gpointer core_new(gchar *elem, gchar *label, struct model_pak *model)
{
struct core_pak *core;
g_assert(elem != NULL);
g_assert(model != NULL);
core = g_malloc(sizeof(struct core_pak));
/* element related initialization */
core_init(elem, core, model);
/* general initialization */
if (label)
core->atom_label = g_strdup(label);
else
core->atom_label = g_strdup(elem);
VEC4SET(core->x, 0.0, 0.0, 0.0, 1.0);
VEC4SET(core->rx, 0.0, 0.0, 0.0, 1.0);
VEC3SET(core->v, 0.0, 0.0, 0.0);
VEC3SET(core->offset, 0.0, 0.0, 0.0);
core->status = NORMAL;
core->primary = TRUE;
core->orig = TRUE;
core->ghost = FALSE;
core->breathe = FALSE;
core->growth = FALSE;
core->translate = FALSE;
core->render_mode = BALL_STICK;
core->render_wire = FALSE;
core->region = REGION1A;
core->radius = 0.0;
core->has_sof = FALSE;
core->sof = 1.0;
core->charge = 0.0;
core->lookup_charge = TRUE;
core->flags = NULL;
core->bonds = NULL;
core->mol = NULL;
core->shell = NULL;
core->primary_core = NULL;
core->vibx_list = NULL;
core->viby_list = NULL;
core->vibz_list = NULL;
/* NEW: hydrogen bond capabilities */
if (g_strrstr(elem, "H") != NULL)
core->hydrogen_bond = TRUE;
else
core->hydrogen_bond = FALSE;
return(core);
}
gpointer shell_new(gchar *elem, gchar *label, struct model_pak *model)
{
gint code;
struct elem_pak elem_data;
struct shel_pak *shell;
g_assert(elem != NULL);
g_assert(model != NULL);
shell = g_malloc(sizeof(struct shel_pak));
/* attempt to match atom type with database */
code = elem_test(elem);
if (!code)
printf("Warning: element [%s] not found.\n", elem);
/* init modifiable element data */
get_elem_data(code, &elem_data, model);
ARR3SET(shell->colour, elem_data.colour);
shell->atom_code = code;
if (label)
shell->shell_label = g_strdup(label);
else
shell->shell_label = g_strdup(elem);
VEC4SET(shell->x, 0.0, 0.0, 0.0, 1.0);
VEC4SET(shell->rx, 0.0, 0.0, 0.0, 1.0);
VEC3SET(shell->v, 0.0, 0.0, 0.0);
VEC3SET(shell->offset, 0.0, 0.0, 0.0);
shell->status = NORMAL;
shell->primary = TRUE;
shell->orig = TRUE;
shell->breathe = FALSE;
shell->translate = FALSE;
shell->region = REGION1A;
shell->core = NULL;
shell->primary_shell = NULL;
shell->radius = 0.0;
shell->charge = 0.0;
shell->has_sof = FALSE;
shell->sof = 1.0;
shell->lookup_charge = TRUE;
shell->flags = NULL;
return(shell);
}
void quat_concat(gdouble *q, gdouble *v, gdouble a)
{
gdouble ha, sa, qr[4];
/* create and apply the desired quaternion rotation */
ha = 0.5*a;
sa = sin(ha);
VEC4SET(qr, cos(ha), v[0]*sa, v[1]*sa, v[2]*sa);
quat_mult(q, qr);
}
void camera_default(gdouble r, gpointer data)
{
struct camera_pak *camera = data;
camera->mode = LOCKED;
camera->perspective = FALSE;
camera->fov = 70.0;
/* FIXME - not sure why the < 1.0 case is needed ... */
if (r < 1.0)
camera->zoom = r;
else
camera->zoom = 1.0;
VEC4SET(camera->q, 1.0, 0.0, 0.0, 0.0);
VEC3SET(camera->x, 0.0, -2.0*r, 0.0);
VEC3SET(camera->o, 0.0, 0.0, 1.0);
VEC3SET(camera->v, 0.0, 1.0, 0.0);
VEC3SET(camera->e, 1.0, 0.0, 0.0);
