static int read_xyz_structure(void *mydata, int *optflags,
molfile_atom_t *atoms) {
int i, j;
char *k;
float coord;
molfile_atom_t *atom;
xyzdata *data = (xyzdata *)mydata;
char buffer[1024], fbuffer[1024];
/* skip over the first two lines */
if (NULL == fgets(fbuffer, 1024, data->file)) return MOLFILE_ERROR;
if (NULL == fgets(fbuffer, 1024, data->file)) return MOLFILE_ERROR;
/* we set atom mass and VDW radius from the PTE. */
*optflags = MOLFILE_ATOMICNUMBER | MOLFILE_MASS | MOLFILE_RADIUS;
for(i=0; i<data->numatoms; i++) {
k = fgets(fbuffer, 1024, data->file);
atom = atoms + i;
j=sscanf(fbuffer, "%s %f %f %f", buffer, &coord, &coord, &coord);
if (k == NULL) {
fprintf(stderr, "xyz structure) missing atom(s) in file '%s'\n", data->file_name);
fprintf(stderr, "xyz structure) expecting '%d' atoms, found only '%d'\n", data->numatoms, i);
return MOLFILE_ERROR;
} else if (j < 4) {
fprintf(stderr, "xyz structure) missing type or coordinate(s) in file '%s' for atom '%d'\n",
data->file_name, i+1);
return MOLFILE_ERROR;
}
/* handle the case if the first item is an ordinal number
* from the PTE */
if (isdigit(buffer[0])) {
int idx;
idx = atoi(buffer);
strncpy(atom->name, get_pte_label(idx), sizeof(atom->name));
atom->atomicnumber = idx;
atom->mass = get_pte_mass(idx);
atom->radius = get_pte_vdw_radius(idx);
} else {
int idx;
strncpy(atom->name, buffer, sizeof(atom->name));
idx = get_pte_idx(buffer);
atom->atomicnumber = idx;
atom->mass = get_pte_mass(idx);
atom->radius = get_pte_vdw_radius(idx);
}
strncpy(atom->type, atom->name, sizeof(atom->type));
atom->resname[0] = '\0';
atom->resid = 1;
atom->chain[0] = '\0';
atom->segid[0] = '\0';
/* skip to the end of line */
}
rewind(data->file);
return MOLFILE_SUCCESS;
}
int main() {
int i;
printf("Periodic table check/dump\n");
printf(" Table contains data for %d elements\n", nr_pte_entries);
printf(" Mass table size check: %d\n", sizeof(pte_mass) / sizeof(float));
printf(" VDW table size check: %d\n", sizeof(pte_vdw_radius) / sizeof(float));
printf("\n");
printf("Symbol Num Mass rVDW\n");
for (i=0; i<nr_pte_entries; i++) {
printf(" %-2s %3d %6.2f %4.2f\n",
get_pte_label(i), i, get_pte_mass(i), get_pte_vdw_radius(i));
}
return 0;
}
static int read_vaspoutcar_structure(void *mydata, int *optflags, molfile_atom_t *atoms)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
FILE *potcar;
char lineptr[LINESIZE], potcarfile[1000];
float atommass[MAXATOMTYPES];
int atomcount, typecount, i;
if (!data || !optflags || !atoms) return MOLFILE_ERROR;
*optflags = MOLFILE_MASS; /* we set atom mass from the PTE. */
*optflags |= MOLFILE_ATOMICNUMBER | MOLFILE_RADIUS;
typecount = 0;
atomcount = 0;
while (fgets(lineptr, LINESIZE, data->file) && atomcount < data->numatoms) {
if (strstr(lineptr, "POMASS") != NULL) sscanf(lineptr, " POMASS = %f;", &atommass[typecount++]);
if (strstr(lineptr, "ions per type =") != NULL) {
char const *token = strtok(lineptr, "=");
for (i = 0; i < typecount; ++i) {
token = strtok(NULL, " ");
atomcount += data->eachatom[i] = atoi(token);
}
}
}
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP OUTCAR read) ERROR: file '%s' does not have number of each atom.\n", data->filename);
return MOLFILE_ERROR;
}
/* Read POTCAR file to determine atom types.
