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/****************************************************************************
* Copyright (C) 2009-2015 EPAM Systems
*
* 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_cis_trans__
#define __molecule_cis_trans__
#include "base_cpp/red_black.h"
#include "math/algebra.h"
#ifdef _WIN32
#pragma warning(push)
#pragma warning(disable:4251)
#endif
namespace indigo {
class BaseMolecule;
class Filter;
class DLLEXPORT MoleculeCisTrans
{
public:
enum
{
CIS = 1,
TRANS = 2
};
void clear ();
void build (int *exclude_bonds);
void buildFromSmiles (int *dirs);
bool exists () const;
int count ();
void setParity (int bond_idx, int parity);
int getParity (int bond_idx) const;
bool isIgnored (int bond_idx) const;
void ignore (int bond_idx);
void registerBond (int idx);
void flipBond (int atom_parent, int atom_from, int atom_to);
const int * getSubstituents (int bond_idx) const;
void getSubstituents_All (int bond_idx, int subst[4]);
void add (int bond_idx, int substituents[4], int parity);
bool registerBondAndSubstituents (int idx);
int applyMapping (int idx, const int *mapping, bool sort) const;
static int applyMapping (int parity, const int *substituents, const int *mapping, bool sort);
// Returns -2 if mapping is not valid
static int getMappingParitySign (BaseMolecule &query, BaseMolecule &target,
int bond_idx, const int *mapping);
static bool checkSub (BaseMolecule &query, BaseMolecule &target, const int *mapping);
void buildOnSubmolecule (BaseMolecule &super, int *mapping);
static bool sortSubstituents (BaseMolecule &mol, int *substituents, bool *parity_changed);
void restoreSubstituents (int bond_idx);
void registerUnfoldedHydrogen (int atom_idx, int added_hydrogen);
static bool isAutomorphism (BaseMolecule &mol, const Array<int> &mapping, const Filter *edge_filter = NULL);
bool isRingTransBond (int bond_idx);
bool convertableToImplicitHydrogen (int idx);
void validate ();
DECL_ERROR;
static bool isGeomStereoBond (BaseMolecule &mol, int bond_idx, int *substituents, bool have_xyz);
static int sameside (const Vec3f &beg, const Vec3f &end, const Vec3f &nei_beg, const Vec3f &nei_end);
static bool sameline (const Vec3f &beg, const Vec3f &end, const Vec3f &nei_beg);
bool sameside (int edge_idx, int v1, int v2);
protected:
BaseMolecule & _getMolecule ();
struct _Bond
{
void clear ()
{
parity = 0;
ignored = 0;
}
int parity; // CIS ot TRANS
int ignored; // explicitly ignored cis-trans configuration on this bond
int substituents[4];
};
Array<_Bond> _bonds;
static bool _pureH (BaseMolecule &mol, int idx);
static int _sameside (BaseMolecule &mol, int i_beg, int i_end, int i_nei_beg, int i_nei_end);
static bool _sameline (BaseMolecule &molecule, int i_beg, int i_end, int i_nei_beg);
static int _getPairParity (int v1, int v2, const int *mapping, bool sort);
static bool _commonHasLonePair (BaseMolecule &mol, int v1, int v2);
static void _fillExplicitHydrogens (BaseMolecule &mol, int bond_idx, int subst[4]);
static void _fillAtomExplicitHydrogens (BaseMolecule &mol, int atom_idx, int subst[2]);
};
}
#ifdef _WIN32
#pragma warning(pop)
#endif
#endif
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