}
void docking_project_create(GtkWidget *w, struct model_pak *model)
{
gint a, b, i, m, n, rx, ry, rz, size, rigid_save;
gint a_max, b_max, rx_max, ry_max, rz_max;
gchar *file, *dump, *dump_save, *rigid_move_save;
gdouble dx, dy, dz, x[3], scale[3], mat[9], dock_centroid[3], q[4];
GString *name, *rigid;
GSList *list, *core_list, *shell_list;
struct dock_pak *dock;
struct core_pak *core, *core2;
struct shel_pak *shell, *shell2;
FILE *fp;
/* checks */
g_assert(model != NULL);
size = g_slist_length(model->selection);
if (!size)
{
gui_text_show(WARNING, "Please select the subset you wish to dock.\n");
return;
}
/* create new docking project */
dock = g_malloc(sizeof(struct dock_pak));
/* NEW - setup project path */
/*
g_path_get_dirname(model->fullpath);
g_get_current_dir();
*/
/* seek a file name that doesn't exist (avoid background overwriting) */
name = g_string_new(NULL);
i=0;
do
{
g_string_sprintf(name, "project_%06d", i);
i++;
}
while (g_file_test(name->str, G_FILE_TEST_EXISTS));
dock->path = g_build_path(sysenv.cwd, name->str, NULL);
printf("creating new project: [%s]\n", dock->path);
#if WIN32
if (mkdir(dock->path))
#else
if (mkdir(dock->path, 0700))
#endif
{
gui_text_show(ERROR, "Failed to create project directory.\n");
g_free(dock->path);
g_free(dock);
return;
}
/* project control file */
g_string_sprintf(name, "%s%sproject.pcf", dock->path, DIR_SEP);
fp = fopen(name->str, "wt");
/* save original variables */
dump_save = model->gulp.dump_file;
model->gulp.dump_file = NULL;
rigid_save = model->gulp.rigid;
model->gulp.rigid = dock_rigid_on;
rigid_move_save = model->gulp.rigid_move;
model->gulp.rigid_move = NULL;
if (model->gulp.rigid)
{
rigid = g_string_new(NULL);
if (dock_rigid_x)
g_string_sprintf(rigid, "x");
if (dock_rigid_y)
g_string_sprintfa(rigid, "y");
if (dock_rigid_z)
g_string_sprintfa(rigid, "z");
model->gulp.rigid_move = g_string_free(rigid, FALSE);
}
/* duplicate selection for docking */
core_list = NULL;
shell_list = NULL;
VEC3SET(dock_centroid, 0.0, 0.0, 0.0);
for (list=model->selection ; list ; list=g_slist_next(list))
{
core2 = dup_core(list->data);
core_list = g_slist_prepend(core_list, core2);
if (core2->shell)
shell_list = g_slist_prepend(shell_list, core2->shell);
/* compute centroid */
ARR3ADD(dock_centroid, core2->x);
}
/* NB: lists must have the same order as original selection */
core_list = g_slist_reverse(core_list);
shell_list = g_slist_reverse(shell_list);
VEC3MUL(dock_centroid, 1.0/(gdouble) size);
/* fractional translation grid units */
scale[0] = dock_cell[0] / dock_grid[0];
scale[1] = dock_cell[1] / dock_grid[1];
/* rotational increments */
dx = PI/dock_rotate[0];
dy = PI/dock_rotate[1];
dz = PI/dock_rotate[2];
/* translational sampling */
if (dock_grid_on)
{
a_max = dock_grid[0];
b_max = dock_grid[1];
}
else
{
a_max = 1;
b_max = 1;
}
/* rotational sampling */
if (dock_rotate_on)
{
rx_max = dock_rotate[0];
ry_max = dock_rotate[1];
rz_max = dock_rotate[2];
