void read_ff_json(const char *json_file, struct atomgrp *ag)
{
json_error_t json_file_error;
json_t *base = json_load_file(json_file, 0, &json_file_error);
if (!base) {
fprintf(stderr,
"error reading json file %s on line %d column %d: %s\n",
json_file, json_file_error.line, json_file_error.column,
json_file_error.text);
}
if (!json_is_object(base)) {
fprintf(stderr, "json file not an object %s\n", json_file);
}
json_t *atoms, *bonds, *angles, *torsions, *impropers;
atoms = json_object_get(base, "atoms");
if (!json_is_array(atoms)) {
fprintf(stderr, "json atoms are not an array %s\n", json_file);
}
size_t natoms = json_array_size(atoms);
if (natoms != (size_t) ag->natoms) {
fprintf(stderr,
"json file has a different number of atoms %zd vs. %d : %s\n",
natoms, ag->natoms, json_file);
}
ag->num_atom_types = 0;
for (size_t i = 0; i < natoms; i++) {
json_t *atom = json_array_get(atoms, i);
if (!json_is_object(atom)) {
fprintf(stderr,
"Atom %zd not an object in json file %s\n", i,
json_file);
}
json_t *ace_volume, *ftype_index, *ftype_name, *eps03;
json_t *name, *radius03, *eps;
json_t *charge, *radius, *element;
ace_volume = json_object_get(atom, "ace_volume");
if (!json_is_real(ace_volume)) {
fprintf(stderr,
"json ace volume is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acevolume = json_real_value(ace_volume);
ftype_index = json_object_get(atom, "ftype_index");
if (!json_is_integer(ftype_index)) {
fprintf(stderr,
"json ftype index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].atom_ftypen = json_integer_value(ftype_index);
if (ag->atoms[i].atom_ftypen > ag->num_atom_types) {
ag->num_atom_types = ag->atoms[i].atom_ftypen;
}
ftype_name = json_object_get(atom, "ftype_name");
if (!json_is_string(ftype_name)) {
fprintf(stderr,
"json ftype name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].ftype_name = strdup(json_string_value(ftype_name));
element = json_object_get(atom, "element");
if (!json_is_string(element)) {
fprintf(stderr,
"json element name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].element = strdup(json_string_value(element));
eps = json_object_get(atom, "eps");
if (!json_is_real(eps)) {
fprintf(stderr,
"json eps is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps = sqrt(-json_real_value(eps));
eps03 = json_object_get(atom, "eps03");
if (!json_is_real(eps03)) {
fprintf(stderr,
"json eps03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps03 = sqrt(-json_real_value(eps03));
radius = json_object_get(atom, "radius");
if (!json_is_real(radius)) {
fprintf(stderr,
"json radius is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh = json_real_value(radius);
radius03 = json_object_get(atom, "radius03");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json radius03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh03 = json_real_value(radius03);
charge = json_object_get(atom, "charge");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json charge is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].chrg = json_real_value(charge);
name = json_object_get(atom, "name");
if (!json_is_string(name)) {
fprintf(stderr,
"json name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].name = strdup(json_string_value(name));
ag->atoms[i].nbonds = 0;
ag->atoms[i].nangs = 0;
ag->atoms[i].ntors = 0;
ag->atoms[i].nimps = 0;
ag->atoms[i].fixed = 0;
}
bonds = json_object_get(base, "bonds");
if (!json_is_array(bonds)) {
fprintf(stderr, "json bonds are not an array %s\n", json_file);
}
size_t nbonds = json_array_size(bonds);
ag->nbonds = nbonds;
ag->bonds = _mol_calloc(nbonds, sizeof(struct atombond));
for (size_t i = 0; i < nbonds; i++) {
json_t *bond = json_array_get(bonds, i);
if (!json_is_object(bond)) {
fprintf(stderr,
"Bond %zd not an object in json file %s\n", i,
json_file);
}
json_t *length, *atom1, *atom2, *spring_constant, *sdf_type;
atom1 = json_object_get(bond, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->bonds[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nbonds)++;
atom2 = json_object_get(bond, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->bonds[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nbonds)++;
length = json_object_get(bond, "length");
if (!json_is_real(length)) {
fprintf(stderr,
"json length is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].l0 = json_real_value(length);
spring_constant = json_object_get(bond, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].k = json_real_value(spring_constant);
sdf_type = json_object_get(bond, "sdf_type");
if (!json_is_integer(sdf_type)) {
fprintf(stderr,
"json sdf_type is not integer for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].sdf_type = json_integer_value(sdf_type);
}
angles = json_object_get(base, "angles");
if (!json_is_array(angles)) {
fprintf(stderr, "json angles are not an array %s\n", json_file);
}
size_t nangles = json_array_size(angles);
ag->nangs = nangles;
ag->angs = _mol_calloc(nangles, sizeof(struct atomangle));
