void PDBSystem::_ParseMolecules() {
for (Mol_it it = begin_mols(); it != end_mols(); it++)
delete *it;
_mols.clear();
MolPtr pmol = (MolPtr)NULL;
int _currentmol = 0;
for (Atom_it it = begin(); it != end(); it++) {
// then, if the atom's molid is different than the one we were just on, then readjust the current molecule to something else
if ((*it)->MolID() != _currentmol) {
MolPtr newmol;
newmol = molecule::MoleculeFactory ((*it)->Residue());
_currentmol = (*it)->MolID();
newmol->MolID (_currentmol);
newmol->Name ((*it)->Residue());
if (pmol != (MolPtr)NULL) {
_mols.push_back (pmol);
}
pmol = newmol;
}
pmol->AddAtom(*it);
}
} // Parse Molecules
distance_pair BondGraph::ClosestAtom (const MolPtr& mol, const Atom::Element_t elmt) const {
distance_vec distances;
for (Atom_it it = mol->begin(); it != mol->end(); it++) {
distances.push_back ((ClosestAtoms (*it, 1, elmt, false))[0]);
}
pair_utility::pair_sort_first(distances.begin(), distances.end());
return distances[0];
}
/* the mol pointers in the topology file list the beginning and end atoms of each molecule. This function will group all atoms in a molecule, form a molecule object, and add it to the _mols vector
*/
void AmberSystem::_ParseMolecules () {
MolPtr newmol;
// Here we run through each mol pointer, create a new molecule, and add in the appropriate atoms
for (int mol = 0; mol < _topfile.NumMols(); mol++) {
// At each new pointer we create a molecule and start adding in atoms
// if the molecule is of a specific type for which a class has been created, then let's use that!
std::string name = _topfile.MolNames()[mol];
newmol = molecule::MoleculeFactory(name);
newmol->Name(name);
//_mols[mol]->Name (name); // set the molecule's residue name
newmol->MolID(mol);
// Then add all the atoms between the indices of the molpointers in the topology file
int molsize = _topfile.MolSizes()[mol];
int molpointer = _topfile.MolPointers()[mol];
for (int atomCount = 0; atomCount < molsize; atomCount++) {
// sets the index of the current atom that's being added to the molecule
int curAtom = molpointer + atomCount - 1;
// Now we're going to bless this new atom with loads of information about itself and its molecule
newmol->AddAtom( _atoms[curAtom] ); // add the atom into the molecule
}
// lastly, tack it into our running list
_mols.push_back(newmol);
/*
// a topology file doesn't give us the type, so that will be determined when creating the new molecules
if (name == "no3") {
_mols.push_back (new Nitrate());
}
else if (name == "hno3") {
_mols.push_back (new NitricAcid());
}
// we might also have water molecules!
else if (name == "h2o") {
_mols.push_back (new Water());
}
else if (name == "so2" || name == "sog" || name == "soq") {
_mols.push_back (new SulfurDioxide());
}
else if (name == "dec" || name == "pds") {
_mols.push_back (new Decane());
}
// otherwise add on a generic molecule
else {
printf ("AmberSystem::_ParseMolecules() -- Couldn't parse the molecule with name '%s'. Don't know what to do with it\n", name.c_str());
exit(1);
}
*/
}
return;
}
distance_vec BondGraph::ClosestAtoms (const MolPtr mol, const int num, const Atom::Element_t elmt) const {
distance_vec distances;
for (Atom_it atom = mol->begin(); atom != mol->end(); atom++) {
distance_vec closest = ClosestAtoms (*atom, 10, elmt, false);
std::copy (closest.begin(), closest.end(), std::back_inserter(distances));
}
pair_utility::pair_sort_first (distances.begin(), distances.end());
distance_vec::const_iterator it = std::unique(distances.begin(), distances.end(), pair_utility::pair_equal_second_pred<distance_pair>());
distances.resize(it - distances.begin());
pair_utility::pair_sort_first (distances.begin(), distances.end());
distances.resize(num);
return distances;
} // closest Atoms - molecular version
// if given a 2nd molecule, this will merge the current and the new molecules into one larger molecule.
MolPtr Molecule::Merge (MolPtr mol) {
printf ("merging two molecules:\n");
this->Print();
printf ("mol 2---\n");
mol->Print();
// the new molecule's name is yet unknown
_name = "undefined";
_moltype = Molecule::NO_MOLECULE;
for (Atom_it it = mol->begin(); it != mol->end(); it++) {
this->AddAtom (*it);
}
return (this);
}