* Each atom type section in POTCAR starts with a line
* that contains the name of the element (H, He, C etc.).
* Otherwise try to find similar mass in periodic table.
*/
if (strstr(potcarfile, "OUTCAR")) {
strcpy(potcarfile, data->filename);
strcpy(strstr(potcarfile, "OUTCAR"), "POTCAR");
potcar = fopen(potcarfile, "r");
} else {
potcar = NULL;
}
for (atomcount = i = 0; atomcount < data->numatoms; ++i) {
char const *label;
float mass, radius;
int k, idx = 0;
if (potcar) {
/* Obtain atom types from POTCAR file */
char atomtype[5] = "X";
if (fgets(lineptr, LINESIZE, potcar)) sscanf(lineptr, "%*s %4[^_. 0-9]", atomtype);
idx = get_pte_idx(atomtype);
/* Skip lines in potcar file until next element */
while (fgets(lineptr, LINESIZE, potcar)) if (strstr(lineptr, "End of Dataset")) break;
}
if (idx == 0) {
/* Try to find atom type by browsing through periodic table */
idx = sizeof(pte_mass)/sizeof(pte_mass[0]);
do idx--;
while (idx > 0 && fabs(get_pte_mass(idx) - atommass[i]) > 0.01);
}
label = get_pte_label(idx);
mass = (idx ? get_pte_mass(idx) : atommass[i]);
radius = get_pte_vdw_radius(idx);
for (k = 0; k < data->eachatom[i]; ++k, ++atomcount) {
molfile_atom_t *atom = &(atoms[atomcount]);
/* Required settings */
strncpy(atom->name, label, sizeof(atom->name));
strncpy(atom->type, atom->name, sizeof(atom->type));
atom->resname[0] = '\0';
atom->resid = 1;
atom->segid[0]='\0';
atom->chain[0]='\0';
/* Optional flags (as defined in *optflags) */
atom->mass = mass;
atom->radius = radius;
atom->atomicnumber = idx;
}
}
if (potcar) fclose(potcar);
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP OUTCAR read) ERROR: file '%s' does contain list of atom names.\n", data->filename);
return MOLFILE_ERROR;
}
atomcount = 0;
while (fgets(lineptr, LINESIZE, data->file) && atomcount == 0) {
if (strstr(lineptr, "position of ions in cartesian coordinates") != NULL) {
for (i = 0; i < data->numatoms; ++i, ++atomcount) {
float coord;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &coord, &coord, &coord)) {
fprintf(stderr, "\n\nVASP OUTCAR read) missing type or coordinate(s) in file '%s' for atom '%d'\n", data->filename, i+1);
return MOLFILE_ERROR;
}
}
}
}
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP OUTCAR read) ERROR: file '%s' does contain list of atom names.\n", data->filename);
return MOLFILE_ERROR;
}
rewind(data->file);
return MOLFILE_SUCCESS;
}
static int read_vasp5xdatcar_structure(void *mydata, int *optflags, molfile_atom_t *atoms)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
FILE *potcar = NULL;
int atomcount, i;
char lineptr[LINESIZE], potcarfile[1000], *cp;
float lc;
if (!data || !optflags || !atoms) return MOLFILE_ERROR;
*optflags = MOLFILE_MASS; /* we set atom mass from the PTE. */
*optflags |= MOLFILE_ATOMICNUMBER | MOLFILE_RADIUS;
strcpy(potcarfile, data->filename);
cp = strstr(potcarfile, "XDATCAR");
if (cp) {
strcpy(cp, "POTCAR");
potcar = fopen(potcarfile, "r");
}
/* Read POTCAR file to determine atom types.
* Each atom type section in POTCAR starts with a line
* that contains the name of the element (H, He, C etc.).
* Otherwise try the title line instead.