for (size_t i = 0; i < nangles; i++) {
json_t *angle = json_array_get(angles, i);
if (!json_is_object(angle)) {
fprintf(stderr,
"Angle %zd not an object in json file %s\n", i,
json_file);
}
json_t *theta, *atom1, *atom2, *atom3, *spring_constant;
atom1 = json_object_get(angle, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->angs[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nangs)++;
atom2 = json_object_get(angle, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->angs[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nangs)++;
atom3 = json_object_get(angle, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->angs[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nangs)++;
theta = json_object_get(angle, "theta");
if (!json_is_real(theta)) {
fprintf(stderr,
"json theta is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].th0 = json_real_value(theta);
spring_constant = json_object_get(angle, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].k = json_real_value(spring_constant);
}
torsions = json_object_get(base, "torsions");
if (!json_is_array(torsions)) {
fprintf(stderr, "json torsions are not an array %s\n",
json_file);
}
size_t ntorsions = json_array_size(torsions);
ag->ntors = ntorsions;
ag->tors = _mol_calloc(ntorsions, sizeof(struct atomtorsion));
for (size_t i = 0; i < ntorsions; i++) {
json_t *torsion = json_array_get(torsions, i);
if (!json_is_object(torsion)) {
fprintf(stderr,
"Torsion %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *minima, *delta_constant,
*spring_constant;
atom1 = json_object_get(torsion, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->tors[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].ntors)++;
atom2 = json_object_get(torsion, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->tors[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].ntors)++;
atom3 = json_object_get(torsion, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->tors[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].ntors)++;
atom4 = json_object_get(torsion, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->tors[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].ntors)++;
minima = json_object_get(torsion, "minima");
if (!json_is_integer(minima)) {
fprintf(stderr,
"json minima is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].n = json_integer_value(minima);
delta_constant = json_object_get(torsion, "delta_constant");
if (!json_is_real(delta_constant)) {
fprintf(stderr,
"json delta_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].d = json_real_value(delta_constant);
spring_constant = json_object_get(torsion, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].k = json_real_value(spring_constant);
}
impropers = json_object_get(base, "impropers");
if (!json_is_array(impropers)) {
fprintf(stderr, "json impropers are not an array %s\n",
json_file);
}
size_t nimpropers = json_array_size(impropers);
ag->nimps = nimpropers;
ag->imps = _mol_calloc(nimpropers, sizeof(struct atomimproper));
for (size_t i = 0; i < nimpropers; i++) {
json_t *improper = json_array_get(impropers, i);
if (!json_is_object(improper)) {
fprintf(stderr,
"Improper %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *phi, *spring_constant;
atom1 = json_object_get(improper, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->imps[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nimps)++;
atom2 = json_object_get(improper, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->imps[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nimps)++;
atom3 = json_object_get(improper, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->imps[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nimps)++;
atom4 = json_object_get(improper, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->imps[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].nimps)++;
phi = json_object_get(improper, "phi");
if (!json_is_real(phi)) {
fprintf(stderr,
"json phi is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].psi0 = json_real_value(phi);
spring_constant = json_object_get(improper, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].k = json_real_value(spring_constant);
}
json_decref(base);
//allocate atom arrays of pointers to parameters
for (size_t i = 0; i < natoms; i++) {
int i1 = ag->atoms[i].nbonds;
ag->atoms[i].bonds = _mol_calloc(i1, sizeof(struct atombond *));
ag->atoms[i].nbonds = 0;
i1 = ag->atoms[i].nangs;
ag->atoms[i].angs = _mol_calloc(i1, sizeof(struct atomangle *));
ag->atoms[i].nangs = 0;
i1 = ag->atoms[i].ntors;
ag->atoms[i].tors =
_mol_calloc(i1, sizeof(struct atomtorsion *));
ag->atoms[i].ntors = 0;
i1 = ag->atoms[i].nimps;
ag->atoms[i].imps =
_mol_calloc(i1, sizeof(struct atomimproper *));
ag->atoms[i].nimps = 0;
}
struct atom *atm;
//fill bonds
for (int i = 0; i < ag->nbonds; i++) {
atm = ag->bonds[i].a0;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
