int colvarproxy_namd::load_atoms(char const *pdb_filename,
cvm::atom_group &atoms,
std::string const &pdb_field_str,
double const pdb_field_value)
{
if (pdb_field_str.size() == 0)
cvm::error("Error: must define which PDB field to use "
"in order to define atoms from a PDB file.\n", INPUT_ERROR);
PDB *pdb = new PDB(pdb_filename);
size_t const pdb_natoms = pdb->num_atoms();
e_pdb_field pdb_field_index = pdb_field_str2enum(pdb_field_str);
for (size_t ipdb = 0; ipdb < pdb_natoms; ipdb++) {
double atom_pdb_field_value = 0.0;
switch (pdb_field_index) {
case e_pdb_occ:
atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
break;
case e_pdb_beta:
atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
break;
case e_pdb_x:
atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
break;
case e_pdb_y:
atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
break;
case e_pdb_z:
atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
break;
default:
break;
}
if ( (pdb_field_value) &&
(atom_pdb_field_value != pdb_field_value) ) {
continue;
} else if (atom_pdb_field_value == 0.0) {
continue;
}
if (atoms.is_enabled(colvardeps::f_ag_scalable)) {
atoms.add_atom_id(ipdb);
} else {
atoms.add_atom(cvm::atom(ipdb+1));
}
}
delete pdb;
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
int colvarproxy_namd::load_coords(char const *pdb_filename,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field_str,
double const pdb_field_value)
{
if (pdb_field_str.size() == 0 && indices.size() == 0) {
cvm::error("Bug alert: either PDB field should be defined or list of "
"atom IDs should be available when loading atom coordinates!\n", BUG_ERROR);
}
e_pdb_field pdb_field_index;
bool const use_pdb_field = (pdb_field_str.size() > 0);
if (use_pdb_field) {
pdb_field_index = pdb_field_str2enum(pdb_field_str);
}
// next index to be looked up in PDB file (if list is supplied)
std::vector<int>::const_iterator current_index = indices.begin();
PDB *pdb = new PDB(pdb_filename);
size_t const pdb_natoms = pdb->num_atoms();
if (pos.size() != pdb_natoms) {
bool const pos_allocated = (pos.size() > 0);
size_t ipos = 0, ipdb = 0;
for ( ; ipdb < pdb_natoms; ipdb++) {
if (use_pdb_field) {
// PDB field mode: skip atoms with wrong value in PDB field
double atom_pdb_field_value = 0.0;
switch (pdb_field_index) {
case e_pdb_occ:
atom_pdb_field_value = (pdb->atom(ipdb))->occupancy();
break;
case e_pdb_beta:
atom_pdb_field_value = (pdb->atom(ipdb))->temperaturefactor();
break;
case e_pdb_x:
atom_pdb_field_value = (pdb->atom(ipdb))->xcoor();
break;
case e_pdb_y:
atom_pdb_field_value = (pdb->atom(ipdb))->ycoor();
break;
case e_pdb_z:
atom_pdb_field_value = (pdb->atom(ipdb))->zcoor();
break;
default:
break;
}
if ( (pdb_field_value) &&
(atom_pdb_field_value != pdb_field_value) ) {
continue;
} else if (atom_pdb_field_value == 0.0) {
continue;
}
} else {
// Atom ID mode: use predefined atom IDs from the atom group
if (((int) ipdb) != *current_index) {
// Skip atoms not in the list
continue;
} else {
current_index++;
}
}
if (!pos_allocated) {
pos.push_back(cvm::atom_pos(0.0, 0.0, 0.0));
} else if (ipos >= pos.size()) {
cvm::error("Error: the PDB file \""+
std::string(pdb_filename)+
"\" contains coordinates for "
"more atoms than needed.\n", BUG_ERROR);
}
pos[ipos] = cvm::atom_pos((pdb->atom(ipdb))->xcoor(),
(pdb->atom(ipdb))->ycoor(),
(pdb->atom(ipdb))->zcoor());
ipos++;
if (!use_pdb_field && current_index == indices.end())
break;
}
if (ipos < pos.size() || (!use_pdb_field && current_index != indices.end())) {
size_t n_requested = use_pdb_field ? pos.size() : indices.size();
cvm::error("Error: number of matching records in the PDB file \""+
std::string(pdb_filename)+"\" ("+cvm::to_str(ipos)+
") does not match the number of requested coordinates ("+
cvm::to_str(n_requested)+").\n", INPUT_ERROR);
return COLVARS_ERROR;
}
} else {
// when the PDB contains exactly the number of atoms of the array,
// ignore the fields and just read coordinates
for (size_t ia = 0; ia < pos.size(); ia++) {
pos[ia] = cvm::atom_pos((pdb->atom(ia))->xcoor(),
(pdb->atom(ia))->ycoor(),
(pdb->atom(ia))->zcoor());
}
}
delete pdb;
return COLVARS_OK;
}
