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sys.c
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sys.c
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/*
* Copyright (c) 2013-2017 Ilya Kaliman
*
* Permission to use, copy, modify, and distribute this software for any
* purpose with or without fee is hereby granted, provided that the above
* copyright notice and this permission notice appear in all copies.
*
* THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
* WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
* MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
* ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
* WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
* ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
* OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#include "vimol.h"
struct sys {
int is_modified;
struct atoms *atoms;
struct graph *graph;
struct sel *sel;
struct sel *visible;
};
static const vec_t h_table[] = {
{ 1.090, 0.000, 0.000 }, /* 0 C(sp3) H-1 */
{ -0.360, 1.029, 0.000 }, /* 1 C(sp3) H-2 */
{ -0.350, -0.523, 0.890 }, /* 2 C(sp3) H-3 */
{ -0.350, -0.523, -0.890 }, /* 3 C(sp3) H-4 */
{ -0.542, 0.946, 0.000 }, /* 4 C(sp2) H-1 */
{ -0.542, -0.946, 0.000 }, /* 5 C(sp2) H-2 */
{ -1.090, 0.000, 0.000 }, /* 6 C(sp) H-1 */
{ 1.070, 0.000, 0.000 }, /* 7 N H-1 */
{ -0.353, 1.010, 0.000 }, /* 8 N H-2 */
{ -0.350, -0.510, 0.873 }, /* 9 N H-3 */
{ 1.380, 0.000, 0.000 }, /* 10 P H-1 */
{ -0.455, 1.303, 0.000 }, /* 11 P H-2 */
{ -0.451, -0.658, 1.126 }, /* 12 P H-3 */
{ 1.050, 0.000, 0.000 }, /* 13 O H-1 */
{ -0.350, 0.990, 0.000 }, /* 14 O H-2 */
{ 1.340, 0.000, 0.000 }, /* 15 S H-1 */
{ -0.447, 1.263, 0.000 }, /* 16 S H-2 */
};
static void
add_hydrogens(struct sys *sys, int i, int j, int k, int offset, int count)
{
mat_t rotmat;
vec_t pi, pj, pk;
pi = sys_get_atom_xyz(sys, i);
if (j < 0) {
pj = vec_random();
pj = vec_add(&pj, &pi);
} else
pj = sys_get_atom_xyz(sys, j);
if (k < 0) {
pk = vec_random();
pk = vec_add(&pk, &pi);
} else
pk = sys_get_atom_xyz(sys, k);
rotmat = mat_align(&pi, &pj, &pk);
for (k = 0; k < count; k++) {
pk = h_table[offset + k];
pk = mat_vec(&rotmat, &pk);
pk = vec_add(&pk, &pi);
sys_add_atom(sys, "H", pk);
j = sys_get_atom_count(sys) - 1;
graph_edge_create(sys->graph, i, j, 1);
}
}
static int
get_bond_count(struct graph *graph, int idx)
{
struct graphedge *edge;
int count = 0;
edge = graph_get_edges(graph, idx);
while (edge) {
count += graph_edge_get_type(edge);
edge = graph_edge_next(edge);
}
return (count);
}
struct sys *
sys_create(const char *path)
{
struct sys *sys;
int i;
sys = xcalloc(1, sizeof *sys);
sys->graph = graph_create();
sys->sel = sel_create(0);
sys->visible = sel_create(0);
if (path == NULL || !util_file_exists(path)) {
sys->atoms = atoms_create();
return (sys);
}
if ((sys->atoms = formats_load(path)) == NULL) {
sys_free(sys);
return (NULL);
}
for (i = 0; i < sys_get_atom_count(sys); i++) {
graph_vertex_add(sys->graph);
sel_expand(sys->sel);
sel_expand(sys->visible);
sel_add(sys->visible, sel_get_size(sys->visible) - 1);
}
sys_reset_bonds(sys);
return (sys);
}
struct sys *
sys_copy(struct sys *sys)
{
struct sys *copy;
copy = xcalloc(1, sizeof *sys);
copy->is_modified = sys->is_modified;
copy->atoms = atoms_copy(sys->atoms);
copy->graph = graph_copy(sys->graph);