atm = ag->bonds[i].a1;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
}
//fill angles
for (int i = 0; i < ag->nangs; i++) {
atm = ag->angs[i].a0;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a1;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a2;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
}
//fill torsions
for (int i = 0; i < ag->ntors; i++) {
atm = ag->tors[i].a0;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a1;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a2;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a3;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
}
//fill impropers
for (int i = 0; i < ag->nimps; i++) {
atm = ag->imps[i].a0;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a1;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a2;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a3;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
}
//atom indices in the group
fill_ingrp(ag);
ag->is_psf_read = true;
// copy vals from deprecated to new data structures
int atomsi;
for (atomsi = 0; atomsi < ag->natoms; atomsi++) {
_mol_atom_create_bond_indices(&ag->atoms[atomsi],
ag->atoms[atomsi].nbonds);
}
_mol_atom_group_copy_from_deprecated(ag);
}
struct atomgrp *join_rec_lig_ff(struct atomgrp *rec, struct atomgrp *lig)
{
int i;
int j;
struct atomgrp *ag =
(struct atomgrp *)_mol_calloc(1, sizeof(struct atomgrp));
//sum counts
ag->natoms = rec->natoms + lig->natoms;
ag->nbonds = rec->nbonds + lig->nbonds;
ag->nangs = rec->nangs + lig->nangs;
ag->ntors = rec->ntors + lig->ntors;
ag->nimps = rec->nimps + lig->nimps;
ag->num_atom_types = rec->num_atom_types + lig->num_atom_types;
//don't think we need actives yet
//ag->nactives = rec->nactives + lig->nactives;
//ag->nbact = rec->nbact + lig->nbact;
//ag->nangact = rec->nangact + lig->nangact;
//ag->ntoract = rec->ntoract + lig->ntoract;
//ag->nimpact = rec->nimpact + lig->nimpact;
//allocate first level
ag->atoms =
(struct atom *)_mol_malloc(sizeof(struct atom) * ag->natoms);
ag->bonds =
(struct atombond *)_mol_malloc(sizeof(struct atombond) *
ag->nbonds);
ag->angs =
(struct atomangle *)_mol_malloc(sizeof(struct atomangle) *
ag->nangs);
ag->tors =
(struct atomtorsion *)_mol_malloc(sizeof(struct atomtorsion) *
ag->ntors);
ag->imps =
(struct atomimproper *)_mol_malloc(sizeof(struct atomimproper) *
ag->nimps);
//copy rec items
memcpy(ag->atoms, rec->atoms, sizeof(struct atom) * rec->natoms);
memcpy(ag->bonds, rec->bonds, sizeof(struct atombond) * rec->nbonds);
memcpy(ag->angs, rec->angs, sizeof(struct atomangle) * rec->nangs);
memcpy(ag->tors, rec->tors, sizeof(struct atomtorsion) * rec->ntors);
memcpy(ag->imps, rec->imps, sizeof(struct atomimproper) * rec->nimps);
//point to correct atoms
for (i = 0; i < rec->nbonds; i++) {
ptrdiff_t a0_offset = ag->bonds[i].a0 - rec->atoms;
ptrdiff_t a1_offset = ag->bonds[i].a1 - rec->atoms;
ag->bonds[i].a0 = ag->atoms + a0_offset;
ag->bonds[i].a1 = ag->atoms + a1_offset;
}
for (i = 0; i < rec->nangs; i++) {
ptrdiff_t a0_offset = ag->angs[i].a0 - rec->atoms;
ptrdiff_t a1_offset = ag->angs[i].a1 - rec->atoms;
ptrdiff_t a2_offset = ag->angs[i].a2 - rec->atoms;
ag->angs[i].a0 = ag->atoms + a0_offset;
ag->angs[i].a1 = ag->atoms + a1_offset;
ag->angs[i].a2 = ag->atoms + a2_offset;
}
for (i = 0; i < rec->ntors; i++) {
ptrdiff_t a0_offset = ag->tors[i].a0 - rec->atoms;
ptrdiff_t a1_offset = ag->tors[i].a1 - rec->atoms;
ptrdiff_t a2_offset = ag->tors[i].a2 - rec->atoms;
ptrdiff_t a3_offset = ag->tors[i].a3 - rec->atoms;
ag->tors[i].a0 = ag->atoms + a0_offset;
ag->tors[i].a1 = ag->atoms + a1_offset;
ag->tors[i].a2 = ag->atoms + a2_offset;
ag->tors[i].a3 = ag->atoms + a3_offset;
}
for (i = 0; i < rec->nimps; i++) {
ptrdiff_t a0_offset = ag->imps[i].a0 - rec->atoms;
ptrdiff_t a1_offset = ag->imps[i].a1 - rec->atoms;
ptrdiff_t a2_offset = ag->imps[i].a2 - rec->atoms;
ptrdiff_t a3_offset = ag->imps[i].a3 - rec->atoms;
ag->imps[i].a0 = ag->atoms + a0_offset;
ag->imps[i].a1 = ag->atoms + a1_offset;
ag->imps[i].a2 = ag->atoms + a2_offset;
ag->imps[i].a3 = ag->atoms + a3_offset;
}
//point to atoms to correct bonds, angs, tors, imps
for (i = 0; i < rec->natoms; i++) {
ag->atoms[i].name = strdup(rec->atoms[i].name);
if (rec->atoms[i].residue_name != NULL) {
ag->atoms[i].residue_name = strdup(rec->atoms[i].residue_name);
}
ag->atoms[i].ftype_name = strdup(rec->atoms[i].ftype_name);
ag->atoms[i].bonds =
_mol_malloc(rec->atoms[i].nbonds *
sizeof(struct atombond *));
memcpy(ag->atoms[i].bonds, rec->atoms[i].bonds,
sizeof(struct atombond *) * rec->atoms[i].nbonds);
for (j = 0; j < ag->atoms[i].nbonds; j++) {
ptrdiff_t bond_offset =
ag->atoms[i].bonds[j] - rec->bonds;
ag->atoms[i].bonds[j] = ag->bonds + bond_offset;
}
ag->atoms[i].angs =
_mol_malloc(rec->atoms[i].nangs *
sizeof(struct atomangle *));
memcpy(ag->atoms[i].angs, rec->atoms[i].angs,
sizeof(struct atomangle *) * rec->atoms[i].nangs);
for (j = 0; j < ag->atoms[i].nangs; j++) {
