/*------------------------------------------------------------*/
void
select_residue_model (void)
{
mol3d *mol;
res3d *res;
int *flags;
int flag, model;
#ifndef NDEBUG
int old = count_residue_selections();
#endif
assert (dstack_size == 1);
model = ival;
clear_dstack();
push_residue_selection();
flags = current_residue_sel->flags;
for (mol = first_molecule; mol; mol = mol->next) {
flag = mol->model == model;
for (res = mol->first; res; res = res->next) *flags++ = flag;
}
#ifdef SELECT_DEBUG
fprintf (stderr, "residue select model: %i\n", select_residue_count());
#endif
#ifndef NDEBUG
assert (count_residue_selections() == old + 1);
#endif
}
/*------------------------------------------------------------*/
void
select_atom_sphere (void)
{
mol3d *mol;
res3d *res;
at3d *at;
vector3 centre;
double sqradius;
int *flags;
#ifndef NDEBUG
int old = count_atom_selections();
#endif
assert (dstack_size == 4);
centre.x = dstack[0];
centre.y = dstack[1];
centre.z = dstack[2];
sqradius = dstack[3];
clear_dstack();
if (sqradius < 0.0) {
yyerror ("invalid radius value");
return;
}
sqradius *= sqradius;
push_atom_selection();
flags = current_atom_sel->flags;
for (mol = first_molecule; mol; mol = mol->next) {
for (res = mol->first; res; res = res->next) {
for (at = res->first; at; at = at->next) {
*flags++ = v3_close (&(at->xyz), ¢re, sqradius);
}
}
}
#ifdef SELECT_DEBUG
fprintf (stderr, "atom select sphere: %i\n", select_atom_count());
#endif
#ifndef NDEBUG
assert (count_atom_selections() == old + 1);
#endif
}
/*------------------------------------------------------------*/
void
select_atom_b_factor (void)
{
mol3d *mol;
res3d *res;
at3d *at;
double lower, upper;
int *flags;
#ifndef NDEBUG
int old = count_atom_selections();
#endif
assert (dstack_size == 2);
lower = dstack[0];
upper = dstack[1];
clear_dstack();
if (upper < lower) {
yyerror ("invalid b-factor range values");
return;
}
push_atom_selection();
flags = current_atom_sel->flags;
for (mol = first_molecule; mol; mol = mol->next) {
for (res = mol->first; res; res = res->next) {
for (at = res->first; at; at = at->next) {
*flags++ = ((lower <= at->bfactor) && (at->bfactor <= upper));
}
}
}
#ifdef SELECT_DEBUG
fprintf (stderr, "atom select b-factor: %i\n", select_atom_count());
#endif
#ifndef NDEBUG
assert (count_atom_selections() == old + 1);
#endif
}
/*------------------------------------------------------------*/
void
select_atom_close (void)
{
double sqdistance;
int slot, atom_count;
int *flags;
#ifndef NDEBUG
int old = count_atom_selections();
#endif
assert (dstack_size == 1);
sqdistance = dstack[0];
clear_dstack();
if (sqdistance < 0.0) {
yyerror ("invalid distance value");
return;
}
sqdistance *= sqdistance;
atom_count = select_atom_count();
if (atom_count == 0) {
flags = current_atom_sel->flags;
for (slot = 0; slot < total_atoms; slot++) *flags++ = FALSE;
} else {
mol3d *mol;
res3d *res;
at3d *at;
int flag;
at3d **atoms, **close_atoms;
close_atoms = malloc (atom_count * sizeof (at3d *));
atoms = close_atoms;
flags = current_atom_sel->flags;
for (mol = first_molecule; mol; mol = mol->next) {
for (res = mol->first; res; res = res->next) {
for (at = res->first; at; at = at->next) {
if (*flags++) *atoms++ = at;
}
}
}
select_atom_not();
push_atom_selection();
flags = current_atom_sel->flags;
for (mol = first_molecule; mol; mol = mol->next) {
for (res = mol->first; res; res = res->next) {
for (at = res->first; at; at = at->next) {
flag = FALSE;
atoms = close_atoms;
for (slot = 0; slot < atom_count; slot++, atoms++) {
if (v3_close (&(at->xyz), &((*atoms)->xyz), sqdistance)) {
flag = TRUE;
break;
}
}
*flags++ = flag;
}
}
}
select_atom_and();
free (close_atoms);
}
#ifdef SELECT_DEBUG
fprintf (stderr, "atom select close: %i\n", select_atom_count());
#endif
#ifndef NDEBUG
assert (count_atom_selections() == old);
#endif
}
double stack_eval(double t, double *c_in, double *x_in, D_Stack *d_stack, StackExpr expr ) {