copy->sel = sel_copy(sys->sel);
copy->visible = sel_copy(sys->visible);
return (copy);
}
void
sys_free(struct sys *sys)
{
if (sys) {
atoms_free(sys->atoms);
graph_free(sys->graph);
sel_free(sys->sel);
sel_free(sys->visible);
free(sys);
}
}
struct graph *
sys_get_graph(struct sys *sys)
{
return (sys->graph);
}
struct sel *
sys_get_sel(struct sys *sys)
{
return (sys->sel);
}
struct sel *
sys_get_visible(struct sys *sys)
{
return (sys->visible);
}
int
sys_is_modified(struct sys *sys)
{
return (sys->is_modified);
}
int
sys_get_frame(struct sys *sys)
{
return (atoms_get_frame(sys->atoms));
}
void
sys_set_frame(struct sys *sys, int frame)
{
atoms_set_frame(sys->atoms, frame);
}
int
sys_get_frame_count(struct sys *sys)
{
return (atoms_get_frame_count(sys->atoms));
}
void
sys_add_atom(struct sys *sys, const char *name, vec_t xyz)
{
atoms_add(sys->atoms, name, xyz);
graph_vertex_add(sys->graph);
sel_expand(sys->sel);
sel_expand(sys->visible);
sel_add(sys->visible, sel_get_size(sys->visible)-1);
sys->is_modified = 1;
}
void
sys_remove_atom(struct sys *sys, int idx)
{
atoms_remove(sys->atoms, idx);
graph_vertex_remove(sys->graph, idx);
sel_contract(sys->sel, idx);
sel_contract(sys->visible, idx);
sys->is_modified = 1;
}
int
sys_get_atom_count(struct sys *sys)
{
return (atoms_get_count(sys->atoms));
}
const char *
sys_get_atom_name(struct sys *sys, int idx)
{
return (atoms_get_name(sys->atoms, idx));
}
int
sys_get_atom_type(struct sys *sys, int idx)
{
return (atoms_get_type(sys->atoms, idx));
}
void
sys_set_atom_name(struct sys *sys, int idx, const char *name)
{
atoms_set_name(sys->atoms, idx, name);
sys->is_modified = 1;
}
vec_t
sys_get_atom_xyz(struct sys *sys, int idx)
{
return (atoms_get_xyz(sys->atoms, idx));
}
void
sys_set_atom_xyz(struct sys *sys, int idx, vec_t xyz)
{
atoms_set_xyz(sys->atoms, idx, xyz);
sys->is_modified = 1;
}
void
sys_add_hydrogens(struct sys *sys, struct sel *sel)
{
int i, j, k, l, n_bond, n_neig;
sel_iter_start(sel);
while (sel_iter_next(sel, &i)) {
if (sys_get_atom_type(sys, i) == 6) { /* C */
n_neig = graph_get_edge_count(sys->graph, i);
n_bond = get_bond_count(sys->graph, i);
j = k = -1;
if (n_bond == 0) {
/* add 4 sp3 */
add_hydrogens(sys, i, j, k, 0, 4);
} else if (n_bond == 1) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
/* add 3 sp3 */
add_hydrogens(sys, i, j, k, 1, 3);
} else if (n_bond == 2) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
if (n_neig == 1) {
/* keep double bond atoms in plane */
if (graph_get_edge_count(sys->graph, j) > 1) {
if ((k = graph_edge_j(graph_get_edges(sys->graph, j))) == i)
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, j)));
}
/* add 2 sp2 */
add_hydrogens(sys, i, j, k, 4, 2);
} else if (n_neig == 2) {
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, i)));
/* add 2 sp3 */
add_hydrogens(sys, i, j, k, 2, 2);
}
} else if (n_bond == 3) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
if (n_neig == 1) {
/* add 1 sp */
add_hydrogens(sys, i, j, k, 6, 1);
} else if (n_neig == 2) {
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, i)));
/* add 1 sp2 */
add_hydrogens(sys, i, j, k, 5, 1);
} else if (n_neig == 3) {
vec_t pl, ph1, ph2;
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, i)));
l = graph_edge_j(graph_edge_next(graph_edge_next(graph_get_edges(sys->graph, i))));