ptrdiff_t ang_offset = ag->atoms[i].angs[j] - rec->angs;
ag->atoms[i].angs[j] = ag->angs + ang_offset;
}
ag->atoms[i].tors =
_mol_malloc(rec->atoms[i].ntors *
sizeof(struct atomtorsion *));
memcpy(ag->atoms[i].tors, rec->atoms[i].tors,
sizeof(struct atomtorsion *) * rec->atoms[i].ntors);
for (j = 0; j < ag->atoms[i].ntors; j++) {
ptrdiff_t tor_offset = ag->atoms[i].tors[j] - rec->tors;
ag->atoms[i].tors[j] = ag->tors + tor_offset;
}
ag->atoms[i].imps =
_mol_malloc(rec->atoms[i].nimps *
sizeof(struct atomimproper *));
memcpy(ag->atoms[i].imps, rec->atoms[i].imps,
sizeof(struct atomimproper *) * rec->atoms[i].nimps);
for (j = 0; j < ag->atoms[i].nimps; j++) {
ptrdiff_t imp_offset = ag->atoms[i].imps[j] - rec->imps;
ag->atoms[i].imps[j] = ag->imps + imp_offset;
}
}
//copy lig items
memcpy(ag->atoms + rec->natoms, lig->atoms,
sizeof(struct atom) * lig->natoms);
memcpy(ag->bonds + rec->nbonds, lig->bonds,
sizeof(struct atombond) * lig->nbonds);
memcpy(ag->angs + rec->nangs, lig->angs,
sizeof(struct atomangle) * lig->nangs);
memcpy(ag->tors + rec->ntors, lig->tors,
sizeof(struct atomtorsion) * lig->ntors);
memcpy(ag->imps + rec->nimps, lig->imps,
sizeof(struct atomimproper) * lig->nimps);
//point to correct atoms
struct atom *newlig_atoms = ag->atoms + rec->natoms;
for (i = rec->nbonds; i < ag->nbonds; i++) {
ptrdiff_t a0_offset = ag->bonds[i].a0 - lig->atoms;
ptrdiff_t a1_offset = ag->bonds[i].a1 - lig->atoms;
ag->bonds[i].a0 = newlig_atoms + a0_offset;
ag->bonds[i].a1 = newlig_atoms + a1_offset;
ag->bonds[i].ai += rec->natoms;
ag->bonds[i].aj += rec->natoms;
}
for (i = rec->nangs; i < ag->nangs; i++) {
ptrdiff_t a0_offset = ag->angs[i].a0 - lig->atoms;
ptrdiff_t a1_offset = ag->angs[i].a1 - lig->atoms;
ptrdiff_t a2_offset = ag->angs[i].a2 - lig->atoms;
ag->angs[i].a0 = newlig_atoms + a0_offset;
ag->angs[i].a1 = newlig_atoms + a1_offset;
ag->angs[i].a2 = newlig_atoms + a2_offset;
}
for (i = rec->ntors; i < ag->ntors; i++) {
ptrdiff_t a0_offset = ag->tors[i].a0 - lig->atoms;
ptrdiff_t a1_offset = ag->tors[i].a1 - lig->atoms;
ptrdiff_t a2_offset = ag->tors[i].a2 - lig->atoms;
ptrdiff_t a3_offset = ag->tors[i].a3 - lig->atoms;
ag->tors[i].a0 = newlig_atoms + a0_offset;
ag->tors[i].a1 = newlig_atoms + a1_offset;
ag->tors[i].a2 = newlig_atoms + a2_offset;
ag->tors[i].a3 = newlig_atoms + a3_offset;
}
for (i = rec->nimps; i < ag->nimps; i++) {
ptrdiff_t a0_offset = ag->imps[i].a0 - lig->atoms;
ptrdiff_t a1_offset = ag->imps[i].a1 - lig->atoms;
ptrdiff_t a2_offset = ag->imps[i].a2 - lig->atoms;
ptrdiff_t a3_offset = ag->imps[i].a3 - lig->atoms;
ag->imps[i].a0 = newlig_atoms + a0_offset;
ag->imps[i].a1 = newlig_atoms + a1_offset;
ag->imps[i].a2 = newlig_atoms + a2_offset;
ag->imps[i].a3 = newlig_atoms + a3_offset;
}
int max_rec_res_seq = rec->atoms[rec->natoms-1].comb_res_seq;
//point to atoms to correct bonds, angs, tors, imps
struct atombond *newlig_bonds = ag->bonds + rec->nbonds;
struct atomangle *newlig_angs = ag->angs + rec->nangs;
struct atomtorsion *newlig_tors = ag->tors + rec->ntors;
struct atomimproper *newlig_imps = ag->imps + rec->nimps;
for (i = rec->natoms; i < ag->natoms; i++) {
// struct atom local_atom = ag->atoms[i];
ag->atoms[i].comb_res_seq += 100 + max_rec_res_seq;
ag->atoms[i].atom_ftypen += rec->num_atom_types;
ag->atoms[i].name = strdup(lig->atoms[i - (rec->natoms)].name);
if (lig->atoms[i - (rec->natoms)].residue_name != NULL) {
ag->atoms[i].residue_name =
strdup(lig->atoms[i - (rec->natoms)].residue_name);
}
ag->atoms[i].ftype_name =
strdup(lig->atoms[i - (rec->natoms)].ftype_name);
ag->atoms[i].bonds =
_mol_malloc(lig->atoms[i - (rec->natoms)].nbonds *
sizeof(struct atombond *));
memcpy(ag->atoms[i].bonds, lig->atoms[i - (rec->natoms)].bonds,
sizeof(struct atombond *) * lig->atoms[i -
(rec->natoms)].
nbonds);
for (j = 0; j < ag->atoms[i].nbonds; j++) {
ptrdiff_t bond_offset =
ag->atoms[i].bonds[j] - lig->bonds;
ag->atoms[i].bonds[j] = newlig_bonds + bond_offset;
}
ag->atoms[i].angs =
_mol_malloc(lig->atoms[i - (rec->natoms)].nangs *
sizeof(struct atomangle *));
memcpy(ag->atoms[i].angs, lig->atoms[i - (rec->natoms)].angs,
sizeof(struct atomangle *) * lig->atoms[i -
(rec->natoms)].
nangs);
for (j = 0; j < ag->atoms[i].nangs; j++) {
ptrdiff_t ang_offset = ag->atoms[i].angs[j] - lig->angs;
ag->atoms[i].angs[j] = newlig_angs + ang_offset;
}
ag->atoms[i].tors =
_mol_malloc(lig->atoms[i - (rec->natoms)].ntors *
sizeof(struct atomtorsion *));
memcpy(ag->atoms[i].tors, lig->atoms[i - (rec->natoms)].tors,
sizeof(struct atomtorsion *) * lig->atoms[i -
(rec->natoms)].
ntors);
for (j = 0; j < ag->atoms[i].ntors; j++) {
ptrdiff_t tor_offset = ag->atoms[i].tors[j] - lig->tors;
ag->atoms[i].tors[j] = newlig_tors + tor_offset;
}
ag->atoms[i].imps =
_mol_malloc(lig->atoms[i - (rec->natoms)].nimps *
sizeof(struct atomimproper *));
memcpy(ag->atoms[i].imps, lig->atoms[i - (rec->natoms)].imps,
sizeof(struct atomimproper *) * lig->atoms[i -
(rec->
natoms)].
