static HashSet *
frt_get_fields(VALUE rfields)
{
VALUE rval;
HashSet *fields;
char *s, *p, *str;
if (rfields == Qnil) return NULL;
fields = hs_new_str(&free);
if (TYPE(rfields) == T_ARRAY) {
int i;
for (i = 0; i < RARRAY(rfields)->len; i++) {
rval = rb_obj_as_string(RARRAY(rfields)->ptr[i]);
hs_add(fields, estrdup(RSTRING(rval)->ptr));
}
} else {
rval = rb_obj_as_string(rfields);
if (strcmp("*", RSTRING(rval)->ptr) == 0) {
hs_destroy(fields);
fields = NULL;
} else {
s = str = estrdup(RSTRING(rval)->ptr);
while ((p = strchr(s, '|')) != '\0') {
*p = '\0';
hs_add(fields, estrdup(s));
s = p + 1;
}
hs_add(fields, estrdup(s));
free(str);
}
}
return fields;
}
void
hs_test (void)
{
array_t *arr;
struct hs *a = hs_create (1);
hs_add (a, array_from_str ("0011xx00"));
hs_add (a, array_from_str ("10100x0x"));
arr = array_from_str ("10100x01");
hs_diff (a, arr);
hs_print (a);
struct hs *b = hs_copy_a (a);
hs_print (b);
hs_free (b);
free (arr);
b = hs_create (1);
hs_add (b, array_from_str ("xxxx1x00"));
hs_add (b, array_from_str ("xxxxx1x0"));
hs_print (b);
hs_isect (b, a);
hs_print (b);
hs_free (b);
hs_free (a);
a = hs_create (1);
hs_add (a, array_from_str ("10xxxxxx"));
hs_add (a, array_from_str ("xxxxxx10"));
arr = array_from_str ("11111111");
hs_diff (a, arr);
hs_print (a);
hs_cmpl (a);
hs_print (a);
hs_free (a);
a = hs_create (1);
hs_add (a, array_from_str ("10xxxxxx"));
hs_add (a, array_from_str ("xxxxxx10"));
b = hs_create (1);
hs_add (b, array_from_str ("11111111"));
hs_minus (a, b);
hs_print (a);
hs_free (a);
hs_free (b);
a = hs_create (1);
hs_add (a, array_from_str ("11111111"));
//hs_add (a, array_from_str ("xxxxxxx1"));
hs_diff (a, arr);
hs_print (a);
hs_comp_diff (a);
char *s = hs_to_str (a);
printf ("S: %s\n", s);
free (s);
hs_free (a);
free (arr);
}
void cw_add_file(CompoundWriter *cw, char *id)
{
id = estrdup(id);
if (hs_add(cw->ids, id) != HASH_KEY_DOES_NOT_EXIST) {
RAISE(IO_ERROR, "Tried to add file \"%s\" which has already been "
"added to the compound store", id);
}
ary_grow(cw->file_entries);
ary_last(cw->file_entries).name = id;
}
Query *index_get_query(Index *self, char *qstr)
{
int i;
FieldInfos *fis;
ensure_searcher_open(self);
fis = self->ir->fis;
for (i = fis->size - 1; i >= 0; i--) {
hs_add(self->qp->all_fields, (char *)fis->fields[i]->name);
}
return qp_parse(self->qp, qstr);
}
void
hs_cmpl (struct hs *hs)
{
if (!hs->list.used) {
hs_add (hs, array_create (hs->len, BIT_X));
return;
}
struct hs_vec *v = &hs->list, new_list = {0};
for (int i = 0; i < v->used; i++) {
struct hs_vec tmp = {0};
tmp.elems = array_cmpl_a (v->elems[i], hs->len, &tmp.used);
tmp.alloc = tmp.used;
/* If complement is empty, result will be empty. */
if (!tmp.elems) {
vec_destroy (&new_list);
vec_destroy (&hs->list);
memset (&hs->list, 0, sizeof hs->list);
return;
}
tmp.diff = xcalloc (tmp.alloc, sizeof *tmp.diff);
if (v->diff) { /* NULL if called from comp_diff */
struct hs_vec *d = &v->diff[i];
for (int j = 0; j < d->used; j++)
vec_append (&tmp, d->elems[j], false);
}
if (!new_list.used) new_list = tmp;
else {
vec_isect (&new_list, &tmp, hs->len);
vec_destroy (&tmp);
}
}
vec_destroy (v);
hs->list = new_list;
}
/* scan trajectory and accumulate data */
static int dotrj(hist_t *hsrms, bb_t *bb, int rescnt, FILE *fplog,
trj_t *trj, const char *fxtc, rvec *xrefbb,
int nat, matrix box, double *wtot)
{
int nfr, match, natoms;
int fpxtc = 0; /* gromacs file handle for trj */
rvec *x = NULL, *xbb;
double t1, w, rmsd;
real t = 0.f;
xnew(xbb, rescnt * 3);
/* loop over xtc frames */
for (nfr = 0; ; nfr++) {
if (nfr == 0) {
/* first frame, get the file handle fpxtc, allocate x
* and check the number of atoms */
natoms = read_first_x(&fpxtc, fxtc, &t, &x, box);
if (natoms != nat) {
fprintf(stderr, "natoms mismatch! top %d, xtc %d\n", nat, natoms);
return -1;
}
} else {
if (!read_next_x(fpxtc, &t, natoms, x, box))
break;
}
if (ctmd) { /* each frame has a weight */
w = 1.;
} else {
/* for each xtc frame, we search a corresponding
* frame in trj at the same time */
for (match = 0; trj->pos < trj->n; trj->pos++) {
t1 = trj->fr[trj->pos].t;
if (fabs(t1 - t) < 0.5) {
match = 1;
break;
} else if (t1 > t + 0.5) {
fprintf(stderr, "time difference %g (trace), %g (xtc)\n", t1, t);
return -1;
}
}
if (!match) {
fprintf(stderr, "cannot find a frame for t = %g\n", t);
break;
}
if (!trj->fr[trj->pos].in) {
w = 0.0;
} else {
w = exp(trj->fr[trj->pos].lnw);
}
}
/* skip trivial frames */
if (fplog == NULL && w < 1e-6) continue;
/* extract backbone indices */
xgetbb(xbb, x, bb, rescnt);
/* fit x to xref */
rmsd = rv3_rmsd(xbb, NULL, xrefbb, vmass, rescnt*3, 0, NULL, NULL);
if (fplog) {
fprintf(fplog, "%10.0f %8.4f %g %d\n", t, rmsd, w, trj->fr[trj->pos].dataid);
}
hs_add(hsrms, &rmsd, w, HIST_VERBOSE);
*wtot += w;
}
free(xbb);
return 0;
}