/* add 2 sp3 and remove the wrong one */
add_hydrogens(sys, i, j, k, 2, 2);
pl = sys_get_atom_xyz(sys, l);
ph1 = sys_get_atom_xyz(sys, sys_get_atom_count(sys) - 2);
ph2 = sys_get_atom_xyz(sys, sys_get_atom_count(sys) - 1);
k = vec_dist(&pl, &ph1) < vec_dist(&pl, &ph2) ? 2 : 1;
sys_remove_atom(sys, sys_get_atom_count(sys) - k);
}
}
} else if (sys_get_atom_type(sys, i) == 7) { /* N */
n_neig = graph_get_edge_count(sys->graph, i);
n_bond = get_bond_count(sys->graph, i);
j = k = -1;
if (n_bond == 0) {
/* add 3 */
add_hydrogens(sys, i, j, k, 7, 3);
} else if (n_bond == 1) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
/* add 2 */
add_hydrogens(sys, i, j, k, 8, 2);
} else if (n_bond == 2) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
if (n_neig > 1)
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, i)));
/* add 1 */
add_hydrogens(sys, i, j, k, 9, 1);
}
} else if (sys_get_atom_type(sys, i) == 8) { /* O */
n_bond = get_bond_count(sys->graph, i);
j = k = -1;
if (n_bond == 0) {
/* add 2 */
add_hydrogens(sys, i, j, k, 13, 2);
} else if (n_bond == 1) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
/* add 1 */
add_hydrogens(sys, i, j, k, 14, 1);
}
} else if (sys_get_atom_type(sys, i) == 15) { /* P */
n_neig = graph_get_edge_count(sys->graph, i);
n_bond = get_bond_count(sys->graph, i);
j = k = -1;
if (n_bond == 0) {
/* add 3 */
add_hydrogens(sys, i, j, k, 10, 3);
} else if (n_bond == 1) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
/* add 2 */
add_hydrogens(sys, i, j, k, 11, 2);
} else if (n_bond == 2) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
if (n_neig > 1)
k = graph_edge_j(graph_edge_next(graph_get_edges(sys->graph, i)));
/* add 1 */
add_hydrogens(sys, i, j, k, 12, 1);
}
} else if (sys_get_atom_type(sys, i) == 16) { /* S */
n_bond = get_bond_count(sys->graph, i);
j = k = -1;
if (n_bond == 0) {
/* add 2 */
add_hydrogens(sys, i, j, k, 15, 2);
} else if (n_bond == 1) {
j = graph_edge_j(graph_get_edges(sys->graph, i));
/* add 1 */
add_hydrogens(sys, i, j, k, 16, 1);
}
}
}
}
vec_t
sys_get_sel_center(struct sys *sys, struct sel *sel)
{
vec_t center, xyz;
int idx;
center = vec_zero();
if (sel_get_count(sel) == 0)
return (center);
sel_iter_start(sel);
while (sel_iter_next(sel, &idx)) {
xyz = sys_get_atom_xyz(sys, idx);
center = vec_add(¢er, &xyz);
}
vec_scale(¢er, 1.0 / sel_get_count(sel));
return (center);
}
void
sys_reset_bonds(struct sys *sys)
{
struct pair pair;
struct spi *spi;
int i, j, k, n, np;
n = sys_get_atom_count(sys);
spi = spi_create();
for (i = 0; i < n; i++) {
graph_remove_vertex_edges(sys->graph, i);
spi_add_point(spi, sys_get_atom_xyz(sys, i));
}
spi_compute(spi, 1.6);
np = spi_get_pair_count(spi);
for (k = 0; k < np; k++) {
pair = spi_get_pair(spi, k);
i = pair.i;
j = pair.j;
/* No bond between two Hydrogen atoms */
if (sys_get_atom_type(sys, i) == 1 &&
sys_get_atom_type(sys, j) == 1)
continue;
if (graph_edge_find(sys->graph, i, j) == NULL)
graph_edge_create(sys->graph, i, j, 1);
}
for (i = 0; i < n; i++) {
/* Double bond for Oxygen */
if (sys_get_atom_type(sys, i) == 8 &&
graph_get_edge_count(sys->graph, i) == 1)
graph_edge_set_type(graph_get_edges(sys->graph, i), 2);
}
spi_free(spi);
}
int
sys_save_to_file(struct sys *sys, const char *path)
{
int rc;
if ((rc = formats_save(sys->atoms, path)))
sys->is_modified = 0;
return (rc);
}