nimps);
for (j = 0; j < ag->atoms[i].nimps; j++) {
ptrdiff_t imp_offset = ag->atoms[i].imps[j] - lig->imps;
ag->atoms[i].imps[j] = newlig_imps + imp_offset;
}
}
//copy into ryan's structure
// _mol_atom_group_copy_from_deprecated(ag);
fill_ingrp(ag);
return ag;
}
struct atomgrp *read_json_ag(const char *json_file)
{
struct atomgrp *ag =
(struct atomgrp *)_mol_calloc(1, sizeof(struct atomgrp));
json_error_t json_file_error;
json_t *base = json_load_file(json_file, 0, &json_file_error);
if (!base) {
fprintf(stderr,
"error reading json file %s on line %d column %d: %s\n",
json_file, json_file_error.line, json_file_error.column,
json_file_error.text);
}
if (!json_is_object(base)) {
fprintf(stderr, "json file not an object %s\n", json_file);
}
json_t *atoms, *bonds, *angles, *torsions, *impropers;
atoms = json_object_get(base, "atoms");
if (!json_is_array(atoms)) {
fprintf(stderr, "json atoms are not an array %s\n", json_file);
}
size_t natoms = json_array_size(atoms);
ag->natoms = natoms;
ag->atoms = (struct atom *)_mol_calloc(ag->natoms, sizeof(struct atom));
ag->num_atom_types = 0;
char *prev_segment = _mol_calloc(1, sizeof(char));
char *prev_residue = _mol_calloc(1, sizeof(char));
int prev_residue_seq = -107;
ag->nres = 0;
int alloc_res = 250;
ag->iares = _mol_malloc(alloc_res*sizeof(int));
for (size_t i = 0; i < natoms; i++) {
json_t *atom = json_array_get(atoms, i);
if (!json_is_object(atom)) {
fprintf(stderr,
"Atom %zd not an object in json file %s\n", i,
json_file);
}
json_t *ace_volume, *ftype_index, *ftype_name, *eps03;
json_t *name, *radius03, *eps, *acp_type, *residue_name;
json_t *charge, *radius, *element;
json_t *x, *y, *z;
json_t *yeti_type, *sybyl_type;
json_t *backbone, *hb_acceptor, *hb_donor, *hb_weight;
json_t *segment, *residue;
segment = json_object_get(atom, "segment");
residue = json_object_get(atom, "residue");
if ((segment != NULL) && (residue != NULL)) {
if (!json_is_string(segment)) {
fprintf(stderr,
"json segment is not string for atom %zd in json_file %s\n",
i, json_file);
}
if (!json_is_string(residue)) {
fprintf(stderr,
"json residue is not string for atom %zd in json_file %s\n",
i, json_file);
}
const char *cur_segment = json_string_value(segment);
const char *cur_residue = json_string_value(residue);
if (strcmp(cur_segment, prev_segment) != 0) {
prev_residue_seq += 100;
free(prev_segment);
prev_segment = strdup(cur_segment);
}
if (strcmp(cur_residue, prev_residue) != 0) {
int cur_residue_int = atoi(cur_residue);
int prev_residue_int = atoi(prev_residue);
if ((cur_residue_int - prev_residue_int) > 1) {
prev_residue_seq +=
(cur_residue_int -
prev_residue_int);
} else {
prev_residue_seq += 1;
}
free(prev_residue);
prev_residue = strdup(cur_residue);
if (ag->nres +1 == alloc_res) {
alloc_res *= 2;
ag->iares = _mol_realloc(ag->iares, alloc_res * i);
}
ag->iares[ag->nres] = i;
ag->nres++;
}
ag->atoms[i].comb_res_seq = prev_residue_seq;
} else {
ag->atoms[i].comb_res_seq = prev_residue_seq;
}
ace_volume = json_object_get(atom, "ace_volume");
if (!json_is_real(ace_volume)) {
fprintf(stderr,
"json ace volume is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acevolume = json_real_value(ace_volume);
ftype_index = json_object_get(atom, "ftype_index");
if (!json_is_integer(ftype_index)) {
fprintf(stderr,
"json ftype index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].atom_ftypen = json_integer_value(ftype_index);
if (ag->atoms[i].atom_ftypen > ag->num_atom_types) {
ag->num_atom_types = ag->atoms[i].atom_ftypen;
}
ftype_name = json_object_get(atom, "ftype_name");
if (!json_is_string(ftype_name)) {
fprintf(stderr,
"json ftype name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].ftype_name = strdup(json_string_value(ftype_name));
element = json_object_get(atom, "element");
if (!json_is_string(element)) {
fprintf(stderr,
"json element name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].element = strdup(json_string_value(element));
eps = json_object_get(atom, "eps");
if (!json_is_real(eps)) {
fprintf(stderr,
"json eps is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps = sqrt(-json_real_value(eps));
eps03 = json_object_get(atom, "eps03");
if (!json_is_real(eps03)) {
fprintf(stderr,
"json eps03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].eps03 = sqrt(-json_real_value(eps03));
radius = json_object_get(atom, "radius");
if (!json_is_real(radius)) {
fprintf(stderr,
"json radius is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh = json_real_value(radius);
radius03 = json_object_get(atom, "radius03");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json radius03 is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].rminh03 = json_real_value(radius03);
charge = json_object_get(atom, "charge");
if (!json_is_real(radius03)) {
fprintf(stderr,
"json charge is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].chrg = json_real_value(charge);
name = json_object_get(atom, "name");
if (!json_is_string(name)) {
fprintf(stderr,
"json name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].name = strdup(json_string_value(name));
residue_name = json_object_get(atom, "residue_name");
if (residue_name != NULL) {
