Conformer.h
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//
// Copyright (C) 2001-2008 Greg Landrum and 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.
//
#include <RDGeneral/export.h>
#ifndef _RD_CONFORMER_H
#define _RD_CONFORMER_H
#include <Geometry/point.h>
#include <RDGeneral/types.h>
#include <boost/smart_ptr.hpp>
#include <RDGeneral/RDProps.h>
namespace RDKit {
class ROMol;
//! used to indicate errors from incorrect confomer access
class RDKIT_GRAPHMOL_EXPORT ConformerException : public std::exception {
public:
//! construct with an error message
ConformerException(const char *msg) : _msg(msg){};
//! construct with an error message
ConformerException(const std::string &msg) : _msg(msg){};
//! get the error message
const char *message() const { return _msg.c_str(); };
~ConformerException() throw(){};
private:
std::string _msg;
};
//! The class for representing 2D or 3D conformation of a molecule
/*!
This class contains
- a pointer to the owing molecule
- a vector of 3D points (positions of atoms)
*/
class RDKIT_GRAPHMOL_EXPORT Conformer : public RDProps {
public:
friend class ROMol;
//! Constructor
Conformer() : df_is3D(true), d_id(0), dp_mol(NULL) { d_positions.clear(); };
//! Constructor with number of atoms specified ID specification
Conformer(unsigned int numAtoms) : df_is3D(true), d_id(0), dp_mol(NULL) {
if (numAtoms) {
d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
} else {
d_positions.resize(0);
d_positions.clear();
}
};
//! Copy Constructor: initialize from a second conformation.
Conformer(const Conformer &other);
Conformer &operator=(const Conformer &other);
//! Destructor
~Conformer(){};
//! Resize the conformer so that more atoms location can be added.
//! Useful, for e.g., when adding hydrogens
void resize(unsigned int size) { d_positions.resize(size); }
//! Reserve more space for atom position
void reserve(unsigned int size) { d_positions.reserve(size); }
//! returns whether or not this instance belongs to a molecule
bool hasOwningMol() const { return dp_mol != nullptr; };
//! Get the molecule that owns this instance
ROMol &getOwningMol() const {
PRECONDITION(dp_mol, "no owner");
return *dp_mol;
}
//! Get a const reference to the vector of atom positions
const RDGeom::POINT3D_VECT &getPositions() const;
//! Get a reference to the atom positions
RDGeom::POINT3D_VECT &getPositions();
//! Get the position of the specified atom
const RDGeom::Point3D &getAtomPos(unsigned int atomId) const;
//! overload
template <class U>
const RDGeom::Point3D &getAtomPos(U atomId) const {
return getAtomPos(rdcast<unsigned int>(atomId));
}
//! Get the position of the specified atom
RDGeom::Point3D &getAtomPos(unsigned int atomId);
//! overload
template <class U>
RDGeom::Point3D &getAtomPos(U atomId) {
return getAtomPos(rdcast<unsigned int>(atomId));
}
//! Set the position of the specified atom
inline void setAtomPos(unsigned int atomId, const RDGeom::Point3D &position) {
// RANGE_CHECK(0,atomId,d_positions.size()-1);
if (atomId >= d_positions.size()) {
d_positions.resize(atomId + 1, RDGeom::Point3D(0.0, 0.0, 0.0));
}
d_positions[atomId] = position;
}
//! overload
template <class U>
void setAtomPos(U atomId, const RDGeom::Point3D &position) {
return setAtomPos(rdcast<unsigned int>(atomId), position);
}
//! get the ID of this conformer
inline unsigned int getId() const { return d_id; }
//! set the ID of this conformer
inline void setId(unsigned int id) { d_id = id; }
//! Get the number of atoms
inline unsigned int getNumAtoms() const {
return rdcast<unsigned int>(d_positions.size());
}
inline bool is3D() const { return df_is3D; }
inline void set3D(bool v) { df_is3D = v; }
protected:
//! Set owning moelcule
void setOwningMol(ROMol *mol);
//! Set owning moelcule
void setOwningMol(ROMol &mol);
private:
bool df_is3D; // is this a 3D conformation?
unsigned int d_id; // id is the conformation
ROMol *dp_mol; // owning molecule
RDGeom::POINT3D_VECT d_positions; // positions of the atoms
void initFromOther(const Conformer &conf);
};
typedef boost::shared_ptr<Conformer> CONFORMER_SPTR;
//! Returns true if any of the z coords are non zero, false otherwise
/*!