// I_Stack *serial = new_istack();
// I_Stack istack;
// I_Stack *serial = &istack;
clear_dstack(d_stack);
int* serial = expr.serial;
#ifdef print_stack_eval
printf("Serial: |%d|", expr.s_len);
#endif
int s;
for( s=0; s < expr.s_len; s++ ) {
// #ifdef print_stack_eval
// printf( "%d ", expr.serial[s]);
// #endif
// push_istack(serial,expr.serial[expr.s_len-s-1]);
// }
// #ifdef print_stack_eval
// printf("\n");
// #endif
// clear_dstack(d_stack);
// // fill i_stack with cmds and d_stack with leaves
// while ( !is_empty_istack(serial) ) {
// // printf( "processing serial\n");
// int val = top_istack(serial);
// pop_istack(serial);
int val = serial[s];
#ifdef print_stack_eval
int dlen = len_dstack(d_stack);
int slen = len_istack(serial);
printf( "S: %d val: %d \n", slen, val );
printf( "serial(%d): [ ", slen);
for( i=0; i < slen; i++ )
printf( "%d ", get_istack(serial,i) );
printf(" ]\n");
printf( "d_stack(%d): [ ", dlen);
for( i=0; i < dlen; i++ )
printf( "%.2f ", get_dstack(d_stack,i) );
printf(" ]\n");
#endif
switch (val) {
// CONSTANT: 2
case 2: {
s++;
int p = serial[s];
// int p = top_istack(serial);
// pop_istack(serial);
push_dstack(d_stack,c_in[p]);
}
break;
// HACK***
// CONSTANTF: 3
case 3: {
s++;
int p = serial[s];
// int p = top_istack(serial);
// pop_istack(serial);
push_dstack(d_stack,p);
}
break;
// TIME: 4
case 4:
push_dstack(d_stack,t);
break;
// SYSTEM: 5
// case 5:
// s++;
// push_dstack(d_stack,sys_in[serial[s]]);
// VAR: 6 should already be transformed, but just in case
case 6: {
s++;
int p = serial[s];
// int p = top_istack(serial);
// pop_istack(serial);
push_dstack(d_stack,x_in[p]);
break;
}
// NEG: 9
case 9: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, -top);
}
break;
// ABS: 10
case 10: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, fabs(top));
}
break;
// SQRT: 11
case 11: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, sqrt(top));
}
break;
// SIN: 12
case 12: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, sin(top));
}
break;
// COS: 13
case 13: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, cos(top));
}
break;
// TAN: 14
case 14: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, tan(top));
}
break;
// EXP: 15
case 15: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, exp(top));
}
break;
// LOG: 16
case 16: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, log(top));
}
break;
// POWI: 18
case 18: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
s++;
int pwr = serial[s];
// int pwr = top_istack(serial);
// pop_istack(serial);
push_dstack(d_stack, pow(top,pwr));
}
break;
// POWE: 20
case 20: {
double top = top_dstack(d_stack);
pop_dstack(d_stack);
double pwr = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, pow(top,pwr));
}
break;
// DIV: 21
case 21: {
double denom = top_dstack(d_stack);
pop_dstack(d_stack);
double numer = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, numer / denom);
}
break;
// ADD: 22
case 22: {
double lhs = top_dstack(d_stack);
pop_dstack(d_stack);
double rhs = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, lhs + rhs);
// printf( "%f + %f = %f\n", lhs, rhs, top_dstack(d_stack));
}
break;
// MUL: 23
case 23: {
double lhs = top_dstack(d_stack);
pop_dstack(d_stack);
double rhs = top_dstack(d_stack);
pop_dstack(d_stack);
push_dstack(d_stack, lhs * rhs);
// printf( "%f * %f = %f\n", lhs, rhs, top_dstack(d_stack));
}
break;
case 0:
default:
// STARTVAR: 25
if (val >= 25) {
push_dstack(d_stack,x_in[val-25]); // x_dim_of_var = val - STARTVAR
} else {
printf("pushing unknown cmd %d\n", val);
int s;
for( s=0; s < expr.s_len; s++ ) {
printf( "%d ", expr.serial[s]);
}
printf( "\n");
abort();
}
}
#ifdef print_stack_eval
dlen = len_dstack(d_stack);
printf( "S: %d val: %d\n", s, val);
printf( "d_stack(%d): [ ", dlen);
for( i=0; i < dlen; i++ )
printf( "%.2f ", get_dstack(d_stack,i) );
printf(" ]\n\n");
#endif
}
// free(serial);
return top_dstack(d_stack);
}