}
else
{
rx_max = 1;
ry_max = 1;
rz_max = 1;
}
/* project header */
fprintf(fp, "%%title solvent mapping project\n");
fprintf(fp, "%%set %d %d %f %f\n", a_max, b_max, dock_cell[0], dock_cell[1]);
/* loop over all grid translations */
m = n = 0;
for (a=0 ; a<a_max ; a++)
{
for (b=0 ; b<b_max ; b++)
{
VEC3SET(x, a, b, 0.0);
x[0] *= scale[0];
x[1] *= scale[1];
/* loop over rotations */
VEC4SET(q, 1.0, 0.0, 0.0, 0.0);
for (rx=0 ; rx<rx_max ; rx++)
{
if (rx)
quat_concat_euler(q, PITCH, dx);
for (ry=0 ; ry<ry_max ; ry++)
{
if (ry)
quat_concat_euler(q, ROLL, dy);
for (rz=0 ; rz<rz_max ; rz++)
{
if (rz)
quat_concat_euler(q, YAW, dz);
/* build total rotation matrix */
quat_matrix(mat, q);
/* transform the cores and shells */
i = 0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
core = list->data;
/* FIXME - should we restore this after? how? */
core->region = 2;
/* get original selection core coordinates */
core2 = g_slist_nth_data(core_list, i);
ARR3SET(core->x, core2->x);
/* perform the rotation (NB: must be done about origin in cartesian space) */
ARR3SUB(core->x, dock_centroid);
vecmat(model->latmat, core->x);
vecmat(mat, core->x);
vecmat(model->ilatmat, core->x);
ARR3ADD(core->x, dock_centroid);
/* add the current translation offset */
ARR3ADD(core->x, x);
/* as above, for the associated shell */
if (core->shell)
{
shell = core->shell;
shell->region = 2;
shell2 = core2->shell;
g_assert(shell2 != NULL);
ARR3SET(shell->x, shell2->x);
ARR3SUB(shell->x, dock_centroid);
vecmat(model->latmat, shell->x);
vecmat(mat, shell->x);
vecmat(model->ilatmat, shell->x);
ARR3ADD(shell->x, dock_centroid);
ARR3ADD(shell->x, x);
}
i++;
}
/* write docking configuration */
/*
file = g_strdup_printf("%s_%06d.gin", model->basename, n);
*/
/* m identifies grid points (for later minimum check) */
fprintf(fp, "%s_%06d.gin %f %f %d\n", model->basename, n, x[0], x[1], m);
file = g_strdup_printf("%s%s%s_%06d.gin", dock->path, DIR_SEP, model->basename, n);
dump = g_strdup_printf("%s_%06d.res", model->basename, n);
model->gulp.dump_file = dump;
write_gulp(file, model);
g_free(file);
g_free(dump);
n++;
}
}
}
m++;
}
}
/* restore original variables */
model->gulp.dump_file = dump_save;
model->gulp.rigid = rigid_save;
g_free(model->gulp.rigid_move);
model->gulp.rigid_move = rigid_move_save;
/* restore original selection (delete, then concat saved list) */
i = 0;
for (list=model->selection ; list ; list=g_slist_next(list))
{
core = list->data;
core2 = g_slist_nth_data(core_list, i);
ARR3SET(core->x, core2->x);
if (core->shell)
{
shell = core->shell;
shell2 = core2->shell;
g_assert(shell2 != NULL);
ARR3SET(shell->x, shell2->x);
}
i++;
}
/* free docking core/shell lists */
free_slist(core_list);
free_slist(shell_list);
g_string_free(name, TRUE);
fclose(fp);
/* run docking in background unless told to stop after setup */
/*
if (!dock_no_execute)
submit_task("Docking", &docking_execute, dock, &docking_cleanup, dock, model);
*/
}
