int make_asa_list(LinusProtein *p, int hphob, int hphil, int hydrogens, int *flags)
{
int PRESENT = 1;
int CONTRIB = 2;
/*
// This should be in Main/Calling function
int flags[p->num_atoms];
*/
if(hphob < 0)
hphob = 1;
if(hphil < 0)
hphil = 0;
if(hydrogens <0)
hydrogens=0;
int i;
for (i=0; i<p->num_atoms; i++)
{
flags[i] = 0;
}
int minres,maxres;
get_res_extents(p,&minres,&maxres);
int r;
for(r=minres; r<maxres; r++)
{
int first = p->res_fai[r];
int last = p->res_fai[r+1];
int at;
for(at=first; at<last; at++)
{
if(!hydrogens && is_hydrogen(p->atoms[at].name))
continue;
int hydrophobic = is_hydrophobic(p->atoms[at].name);
//printf("HPhobic - Atom %s %d is %d\n",p->atoms[at].name,p->atoms[at].resnum,hydrophobic);
flags[at] = PRESENT;
if(hphob && hydrophobic)
{
//printf("1 Flag for atom %s %d is %d\n",p->atoms[at].name,p->atoms[at].resnum,flags[at]);
flags[at] = flags[at] | CONTRIB;
//printf("2 Flag for atom %s %d is %d\n",p->atoms[at].name,p->atoms[at].resnum,flags[at]);
}
if(hphil && !hydrophobic)
{
//printf("3 Flag for atom %s %d is %d\n",p->atoms[at].name,p->atoms[at].resnum,flags[at]);
flags[at] = flags[at] | CONTRIB;
//printf("4 Flag for atom %s %d is %d\n",p->atoms[at].name,p->atoms[at].resnum,flags[at]);
}
}
}//r minres maxres
}// make_asa_list
void rm_res_pbc(t_atoms *atoms, rvec *x, matrix box)
{
int i, start, n, d, nat;
rvec xcg;
start = 0;
nat = 0;
clear_rvec(xcg);
for (n = 0; n < atoms->nr; n++)
{
if (!is_hydrogen(*(atoms->atomname[n])))
{
nat++;
rvec_inc(xcg, x[n]);
}
if ( (n+1 == atoms->nr) ||
(atoms->atom[n+1].resind != atoms->atom[n].resind) )
{
/* if nat==0 we have only hydrogens in the solvent,
we take last coordinate as cg */
if (nat == 0)
{
nat = 1;
copy_rvec(x[n], xcg);
}
svmul(1.0/nat, xcg, xcg);
for (d = 0; d < DIM; d++)
{
while (xcg[d] < 0)
{
for (i = start; i <= n; i++)
{
x[i][d] += box[d][d];
}
xcg[d] += box[d][d];
}
while (xcg[d] >= box[d][d])
{
for (i = start; i <= n; i++)
{
x[i][d] -= box[d][d];
}
xcg[d] -= box[d][d];
}
}
start = n+1;
nat = 0;
clear_rvec(xcg);
}
}
}
void
sys_reset_bonds(struct sys *sys, struct sel *sel)
{
struct spi *spi;
struct pair pair;
int i, j, k, n, *map;
spi = spi_create();
n = sel_get_count(sel);
map = calloc(n, sizeof(int));
sel_iter_start(sel);
for (k = 0; sel_iter_next(sel, &i); k++) {
spi_add_point(spi, sys_get_atom_xyz(sys, i));
map[k] = i;
}
spi_compute(spi, 1.6);
n = spi_get_pair_count(spi);
for (k = 0; k < n; k++) {
pair = spi_get_pair(spi, k);
i = map[pair.i];
j = map[pair.j];
if (is_hydrogen(sys_get_atom_name(sys, i)) &&
is_hydrogen(sys_get_atom_name(sys, j)))
continue;
if (graph_edge_find(sys->graph, i, j) == NULL)
graph_edge_create(sys->graph, i, j, 1);
}
spi_free(spi);
free(map);
}
//! Returns true if the current atom is a mutable atom.
bool atom::is_mutable() const
{
return is_hydrogen() || is_halogen();
}