if (!json_is_string(residue_name)) {
fprintf(stderr,
"json residue_name is not string for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].residue_name =
strdup(json_string_value(residue_name));
} else {
ag->atoms[i].residue_name = NULL;
}
x = json_object_get(atom, "x");
if (!json_is_real(x)) {
fprintf(stderr,
"json coordinate x is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].X = json_real_value(x);
y = json_object_get(atom, "y");
if (!json_is_real(y)) {
fprintf(stderr,
"json coordinate y is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].Y = json_real_value(y);
z = json_object_get(atom, "z");
if (!json_is_real(z)) {
fprintf(stderr,
"json coordinate z is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].Z = json_real_value(z);
acp_type = json_object_get(atom, "acp_type");
if (acp_type != NULL) {
if (!json_is_integer(acp_type)) {
fprintf(stderr,
"json acp_type index is not integer for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].acp_type = json_integer_value(acp_type);
} else {
ag->atoms[i].acp_type = -1;
}
yeti_type = json_object_get(atom, "yeti_type");
if (yeti_type != NULL) {
const char *yeti_type_string;
if (!json_is_string(yeti_type)) {
fprintf(stderr,
"json yeti_type is not string for atom %zd in json_file %s\n",
i, json_file);
}
yeti_type_string = json_string_value(yeti_type);
if (strcmp("carbonyl", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_CARBONYL;
} else if (strcmp("hydroxyl", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_HYDROXYL;
} else if (strcmp("sulfonamide", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_SULFONAMIDE;
} else if (strcmp("N5_aromatic", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_N5_AROMATIC;
} else if (strcmp("N6_aromatic", yeti_type_string) == 0) {
ag->atoms[i].yeti_type = MOL_YETI_N6_AROMATIC;
} else {
fprintf(stderr,
"unknown json yeti_type %s for atom %zd in json_file %s\n",
yeti_type_string, i, json_file);
ag->atoms[i].yeti_type = MOL_YETI_NONE;
}
} else {
ag->atoms[i].yeti_type = MOL_YETI_NONE;
}
sybyl_type = json_object_get(atom, "sybyl_type");
if (sybyl_type != NULL) {
const char *sybyl_type_string;
if (!json_is_string(sybyl_type)) {
fprintf(stderr,
"json sybyl_type is not string for atom %zd in json_file %s\n",
i, json_file);
}
sybyl_type_string = json_string_value(sybyl_type);
ag->atoms[i].hybridization =
mol_hydridization_from_sybyl(sybyl_type_string);
} else {
ag->atoms[i].hybridization = UNKNOWN_HYBRID;
}
backbone = json_object_get(atom, "backbone");
if (backbone != NULL) {
if (!json_is_boolean(backbone)) {
fprintf(stderr,
"json backbone is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].backbone = json_is_true(backbone);
} else {
ag->atoms[i].backbone = false;
}
ag->atoms[i].hprop = 0;
hb_acceptor = json_object_get(atom, "hb_acceptor");
if (hb_acceptor != NULL) {
if (!json_is_boolean(hb_acceptor)) {
fprintf(stderr,
"json hb_acceptor is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
if (json_is_true(hb_acceptor)) {
ag->atoms[i].hprop |= HBOND_ACCEPTOR;
}
}
hb_donor = json_object_get(atom, "hb_donor");
if (hb_donor != NULL) {
if (!json_is_boolean(hb_donor)) {
fprintf(stderr,
"json hb_donor is not boolean for atom %zd in json_file %s\n",
i, json_file);
}
if (json_is_true(hb_donor)) {
ag->atoms[i].hprop |= DONATABLE_HYDROGEN;
}
}
ag->atoms[i].hbond_weight = 1.0;
hb_weight = json_object_get(atom, "hb_weight");
if (hb_weight != NULL) {
if (!json_is_real(hb_weight)) {
fprintf(stderr,
"json hb_weight is not floating point for atom %zd in json_file %s\n",
i, json_file);
}
ag->atoms[i].hbond_weight = json_real_value(hb_weight);
}
ag->atoms[i].nbonds = 0;
ag->atoms[i].nangs = 0;
ag->atoms[i].ntors = 0;
ag->atoms[i].nimps = 0;
ag->atoms[i].fixed = 0;
ag->atoms[i].sa = -1;
ag->atoms[i].base = -1;
ag->atoms[i].base2 = -1;
}
ag->iares[ag->nres] = ag->natoms;
ag->iares = _mol_realloc(ag->iares, (ag->nres+1) * sizeof(int));
free(prev_segment);
free(prev_residue);
bonds = json_object_get(base, "bonds");
if (!json_is_array(bonds)) {
fprintf(stderr, "json bonds are not an array %s\n", json_file);
}
size_t nbonds = json_array_size(bonds);
ag->nbonds = nbonds;
ag->bonds = _mol_calloc(nbonds, sizeof(struct atombond));
for (size_t i = 0; i < nbonds; i++) {
json_t *bond = json_array_get(bonds, i);
if (!json_is_object(bond)) {
fprintf(stderr,
"Bond %zd not an object in json file %s\n", i,
json_file);
}
json_t *length, *atom1, *atom2, *spring_constant, *sdf_type;
atom1 = json_object_get(bond, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->bonds[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nbonds)++;
atom2 = json_object_get(bond, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for bond %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->bonds[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nbonds)++;
length = json_object_get(bond, "length");
if (!json_is_real(length)) {
fprintf(stderr,
"json length is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].l0 = json_real_value(length);
spring_constant = json_object_get(bond, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].k = json_real_value(spring_constant);
