z2 = 0.0;
}
box[XX][YY] = x1;
box[XX][ZZ] = y1;
box[YY][XX] = z1;
box[YY][ZZ] = x2;
box[ZZ][XX] = y2;
box[ZZ][YY] = z2;
}
return bVel;
}
static int read_atom(t_symtab *symtab,
char line[], int type, int natom,
t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
{
t_atom *atomn;
int j, k;
char nc = '\0';
char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
char xc[12], yc[12], zc[12], occup[12], bfac[12];
unsigned char resic;
char chainid;
int resnr, atomnumber;
if (natom >= atoms->nr)
{
gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
natom+1, atoms->nr);
}
/* Skip over type */
j = 6;
for (k = 0; (k < 5); k++, j++)
{
anr[k] = line[j];
}
anr[k] = nc;
trim(anr);
j++;
for (k = 0; (k < 4); k++, j++)
{
anm[k] = line[j];
}
anm[k] = nc;
std::strcpy(anm_copy, anm);
rtrim(anm_copy);
atomnumber = 0;
trim(anm);
altloc = line[j];
j++;
for (k = 0; (k < 4); k++, j++)
{
resnm[k] = line[j];
}
resnm[k] = nc;
trim(resnm);
chainid = line[j];
j++;
for (k = 0; (k < 4); k++, j++)
{
rnr[k] = line[j];
}
rnr[k] = nc;
trim(rnr);
resnr = std::strtol(rnr, NULL, 10);
resic = line[j];
j += 4;
/* X,Y,Z Coordinate */
for (k = 0; (k < 8); k++, j++)
{
xc[k] = line[j];
}
xc[k] = nc;
for (k = 0; (k < 8); k++, j++)
{
yc[k] = line[j];
}
yc[k] = nc;
for (k = 0; (k < 8); k++, j++)
{
zc[k] = line[j];
}
zc[k] = nc;
/* Weight */
for (k = 0; (k < 6); k++, j++)
{
occup[k] = line[j];
}
occup[k] = nc;
/* B-Factor */
for (k = 0; (k < 7); k++, j++)
{
bfac[k] = line[j];
}
bfac[k] = nc;
/* 10 blanks */
j += 10;
/* Element name */
for (k = 0; (k < 2); k++, j++)
{
elem[k] = line[j];
}
elem[k] = nc;
trim(elem);
if (atoms->atom)
{
atomn = &(atoms->atom[natom]);
if ((natom == 0) ||
atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
(strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm) != 0))
{
if (natom == 0)
{
atomn->resind = 0;
}
else
{
atomn->resind = atoms->atom[natom-1].resind + 1;
}
atoms->nres = atomn->resind + 1;
t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
}
else
{
atomn->resind = atoms->atom[natom-1].resind;
}
if (bChange)
{
xlate_atomname_pdb2gmx(anm);
}
atoms->atomname[natom] = put_symtab(symtab, anm);
atomn->m = 0.0;
atomn->q = 0.0;
atomn->atomnumber = atomnumber;
strncpy(atomn->elem, elem, 4);
}
x[natom][XX] = strtod(xc, NULL)*0.1;
x[natom][YY] = strtod(yc, NULL)*0.1;
x[natom][ZZ] = strtod(zc, NULL)*0.1;
if (atoms->pdbinfo)
{
atoms->pdbinfo[natom].type = type;
atoms->pdbinfo[natom].atomnr = strtol(anr, NULL, 10);
atoms->pdbinfo[natom].altloc = altloc;
strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
atoms->pdbinfo[natom].bfac = strtod(bfac, NULL);
atoms->pdbinfo[natom].occup = strtod(occup, NULL);
}
natom++;
return natom;
}
static int read_g96_pos(char line[], t_symtab *symtab,
FILE *fp, const char *infile,
t_trxframe *fr)
{
t_atoms *atoms;
gmx_bool bEnd;
int nwanted, natoms, atnr, resnr = 0, oldres, newres, shift;
char anm[STRLEN], resnm[STRLEN];
char c1, c2;
double db1, db2, db3;
nwanted = fr->natoms;
atoms = fr->atoms;
natoms = 0;
if (fr->bX)
{
if (fr->bAtoms)
{
shift = CHAR_SHIFT;
}
else
{
shift = 0;
}
newres = -1;
oldres = -666; /* Unlikely number for the first residue! */
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
{
bEnd = (strncmp(line, "END", 3) == 0);
if (!bEnd && (line[0] != '#'))
{
if (sscanf(line+shift, "%15lf%15lf%15lf", &db1, &db2, &db3) != 3)
{
gmx_fatal(FARGS, "Did not find 3 coordinates for atom %d in %s\n",
natoms+1, infile);
}
if ((nwanted != -1) && (natoms >= nwanted))
{
gmx_fatal(FARGS,
"Found more coordinates (%d) in %s than expected %d\n",
natoms, infile, nwanted);
}
if (atoms)
{
if (fr->bAtoms &&
(sscanf(line, "%5d%c%5s%c%5s%7d", &resnr, &c1, resnm, &c2, anm, &atnr)
!= 6))
{
if (oldres >= 0)
{
resnr = oldres;
}
else
{
resnr = 1;
strncpy(resnm, "???", sizeof(resnm)-1);
}
strncpy(anm, "???", sizeof(anm)-1);
}
atoms->atomname[natoms] = put_symtab(symtab, anm);
if (resnr != oldres)
{
oldres = resnr;
newres++;
if (newres >= atoms->nr)
{
gmx_fatal(FARGS, "More residues than atoms in %s (natoms = %d)",
infile, atoms->nr);
}
atoms->atom[natoms].resind = newres;
if (newres+1 > atoms->nres)
{
atoms->nres = newres+1;
}
t_atoms_set_resinfo(atoms, natoms, symtab, resnm, resnr, ' ', 0, ' ');
}
else
{
atoms->atom[natoms].resind = newres;
}
}
if (fr->x)
{
fr->x[natoms][0] = db1;
fr->x[natoms][1] = db2;
fr->x[natoms][2] = db3;
}
natoms++;
}
}
if ((nwanted != -1) && natoms != nwanted)
{
fprintf(stderr,
"Warning: found less coordinates (%d) in %s than expected %d\n",
natoms, infile, nwanted);
}
}
fr->natoms = natoms;
return natoms;
}
