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#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/STRUCTURE/rGroupAssembler.h>
using namespace std;
namespace BALL
{
RGroupAssembler::RGroupAssembler(vector<String>& scaffolds, map<String, vector<String> > &rgroups)
{
SmilesParser smiles_parser;
for (Size i = 0; i < scaffolds.size(); i++)
{
smiles_parser.parse(scaffolds[i]);
scaffolds_.push_back( new System(smiles_parser.getSystem()) );
}
map<String, vector<String> >::iterator iter = rgroups.begin();
for (; iter != rgroups.end(); iter++ )
{
vector<String> smiles = iter->second;
for (Size i = 0; i < smiles.size(); i++)
{
smiles_parser.parse(smiles[i]);
System *sys = new System(smiles_parser.getSystem());
moieties_[iter->first].push_back(sys);
}
}
if (scaffolds_.size() == 0 || moieties_.size() == 0)
not_finished_ = false;
else
not_finished_ = true;
initCounter_();
}
RGroupAssembler::RGroupAssembler(String& scaffoldS, map<String, vector<String> > &rgroups)
{
SmilesParser smiles_parser;
smiles_parser.parse(scaffoldS);
System* scaffold = new System(smiles_parser.getSystem());
map<String, vector<String> >::iterator iter = rgroups.begin();
for (; iter != rgroups.end(); iter++ )
{
vector<String> smiles = iter->second;
for (Size i = 0; i < smiles.size(); i++)
{
smiles_parser.parse(smiles[i]);
System *sys = new System(smiles_parser.getSystem());
moieties_[iter->first].push_back(sys);
}
}
scaffolds_.push_back(scaffold);
if (scaffolds_.size() == 0 || moieties_.size() == 0)
not_finished_ = false;
else
not_finished_ = true;
initCounter_();
}
RGroupAssembler::~RGroupAssembler()
{
map<String, vector<System*> >::iterator iter = moieties_.begin();
for (; iter != moieties_.end(); iter++ )
{
vector<System*> sys = iter->second;
for (Size i = 0; i < sys.size(); i++)
{
sys[i]->destroy();
delete sys[i];
}
}
for (Size i = 0; i < scaffolds_.size(); i++)
{
scaffolds_[i]->destroy();
delete scaffolds_[i];
}
}
void RGroupAssembler::initCounter_()
{
moiety_counter_.clear();
maxcounter_.clear();
scaffold_counter_ = 0;
for (map < String, vector < System* > > ::iterator it = moieties_.begin(); it != moieties_.end(); it++)
{
moiety_counter_[it->first] = 0;
for (Size i = 0; i < scaffolds_.size(); i++)
{
map<String, unsigned int> temp_m;
temp_m[it->first] = 0;
maxcounter_.push_back(temp_m);
System s;
if (scaffolds_[i] != NULL)
s = *scaffolds_[i];
else
{
cerr << "scaffold pointer is null" << endl;
exit(1);
}
for (AtomConstIterator atom_it = s.beginAtom(); +atom_it; atom_it++)
{
if (isPlacemark_(atom_it->getName()))
{
if (atom_it->getName() == it->first)
{
maxcounter_[i][it->first] = it->second.size();
}
}
}
}
}
}
bool RGroupAssembler::incrementCounter_()
{
for (map < String, unsigned int > ::iterator it = moiety_counter_.begin(); it != moiety_counter_.end(); it++)
{
it->second++;
if (it->second < maxcounter_[scaffold_counter_][it->first])
{
return true;
}
else
it->second = 0;
}
scaffold_counter_++;
return scaffold_counter_ < scaffolds_.size();
}
bool RGroupAssembler::isPlacemark_(const String& s)
{
// Placemarks begin with 'R' followed by a digit
return (s[0] == 'R' && s.size() >= 2 && isdigit(s[1]));
}
int countHeavyAtoms(const AtomContainer* molecule)
{
int no = 0;
for (AtomConstIterator atom_it = molecule->beginAtom(); +atom_it; atom_it++)
{
if (atom_it->getElement().getSymbol() != "H") no++;
}
return no;
}
void RGroupAssembler::appendMoiety_(AtomContainer* molecule, AtomContainer* moiety, String pm_atom)
{
AtomContainer* moiety_copy = new AtomContainer;
*moiety_copy = *moiety;
molecule->insert(*moiety_copy);
vector<Atom*> conn_atoms;
for (AtomIterator atom_it = molecule->beginAtom(); +atom_it; atom_it++)
{
if (atom_it->getName() == pm_atom)
{
// find placemark atom ..
conn_atoms.push_back(atom_it->beginBond()->getPartner(*atom_it));
// ... and select placemark atom's partner
atom_it->select();
}
else atom_it->deselect();
}
// remove placemark atoms
molecule->removeSelected();
// create bond between both R-atoms
Bond* bnd = conn_atoms[0]->createBond(*conn_atoms[1]);
bnd->setOrder(1);
}
Molecule* RGroupAssembler::generateNextMolecule()
{
if (!not_finished_) return NULL;
Molecule* mol = new Molecule;
System* scaffold_copy = new System;
if (scaffolds_[scaffold_counter_] != NULL)
{
*scaffold_copy = *scaffolds_[scaffold_counter_];
}
else
{
return 0;
}
mol->insert(*scaffold_copy);
for (AtomIterator atom_it = mol->beginAtom(); +atom_it; )
{
String atom_name = atom_it->getName();
if (isPlacemark_(atom_name))
{
atom_it++;
appendMoiety_(mol, moieties_[atom_name][moiety_counter_[atom_name]], atom_name);
}
else
{
atom_it++;
}
}
not_finished_ = incrementCounter_();
return mol;
}
}
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