*/
for (atomcount = i = 0; atomcount < data->numatoms; ++i) {
int idx, j;
char const *label;
float mass, radius;
if (potcar) {
char atomtype[5] = "X";
/* Obtain atom types from POTCAR file */
if (fgets(lineptr, LINESIZE, potcar)) sscanf(lineptr, "%*s %4[^_. 0-9]", atomtype);
idx = get_pte_idx(atomtype);
/* Skip lines in potcar file until next element */
while (fgets(lineptr, LINESIZE, potcar)) if (strstr(lineptr, "End of Dataset")) break;
} else {
/* Try to obtain atom types from title line */
char const *token = (i == 0 ? strtok(data->titleline, " ") : strtok(NULL, " "));
idx = get_pte_idx(token);
}
label = get_pte_label(idx);
mass = get_pte_mass(idx);
radius = get_pte_vdw_radius(idx);
for (j = 0; j < data->eachatom[i]; ++j, ++atomcount) {
molfile_atom_t *const atom = &(atoms[atomcount]);
/* Required settings */
strncpy(atom->name, label, sizeof(atom->name));
strncpy(atom->type, atom->name, sizeof(atom->type));
atom->resname[0] = '\0';
atom->resid = 1;
atom->segid[0]='\0';
atom->chain[0]='\0';
/* Optional flags (as defined in *optflags) */
atom->mass = mass;
atom->radius = radius;
atom->atomicnumber = idx;
}
}
if (potcar) fclose(potcar);
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP5 XDATCAR read) ERROR: file '%s' doesn't seem to have list of atoms.\n", data->filename);
return MOLFILE_ERROR;
}
for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, "%f", &lc);
fprintf(stderr, "%f\n", lc);
for (i = 0; i < 3; ++i) {
float x, y, z;
fgets(lineptr, LINESIZE, data->file);
sscanf(lineptr, "%f %f %f", &x, &y, &z);
data->cell[i][0] = x*lc;
data->cell[i][1] = y*lc;
data->cell[i][2] = z*lc;
}
vasp_buildrotmat(data);
/* Ignore header until X,Y,Z-coordinates */
for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file);
/* Check whether all coordinates are present in the file */
for (i = 0; i < data->numatoms; ++i) {
float coord;
fgets(lineptr, LINESIZE, data->file);
if (3 != sscanf(lineptr, "%f %f %f", &coord, &coord, &coord)) {
fprintf(stderr, "\n\nVASP5 XDATCAR read) ERROR: structure is missing type or coordinate(s) in file '%s' for atom '%d'\n", data->filename, i+1);
return MOLFILE_ERROR;
}
}
rewind(data->file);
/* Ignore header until X,Y,Z-coordinates */
for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file);
return MOLFILE_SUCCESS;
}
static int read_vaspxml_structure(void *mydata, int *optflags, molfile_atom_t *atoms)
{
vasp_plugindata_t *data = (vasp_plugindata_t *)mydata;
int atomcount, coordscount, finished;
char lineptr[LINESIZE];
/* Verify that input is OK */
if (!data || !optflags || !atoms) return MOLFILE_ERROR;
*optflags = MOLFILE_MASS; /* we set atom mass from the PTE. */
*optflags |= MOLFILE_ATOMICNUMBER | MOLFILE_RADIUS;
/* Scan xml file */
atomcount = coordscount = finished = 0;
while (fgets(lineptr, LINESIZE, data->file) && !finished) {
/* Extract atom types */
if (strstr(lineptr, "atomtype") != NULL && atomcount == 0) {
int i;
fgets(lineptr, LINESIZE, data->file);
for (i = 0; i < data->numatoms; ++i, ++atomcount) {
molfile_atom_t *atom = &(atoms[i]);
char atomtype[5];
int idx;
fgets(lineptr, LINESIZE, data->file);
if (1 != sscanf(lineptr, " <rc><c> %4s </c>", atomtype)) break;