sdf_type = json_object_get(bond, "sdf_type");
if (sdf_type != NULL) {
if (!json_is_integer(sdf_type)) {
fprintf(stderr,
"json sdf_type is not integer for bond %zd in json_file %s\n",
i, json_file);
}
ag->bonds[i].sdf_type = json_integer_value(sdf_type);
} else {
ag->bonds[i].sdf_type = 0;
}
}
angles = json_object_get(base, "angles");
if (!json_is_array(angles)) {
fprintf(stderr, "json angles are not an array %s\n", json_file);
}
size_t nangles = json_array_size(angles);
ag->nangs = nangles;
ag->angs = _mol_calloc(nangles, sizeof(struct atomangle));
for (size_t i = 0; i < nangles; i++) {
json_t *angle = json_array_get(angles, i);
if (!json_is_object(angle)) {
fprintf(stderr,
"Angle %zd not an object in json file %s\n", i,
json_file);
}
json_t *theta, *atom1, *atom2, *atom3, *spring_constant;
atom1 = json_object_get(angle, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->angs[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nangs)++;
atom2 = json_object_get(angle, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->angs[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nangs)++;
atom3 = json_object_get(angle, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for angle %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->angs[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nangs)++;
theta = json_object_get(angle, "theta");
if (!json_is_real(theta)) {
fprintf(stderr,
"json theta is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].th0 = json_real_value(theta);
spring_constant = json_object_get(angle, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for angle %zd in json_file %s\n",
i, json_file);
}
ag->angs[i].k = json_real_value(spring_constant);
}
torsions = json_object_get(base, "torsions");
if (!json_is_array(torsions)) {
fprintf(stderr, "json torsions are not an array %s\n",
json_file);
}
size_t ntorsions = json_array_size(torsions);
ag->ntors = ntorsions;
ag->tors = _mol_calloc(ntorsions, sizeof(struct atomtorsion));
for (size_t i = 0; i < ntorsions; i++) {
json_t *torsion = json_array_get(torsions, i);
if (!json_is_object(torsion)) {
fprintf(stderr,
"Torsion %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *minima, *delta_constant,
*spring_constant;
atom1 = json_object_get(torsion, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->tors[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].ntors)++;
atom2 = json_object_get(torsion, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->tors[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].ntors)++;
atom3 = json_object_get(torsion, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->tors[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].ntors)++;
atom4 = json_object_get(torsion, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->tors[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].ntors)++;
minima = json_object_get(torsion, "minima");
if (!json_is_integer(minima)) {
fprintf(stderr,
"json minima is not integer for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].n = json_integer_value(minima);
delta_constant = json_object_get(torsion, "delta_constant");
if (!json_is_real(delta_constant)) {
fprintf(stderr,
"json delta_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].d = json_real_value(delta_constant);
spring_constant = json_object_get(torsion, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for torsion %zd in json_file %s\n",
i, json_file);
}
ag->tors[i].k = json_real_value(spring_constant);
}
impropers = json_object_get(base, "impropers");
if (!json_is_array(impropers)) {
fprintf(stderr, "json impropers are not an array %s\n",
json_file);
}
size_t nimpropers = json_array_size(impropers);
ag->nimps = nimpropers;
ag->imps = _mol_calloc(nimpropers, sizeof(struct atomimproper));
for (size_t i = 0; i < nimpropers; i++) {
json_t *improper = json_array_get(impropers, i);
if (!json_is_object(improper)) {
fprintf(stderr,
"Improper %zd not an object in json file %s\n",
i, json_file);
}
json_t *atom1, *atom2, *atom3, *atom4, *phi, *spring_constant;
atom1 = json_object_get(improper, "atom1");
if (!json_is_integer(atom1)) {
fprintf(stderr,
"json atom1 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i1 = json_integer_value(atom1) - 1;
ag->imps[i].a0 = &(ag->atoms[i1]);
(ag->atoms[i1].nimps)++;
atom2 = json_object_get(improper, "atom2");
if (!json_is_integer(atom2)) {
fprintf(stderr,
"json atom2 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i2 = json_integer_value(atom2) - 1;
ag->imps[i].a1 = &(ag->atoms[i2]);
(ag->atoms[i2].nimps)++;
atom3 = json_object_get(improper, "atom3");
if (!json_is_integer(atom3)) {
fprintf(stderr,
"json atom3 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i3 = json_integer_value(atom3) - 1;
ag->imps[i].a2 = &(ag->atoms[i3]);
(ag->atoms[i3].nimps)++;
atom4 = json_object_get(improper, "atom4");
if (!json_is_integer(atom4)) {
fprintf(stderr,
"json atom4 is not integer for improper %zd in json_file %s\n",
i, json_file);
}
int i4 = json_integer_value(atom4) - 1;
ag->imps[i].a3 = &(ag->atoms[i4]);
(ag->atoms[i4].nimps)++;
phi = json_object_get(improper, "phi");
if (!json_is_real(phi)) {
fprintf(stderr,
