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/****************************************************************************
* Copyright (C) 2009-2013 GGA Software Services LLC
*
* This file is part of Indigo toolkit.
*
* This file may be distributed and/or modified under the terms of the
* GNU General Public License version 3 as published by the Free Software
* Foundation and appearing in the file LICENSE.GPL included in the
* packaging of this file.
*
* This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
* WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
***************************************************************************/
#ifndef __molecule_inchi_layers_h__
#define __molecule_inchi_layers_h__
#include "base_cpp/array.h"
#include "base_cpp/exception.h"
#include "molecule/molecule_inchi_utils.h"
namespace indigo {
class Molecule;
class Output;
class MoleculeStereocenters;
// Namespace with layers
// Each layers are independent and contains all
// nessesary information
namespace MoleculeInChILayers
{
// Abtract layer
class AbstractLayer
{
public:
AbstractLayer ();
virtual ~AbstractLayer () {};
// Method for constructing internal layer information
void construct (Molecule &mol);
DECL_ERROR;
protected:
Molecule& _getMolecule ();
virtual void _construct () {};
private:
Molecule *_mol;
};
// Main layer formula
class MainLayerFormula : public AbstractLayer
{
public:
void printFormula (Array<char> &result);
static int compareComponentsAtomsCountNoH (MainLayerFormula &comp1,
MainLayerFormula &comp2);
static int compareComponentsTotalHydrogensCount (MainLayerFormula &comp1,
MainLayerFormula &comp2);
protected:
virtual void _construct ();
private:
Array<int> _atoms_count;
void _printAtom (Output &output, int label) const;
void _collectAtomsCount ();
};
// Main layer connections
class MainLayerConnections : public AbstractLayer
{
public:
void printConnectionTable (Array<char> &result);
int compareMappings (const MoleculeInChIUtils::Mapping &m1,
const MoleculeInChIUtils::Mapping &m2);
static int compareComponentsConnectionTables (MainLayerConnections &comp1,
MainLayerConnections &comp2);
protected:
virtual void _construct ();
private:
Array<int> _connection_table;
void _linearizeConnectionTable ();
};
// Layer with hydrogens
class HydrogensLayer : public AbstractLayer
{
public:
static int compareComponentsHydrogens (HydrogensLayer &comp1,
HydrogensLayer &comp2);
bool checkAutomorphism (const Array<int> &mapping);
int compareMappings (MoleculeInChIUtils::Mapping &m1,
MoleculeInChIUtils::Mapping &m2);
void print (Array<char> &result);
protected:
virtual void _construct ();
private:
// Number of immobile hydrogens for each atom
Array<int> _per_atom_immobile;
// Atom indices in the 'mol' to avoid vertexBegin/vertexEnd iterations
// when comparing components
Array<int> _atom_indices;
// TODO: Mobile hydrogens, fixed hydrogens
};
// Cis-trans stereochemistry
class CisTransStereochemistryLayer : public AbstractLayer
{
public:
void print (Array<char> &result);
bool checkAutomorphism (const Array<int> &mapping);
int compareMappings (const MoleculeInChIUtils::Mapping &m1,
const MoleculeInChIUtils::Mapping &m2);
static int compareComponents (CisTransStereochemistryLayer &comp1,
CisTransStereochemistryLayer &comp2);
protected:
virtual void _construct ();
private:
Array<int> bond_is_cis_trans;
};
// Tetrahedral stereochemistry
class TetrahedralStereochemistryLayer : public AbstractLayer
{
public:
void print (Array<char> &result);
void printEnantiomers (Array<char> &result);
bool checkAutomorphism (const Array<int> &mapping);
int compareMappings (const MoleculeInChIUtils::Mapping &m1,
const MoleculeInChIUtils::Mapping &m2);
static int compareComponentsEnantiomers (TetrahedralStereochemistryLayer &comp1,
TetrahedralStereochemistryLayer &comp2);
static int compareComponents (TetrahedralStereochemistryLayer &comp1,
TetrahedralStereochemistryLayer &comp2);
private:
int _getMappingSign (const MoleculeStereocenters &stereocenters,
const MoleculeInChIUtils::Mapping *m, int index);
int _getFirstSign ();
};
};
}
#endif // __molecule_inchi_layers_h__
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