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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/DOCKING/COMMON/flexibleMolecule.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/bond.h>
namespace BALL
{
FlexibleMolecule::FlexibleMolecule(Molecule* mol)
{
molecule_ownership_ = true;
molecule = mol;
Conformation* conf = new Conformation(molecule, molecule);
addConformation(conf);
id = conf->getId();
}
FlexibleMolecule::FlexibleMolecule(const FlexibleMolecule& flexmol)
{
molecule_ownership_ = true;
molecule = new Molecule(*flexmol.molecule);
id = flexmol.id;
for (Size i = 0; i < flexmol.conformations.size(); i++)
{
Conformation* conf_copy = new Conformation(*flexmol.conformations[i]);
addConformation(conf_copy);
}
}
FlexibleMolecule::~FlexibleMolecule()
{
if (molecule_ownership_) delete molecule;
clearConformations();
}
void FlexibleMolecule::removeMoleculeOwnership()
{
molecule_ownership_ = false;
}
void FlexibleMolecule::clearConformations()
{
for (Position i = 0; i < conformations.size(); i++)
{
delete conformations[i];
}
conformations.clear();
conf_ids_.clear();
}
void FlexibleMolecule::addConformation(Conformation* conf)
{
// We don't want to insert any conformation twice, so check
// whether 'conf' has already been added to this FlexibleMolecule
if (conf_ids_.find(conf->getId()) != conf_ids_.end())
{
return;
}
if (checkCompatibility(conf))
{
conformations.push_back(conf);
conf_ids_[conf->getId()] = conf;
}
else
{
throw(Exception::GeneralException(__FILE__, __LINE__, "FlexibleMolecule::addConformation", "conformation not compatible with template molecule"));
}
}
void FlexibleMolecule::calculatePseudoSmile(const Atom* atom, String& smile, HashSet<const Atom*>& visited_atoms, bool ignore_hydrogens)
{
if (!atom || visited_atoms.has(atom)) return;
if (ignore_hydrogens && atom->getElement().getSymbol() == "H")
{
return;
}
smile += atom->getElement().getSymbol();
visited_atoms.insert(atom);
for (Atom::BondConstIterator it = atom->beginBond(); +it; it++)
{
const Atom* partner = it->getPartner(*atom);
if (ignore_hydrogens && partner->getElement().getSymbol() == "H")
{
continue;
}
if (visited_atoms.has(partner))
{
continue;
}
int order = it->getOrder();
String bond_symbol;
if (order == 2) bond_symbol="=";
else if(order==3) bond_symbol="#";
else if (order == 5) bond_symbol="~"; // aromatic bond
if (it != atom->endBond())
{
smile += "("+bond_symbol;
calculatePseudoSmile(partner, smile, visited_atoms, ignore_hydrogens);
smile += ")";
}
else
{
smile += bond_symbol;
calculatePseudoSmile(partner, smile, visited_atoms, ignore_hydrogens);
}
}
}
void FlexibleMolecule::generateTopologyHash(const AtomContainer* mol, String& hashkey, bool ignore_hydrogens)
{
HashSet<const Atom*> visited_atoms;
/* USELESS CODE
* bool more_than_one_atom = 0;
* AtomConstIterator it = mol->beginAtom();
* if (it != mol->endAtom())
* {
* it++;
* if (it != mol->endAtom()) more_than_one_atom = 1;
}
*/
calculatePseudoSmile(&*mol->beginAtom(), hashkey, visited_atoms, ignore_hydrogens);
hashkey = QCryptographicHash::hash(QByteArray(hashkey.c_str()), QCryptographicHash::Sha1).toHex().constData();
}
bool FlexibleMolecule::checkCompatibility(Conformation* conf)
{
// currently only the only compatibility check is whether
// the number of atoms matches with the number of position
// vectors in the Conformation object
return (conf->getNoOfAtoms() == molecule->countAtoms());
}
Size FlexibleMolecule::getNumberOfConformations()
{
return conformations.size();
}
const vector < Conformation* > & FlexibleMolecule::getConformations() const
{
return conformations;
}
String FlexibleMolecule::getConformationId(Position i)
{
if (i < conformations.size())
return conformations[i]->getId();
else
{
throw(Exception::IndexOverflow(__FILE__, __LINE__, i, conformations.size()));
}
}
Conformation* FlexibleMolecule::getConformation(Position i)
{
if (i < conformations.size())
return conformations[i];
else
//throw(Exception::IndexOverflow(__FILE__, __LINE__, i, conformations.size()));
return 0;
}
Molecule* FlexibleMolecule::getConformer(Position i)
{
if (i < conformations.size())
{
Molecule* ret = new Molecule(*molecule);
conformations[i]->applyConformation(*ret);
return ret;
}
else
//throw(Exception::IndexOverflow(__FILE__, __LINE__, i, conformations.size()));
return 0;
}
Molecule* FlexibleMolecule::getConformerById(String id)
{
if (conf_ids_.has(id))
{
Molecule* ret = new Molecule(*molecule);
conf_ids_[id]->applyConformation(*ret);
return ret;
}
else
return 0;
}
Conformation* FlexibleMolecule::getConformationById(String id)
{
if (conf_ids_.has(id))
{
return conf_ids_[id];
}
else
return 0;
}
bool FlexibleMolecule::hasConformation(String id)
{
return conf_ids_.has(id);
}
Molecule* FlexibleMolecule::getParent()
{
return molecule;
}
String FlexibleMolecule::getId() const
{
return id;
}
void FlexibleMolecule::setId(String _id)
{
id = _id;
}
}
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