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//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef __MOLCHEMICALFEATURE_H_11012005_1404__
#define __MOLCHEMICALFEATURE_H_11012005_1404__
#include <string>
#include <vector>
#include <map>
#include <Geometry/point.h>
#include <ChemicalFeatures/ChemicalFeature.h>
namespace RDKit {
class ROMol;
class Atom;
class MolChemicalFeatureFactory;
class MolChemicalFeatureDef;
class MolChemicalFeature : public ChemicalFeatures::ChemicalFeature {
friend class MolChemicalFeatureFactory;
public:
typedef std::vector<const Atom *> AtomPtrContainer;
typedef AtomPtrContainer::const_iterator AtomPtrContainer_CI;
//! Constructor
MolChemicalFeature(const ROMol *mol,
const MolChemicalFeatureFactory *factory,
const MolChemicalFeatureDef *fdef) :
dp_mol(mol), dp_factory(factory), dp_def(fdef), d_activeConf(-1) {};
~MolChemicalFeature() {}
//! \brief return the name of the feature's family
const std::string &getFamily() const;
//! \brief return the name of the feature's type
const std::string &getType() const;
//! \brief return the position of the feature (obtained from
//! from the associated conformation
RDGeom::Point3D getPos() const;
//! \brief return the position of the feature (obtained from
//! from the requested conformation from the associated molecule)
RDGeom::Point3D getPos(int confId) const;
//! \brief return a pointer to our feature factory
const MolChemicalFeatureFactory *getFactory() const { return dp_factory; };
//! \brief return a pointer to our associated molecule
const ROMol *getMol() const { return dp_mol; };
//! \brief return a pointer to our feature definition
const MolChemicalFeatureDef *getFeatDef() const { return dp_def; };
//! \brief returns the number of atoms defining the feature
inline unsigned int getNumAtoms() const {
return d_atoms.size();
}
//! \brief sets the active conformer (in the associated molecule)
void setActiveConformer(int confId);
//! \brief returns the active conformer (in the associated molecule)
int getActiveConformer() const { return d_activeConf;};
//! \brief clears out the internal position cache
void clearCache() { d_locs.clear(); };
//! \brief returns our atom container of
const AtomPtrContainer &getAtoms() const {
return d_atoms;
}
AtomPtrContainer::const_iterator beginAtoms() const { return d_atoms.begin(); };
AtomPtrContainer::const_iterator endAtoms() const { return d_atoms.end(); };
private:
typedef std::map<int,RDGeom::Point3D> PointCacheType;
const ROMol *dp_mol;
const MolChemicalFeatureFactory *dp_factory;
const MolChemicalFeatureDef *dp_def;
//std::string d_type;
//std::string d_family;
int d_activeConf;
AtomPtrContainer d_atoms;
mutable PointCacheType d_locs;
};
}
#endif
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