C++ AtomIterator::getElement方法代码示例

//.........这里部分代码省略.........

		tmp = path.find(polar_radius_rule_file_name);
		if (tmp != "")
		{
			polar_radius_rule_file_name = tmp;
		}
		if (verbosity > 0)
		{
			Log.info() << "Using " << polar_radius_rule_file_name << " as polar radius rule file" << endl;
		}

		INIFile radius_ini(polar_radius_rule_file_name);
		radius_ini.read();
		RadiusRuleProcessor radius_rules(radius_ini);
		system.apply(radius_rules);
	}

	if (verbosity > 8)
	{
		Log.info() << "system statistics:" << endl;
		Log.info() << "molecules: " << system.countMolecules() << endl;
		Log.info() << "proteins:  " << system.countProteins() << endl;
		Log.info() << "fragments: " << system.countFragments() << endl;
		Log.info() << "atoms:     " << system.countAtoms() << endl;
	}


	// check for uassigned type names
	AtomIterator it;
	int count = 0;
	for (it = system.beginAtom(); +it; ++it)
	{
		count++;
		if (it->getElement().getSymbol() == "?")
		{
			Log.info() << "Got symbol \"?\": " << it->getFullName() << endl;
		}
		if (it->getCharge() > 8.0)
		{
			Log.error() << "Mysterious charge: " << it->getCharge() << "\t"
				<< it->getFullName() << "\t" << count << "\t" << it->getElement().getSymbol() << endl;
		}
	}

	// scale charges
	if (verbosity > 0)
	{
		Log.info() << "Scaling receptor charges by " << receptor_charge_scaling_factor << endl;
	}
	if (parpars.has("s"))
	{
		for (it = protein->beginAtom(); +it; ++it)
		{
			it->setCharge(it->getCharge() * receptor_charge_scaling_factor);
		}
	}

	if (verbosity > 0)
	{
		Log.info() << "Scaling ligand charges by " << ligand_charge_scaling_factor << endl;
	}
	if (parpars.has("t"))
	{
		for (it = ligand->beginAtom(); +it; ++it)
		{
			it->setCharge(it->getCharge() * ligand_charge_scaling_factor);

CHECK(AntechamberFile::AntechamberFile(const String& filename, File::OpenMode open_mode))
	// checking for default mode: reading
	AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test1.ac));
	TEST_EQUAL(f.isValid(), true)
RESULT


CHECK(AntechamberFile::read(System& system))
  AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test2.ac));
	System S;
	f.read(S);
	f.close();

	TEST_EQUAL(S.countAtoms(), 2)	
	AtomIterator it = S.beginAtom();
	TEST_EQUAL(it->getElement().getSymbol(), "H")
	TEST_REAL_EQUAL(it->getPosition().x, 0.0)
	TEST_REAL_EQUAL(it->getPosition().y, 1.0)
	TEST_REAL_EQUAL(it->getPosition().z, 2.0)
	it++;
	TEST_EQUAL(it->getElement().getSymbol(), "O")
	TEST_REAL_EQUAL(it->getPosition().x, 3.0)
	TEST_REAL_EQUAL(it->getPosition().y, 4.0)
	TEST_REAL_EQUAL(it->getPosition().z, 5.0)
RESULT


CHECK(AntechamberFile::read(System& system))
  AntechamberFile f(BALL_TEST_DATA_PATH(AntechamberFile_test1.ac));
	System S;
	f.read(S);

double Polarity::updateScore()
{
	score_ = 0.0;
	//float val = 0.0;
	//float distance;
	//float R1;
	//float R2;

	const HashGrid3<Atom*>* hashgrid = scoring_function_->getHashGrid();
	int radius = 1;
	Size no_neighbor_cells = (Size)pow((double)(radius*2+1), 3);  // radius of 1 cell == > 3 cells on each axis

	double total_sum = 0;
	AtomPairVector::const_iterator it;
	for (AtomIterator it = scoring_function_->getLigand()->beginAtom(); +it; it++)
	{
		int no_positive_contacts = 0;
		int no_negative_contacts = 0;
		bool ligandatom_is_lipophilic = isLipophilic_(&*it);

		if (!ligandatom_is_lipophilic)
		{
			continue;
		}

		const HashGridBox3<Atom*>* box = hashgrid->getBox(it->getPosition());

		// ligand atom lies outside of grid
		if (!box) continue;

		Position pos_x, pos_y, pos_z;
		hashgrid->getIndices(*box, pos_x, pos_y, pos_z);

		// indices in HashGrid, where the search for interacting target atoms should begin ( != position of ligand atom)
		int i = ((int)pos_x)-radius; if (i < 0){i = 0; }
		int j0 = ((int)pos_y)-radius; if (j0 < 0){j0 = 0; }
		int k0 = ((int)pos_z)-radius; if (k0 < 0){k0 = 0; }
		int x_size = (int)hashgrid->getSizeX();
		int y_size = (int)hashgrid->getSizeY();
		int z_size = (int)hashgrid->getSizeZ();

		for (; i <= pos_x+radius && i < x_size; i++)
		{
			for (int j = j0; j <= pos_y+radius && j < y_size; j++)
			{
				for (int k = k0; k <= pos_z+radius && k < z_size; k++)
				{
					const HashGridBox3<Atom*>* box = hashgrid->getBox(i, j, k);
					if (!box->isEmpty())
					{
						double cell_score = 0;

						for (HashGridBox3 < Atom* > ::ConstDataIterator d_it = box->beginData(); d_it != box->endData(); d_it++)
						{
							if (isBackboneAtom_(*d_it)) continue;
							bool rec_polar = isPolar_(*d_it);
							bool rec_lipophilic = 0;
							if (!rec_polar) rec_lipophilic = isLipophilic_(*d_it);

							if (!rec_polar && ! rec_lipophilic) continue;

							double distance = ((*d_it)->getPosition()-it->getPosition()).getLength();
							if (distance > (*d_it)->getElement().getVanDerWaalsRadius()+it->getElement().getVanDerWaalsRadius()+1.5) continue;

							double val;
							if (distance > 1) val = 1/distance;
							else val = 1;

							// lipophilic--lipophilic interaction; else polar rec. -- lipophilic ligand atom
							if (rec_lipophilic)
							{
								val *= -1;
							}

							cell_score += val;
							total_sum += val;

							if (scoring_function_->storeInteractionsEnabled())
							{
								val = scaleScore(val);
								it->addInteraction(*d_it, "pol", val);
								(*d_it)->addInteraction(&*it, "pol", val);
							}
						}

						if (cell_score < -0.1) no_positive_contacts++;
						else if (cell_score > 0.1) no_negative_contacts++;
					}
					// if there is no neighboring receptor atom, there will be water ...
// 					else if(i!=pos_x||j!=pos_y||k!=pos_z)
// 					{
// 						if(ligandatom_is_lipophilic)
// 						{
// 							no_negative_contacts++;
// 							double scaled_atom_score = 1.0/no_neighbor_cells;
// 							scaleScore(scaled_atom_score);
// 							total_sum += scaled_atom_score;
// 							it->addInteraction("pol",scaled_atom_score);
// 						}
// 					}
//.........这里部分代码省略.........