idx = get_pte_idx(atomtype);
/* Required settings */
strncpy(atom->name, get_pte_label(idx), sizeof(atom->name));
strncpy(atom->type, atom->name, sizeof(atom->type));
atom->resname[0] = '\0';
atom->resid = 1;
atom->segid[0] ='\0';
atom->chain[0] = '\0';
/* Optional flags (as defined in *optflags) */
atom->mass = get_pte_mass(idx);
atom->radius = get_pte_vdw_radius(idx);
atom->atomicnumber = idx;
}
/* Verify presence of coordinates for all atoms */
} else if (strstr(lineptr, "positions") != NULL && coordscount == 0) {
int i;
for (i = 0; i < data->numatoms && fgets(lineptr, LINESIZE, data->file); ++i) {
float x, y, z;
if (3 != sscanf(lineptr, " <v> %f %f %f <\v>", &x, &y, &z)) break;
}
coordscount = 3 * i;
}
finished = atomcount != 0 && coordscount != 0;
}
if (atomcount != data->numatoms) {
fprintf(stderr, "\n\nVASP xml read) ERROR: file '%s' does not have list of atom names.\n", data->filename);
return MOLFILE_ERROR;
}
if (coordscount != 3 * data->numatoms) {
fprintf(stderr, "\n\nVASP xml read) file '%s' does not contain coordinates of all atoms.\n", data->filename);
return MOLFILE_ERROR;
}
rewind(data->file);
return MOLFILE_SUCCESS;
}
static int read_pdb_structure(void *mydata, int *optflags,
molfile_atom_t *atoms) {
pdbdata *pdb = (pdbdata *)mydata;
molfile_atom_t *atom;
char pdbrec[PDB_BUFFER_LENGTH];
int i, rectype, atomserial, pteidx;
char ridstr[8];
char elementsymbol[3];
int badptecount = 0;
long fpos = ftell(pdb->fd);
*optflags = MOLFILE_INSERTION | MOLFILE_OCCUPANCY | MOLFILE_BFACTOR |
MOLFILE_ALTLOC | MOLFILE_ATOMICNUMBER | MOLFILE_BONDSSPECIAL;
i = 0;
do {
rectype = read_pdb_record(pdb->fd, pdbrec);
switch (rectype) {
case PDB_ATOM:
atom = atoms+i;
get_pdb_fields(pdbrec, strlen(pdbrec), &atomserial,
atom->name, atom->resname, atom->chain, atom->segid,
ridstr, atom->insertion, atom->altloc, elementsymbol,
NULL, NULL, NULL, &atom->occupancy, &atom->bfactor);
if (pdb->idxmap != NULL && atomserial < 100000) {
pdb->idxmap[atomserial] = i; /* record new serial number translation */
}
atom->resid = atoi(ridstr);
/* determine atomic number from the element symbol */
pteidx = get_pte_idx_from_string(elementsymbol);
atom->atomicnumber = pteidx;
if (pteidx != 0) {
atom->mass = get_pte_mass(pteidx);
atom->radius = get_pte_vdw_radius(pteidx);
} else {
badptecount++; /* unrecognized element */
}
strcpy(atom->type, atom->name);
i++;
break;
case PDB_CONECT:
/* only read CONECT records for structures where we know they can */
/* be valid for all of the atoms in the structure */
if (pdb->idxmap != NULL) {
get_pdb_conect(pdbrec, pdb->natoms, pdb->idxmap,
&pdb->maxbnum, &pdb->nbonds, &pdb->from, &pdb->to);
}
break;
default:
/* other record types are ignored in the structure callback */
/* and are dealt with in the timestep callback or elsewhere */
break;
}
} while (rectype != PDB_END && rectype != PDB_EOF);
fseek(pdb->fd, fpos, SEEK_SET);
/* if all atoms are recognized, set the mass and radius flags too, */
/* otherwise let VMD guess these for itself using it's own methods */
if (badptecount == 0) {
*optflags |= MOLFILE_MASS | MOLFILE_RADIUS;
}
return MOLFILE_SUCCESS;
}