\param conf Conformer object to analyze
*/
inline bool hasNonZeroZCoords(const Conformer &conf) {
for (auto p : conf.getPositions()) {
if (p.z != 0.0) return true;
}
return false;
}
} // namespace RDKit
#endif
RDKit::Conformer::setAtomPos
void setAtomPos(U atomId, const RDGeom::Point3D &position)
overload
Definition: Conformer.h:115
point.h
types.h
RDKit::Conformer::getAtomPos
RDGeom::Point3D & getAtomPos(U atomId)
overload
Definition: Conformer.h:101
RDKit::ConformerException
used to indicate errors from incorrect confomer access
Definition: Conformer.h:23
RDKit::Conformer::getAtomPos
const RDGeom::Point3D & getAtomPos(U atomId) const
overload
Definition: Conformer.h:93
RDGeom::Point3D
Definition: point.h:46
RDKit::ConformerException::message
const char * message() const
get the error message
Definition: Conformer.h:30
RDKit::ConformerException::~ConformerException
~ConformerException()
Definition: Conformer.h:31
RDKit::hasNonZeroZCoords
bool hasNonZeroZCoords(const Conformer &conf)
Returns true if any of the z coords are non zero, false otherwise.
Definition: Conformer.h:152
RDKit::Conformer::reserve
void reserve(unsigned int size)
Reserve more space for atom position.
Definition: Conformer.h:72
RDKit::Conformer::getNumAtoms
unsigned int getNumAtoms() const
Get the number of atoms.
Definition: Conformer.h:125
RDKit::Conformer::getPositions
const RDGeom::POINT3D_VECT & getPositions() const
Get a const reference to the vector of atom positions.
RDKit::Conformer::getId
unsigned int getId() const
get the ID of this conformer
Definition: Conformer.h:119
RDKit::ROMol
Definition: ROMol.h:171
RDKit::Conformer::setId
void setId(unsigned int id)
set the ID of this conformer
Definition: Conformer.h:122
RDKit::Conformer::Conformer
Conformer(unsigned int numAtoms)
Constructor with number of atoms specified ID specification.
Definition: Conformer.h:51
RDGeom::POINT3D_VECT
std::vector< Point3D > POINT3D_VECT
Definition: point.h:514
RDKit::Conformer::is3D
bool is3D() const
Definition: Conformer.h:128
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition: export.h:307
RDKit::Conformer::~Conformer
~Conformer()
Destructor.
Definition: Conformer.h:65
RDProps.h
RDKit::Conformer::setAtomPos
void setAtomPos(unsigned int atomId, const RDGeom::Point3D &position)
Set the position of the specified atom.
Definition: Conformer.h:106
RDKit::Conformer
The class for representing 2D or 3D conformation of a molecule.
Definition: Conformer.h:43
RDKit::RDProps
Definition: RDProps.h:10
RDKit::Conformer::Conformer
Conformer()
Constructor.
Definition: Conformer.h:48
RDKit::Conformer::resize
void resize(unsigned int size)
Definition: Conformer.h:69
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::ConformerException::ConformerException
ConformerException(const char *msg)
construct with an error message
Definition: Conformer.h:26
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
RDKit::ConformerException::ConformerException
ConformerException(const std::string &msg)
construct with an error message
Definition: Conformer.h:28
RDKit::Conformer::set3D
void set3D(bool v)
Definition: Conformer.h:129
RDKit::Conformer::hasOwningMol
bool hasOwningMol() const
returns whether or not this instance belongs to a molecule
Definition: Conformer.h:75
RDKit::CONFORMER_SPTR
boost::shared_ptr< Conformer > CONFORMER_SPTR
Definition: Conformer.h:146
RDKit::Conformer::getOwningMol
ROMol & getOwningMol() const
Get the molecule that owns this instance.
Definition: Conformer.h:78
export.h