"json phi is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].psi0 = json_real_value(phi);
spring_constant = json_object_get(improper, "spring_constant");
if (!json_is_real(spring_constant)) {
fprintf(stderr,
"json spring_constant is not floating point for improper %zd in json_file %s\n",
i, json_file);
}
ag->imps[i].k = json_real_value(spring_constant);
}
json_decref(base);
//allocate atom arrays of pointers to parameters
for (size_t i = 0; i < natoms; i++) {
int i1 = ag->atoms[i].nbonds;
ag->atoms[i].bonds = _mol_calloc(i1, sizeof(struct atombond *));
ag->atoms[i].nbonds = 0;
i1 = ag->atoms[i].nangs;
ag->atoms[i].angs = _mol_calloc(i1, sizeof(struct atomangle *));
ag->atoms[i].nangs = 0;
i1 = ag->atoms[i].ntors;
ag->atoms[i].tors =
_mol_calloc(i1, sizeof(struct atomtorsion *));
ag->atoms[i].ntors = 0;
i1 = ag->atoms[i].nimps;
ag->atoms[i].imps =
_mol_calloc(i1, sizeof(struct atomimproper *));
ag->atoms[i].nimps = 0;
}
struct atom *atm;
//fill bonds
for (int i = 0; i < ag->nbonds; i++) {
atm = ag->bonds[i].a0;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
atm = ag->bonds[i].a1;
atm->bonds[(atm->nbonds)++] = &(ag->bonds[i]);
}
//fill angles
for (int i = 0; i < ag->nangs; i++) {
atm = ag->angs[i].a0;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a1;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
atm = ag->angs[i].a2;
atm->angs[(atm->nangs)++] = &(ag->angs[i]);
}
//fill torsions
for (int i = 0; i < ag->ntors; i++) {
atm = ag->tors[i].a0;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a1;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a2;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
atm = ag->tors[i].a3;
atm->tors[(atm->ntors)++] = &(ag->tors[i]);
}
//fill impropers
for (int i = 0; i < ag->nimps; i++) {
atm = ag->imps[i].a0;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a1;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a2;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
atm = ag->imps[i].a3;
atm->imps[(atm->nimps)++] = &(ag->imps[i]);
}
//atom indices in the group
fill_ingrp(ag);
ag->is_psf_read = true;
// copy vals from deprecated to new data structures
int atomsi;
for (atomsi = 0; atomsi < ag->natoms; atomsi++) {
_mol_atom_create_bond_indices(&ag->atoms[atomsi],
ag->atoms[atomsi].nbonds);
}
_mol_atom_group_copy_from_deprecated(ag);
return ag;
}
int main(int argc, char* argv[]){
// Input Files //
/* Intro Message */
printf("\n");
printf("A Program to Repack Protein Side-chains for Protein Docking Refinement Procedures\n");
printf("Copyright (c) 2014, Structural Bioinformatics Laboratory, Boston University\n");
printf("Author: Mohammad Moghadasi ([email protected]) \n");
if(argc!=10){
printf("Usage:\n ./main \n Complex_IN.pdb Complex_IN.psf Complex_IN.mol2 Complex_IN_Ligand.pdb\n Libmol-param-file charmm-param-file.prm charmm-rtf-file.rtf rotamer-library-binary-file.txt\n Complex_OUT.pdb\n \n");
exit(EXIT_FAILURE);
}
char* ifile = argv[1]; //pdb file of both receptor and ligand
char* psffile = argv[2]; //charmm type psf file
char* mol2file = argv[3]; //mol2 file
char* pdbfilelig = argv[4]; //pdb file of ligand
char* atom_prm_file = argv[5]; //libmol parameter file
prmfile = argv[6]; //charmm type parameter file
rtffile = argv[7]; //charmm type connectivity file
char* rotamer_library_file = argv[8]; //rotamer raw library file
char* ofile = argv[9]; //output file
// Filling the atom_group struct //
struct prm *atomprm = read_prm(atom_prm_file,_MOL_VERSION_);
struct atomgrp* ag = read_file_atomgrp(ifile, atomprm, -1);
read_ff_charmm(psffile, prmfile, rtffile, ag);
if(!read_hybridization_states_from_mol2(mol2file,ag)){
exit (EXIT_FAILURE);
}
fix_acceptor_bases(ag,atomprm);
struct List lig_list;
read_fix(pdbfilelig,&lig_list.n,&lig_list.K);
fixed_init(ag);
fixed_update_unfreeze_all(ag);
zero_grads(ag);
fill_ingrp(ag);
struct agsetup* ags;
ags = malloc(sizeof(struct agsetup));
init_nblst(ag,ags);
update_nblst(ag,ags);
// Mark interface residues //
int num_of_res_interface;
int res_list_interface[ag->nres];
mark_interface_residues(ag,ags,lig_list, lig_rec_dist ,&num_of_res_interface,res_list_interface);
// Initialize side chain rotamer library //
//nrotCoef = 3;
nrotCoef = 1;
MAX_ROT = 245;
MAX_RES = ag->nres;//needed for full_pack
cutoff = 3;
// Reslist //
struct ifres_list* reslist;
ifres_list_malloc( &reslist );
reslist->num_of_ifres = num_of_res_interface;
for(int r = 0; r < reslist->num_of_ifres ; r++)
reslist->ifres_num[r] = res_list_interface[r];
// Library //
char *rotamer_lib;
load_file_to_memory(rotamer_library_file, &rotamer_lib);
struct rot_info *rotinf;
init_rotinf(ag, num_of_res_interface, res_list_interface, rotamer_lib, &rotinf);
struct ifres_list* reslist_minor;
ifres_list_malloc( &reslist_minor ) ;
// MAIN FUNCITION //
//
clock_t start, finish;
start = clock();
full_pack(ag,lig_list,rotinf,num_of_res_interface, reslist_minor);
finish = clock();
if(0) printf("Processing Time = %f\n",((double)(finish-start)/CLOCKS_PER_SEC));
// Writing the atom_group into a PDB //
write_pdb_traj_nopar(ag,ifile,ofile);
// Free memory //
Free_ifres_list( &reslist_minor );
free(rotamer_lib);
return 0;
}
