RDKit::Conformer Class Reference

The class for representing 2D or 3D conformation of a molecule. More...

#include <Conformer.h>

Inheritance diagram for RDKit::Conformer:

Public Member Functions
	Conformer ()=default
	Constructor.
	Conformer (unsigned int numAtoms)
	Constructor with number of atoms specified ID specification.
	Conformer (const Conformer &other)=default
	Copy Constructor: initialize from a second conformation.
Conformer &	operator= (const Conformer &other)=default
	Conformer (Conformer &&o) noexcept
Conformer &	operator= (Conformer &&o) noexcept
	~Conformer ()=default
	Destructor.
void	resize (unsigned int size)
void	reserve (unsigned int size)
	Reserve more space for atom position.
bool	hasOwningMol () const
	returns whether or not this instance belongs to a molecule
ROMol &	getOwningMol () const
	Get the molecule that owns this instance.
const RDGeom::POINT3D_VECT &	getPositions () const
	Get a const reference to the vector of atom positions.
RDGeom::POINT3D_VECT &	getPositions ()
	Get a reference to the atom positions.
const RDGeom::Point3D &	getAtomPos (unsigned int atomId) const
	Get the position of the specified atom.
template<class U>
const RDGeom::Point3D &	getAtomPos (U atomId) const
	overload
RDGeom::Point3D &	getAtomPos (unsigned int atomId)
	Get the position of the specified atom.
template<class U>
RDGeom::Point3D &	getAtomPos (U atomId)
	overload
void	setAtomPos (unsigned int atomId, const RDGeom::Point3D &position)
	Set the position of the specified atom.
template<class U>
void	setAtomPos (U atomId, const RDGeom::Point3D &position)
	overload
unsigned int	getId () const
	get the ID of this conformer
void	setId (unsigned int id)
	set the ID of this conformer
unsigned int	getNumAtoms () const
	Get the number of atoms.
bool	is3D () const
void	set3D (bool v)
Public Member Functions inherited from RDKit::RDProps
	RDProps ()
	RDProps (const RDProps &rhs)
RDProps &	operator= (const RDProps &rhs)
	RDProps (RDProps &&o) noexcept=default
RDProps &	operator= (RDProps &&rhs) noexcept=default
void	clear ()
const Dict &	getDict () const
	gets the underlying Dictionary
Dict &	getDict ()
STR_VECT	getPropList (bool includePrivate=true, bool includeComputed=true) const
	returns a list with the names of our properties
template<typename T>
void	setProp (const std::string &key, T val, bool computed=false) const
	sets a property value
template<typename T>
void	getProp (const std::string &key, T &res) const
	allows retrieval of a particular property value
template<typename T>
T	getProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<typename T>
bool	getPropIfPresent (const std::string &key, T &res) const
bool	hasProp (const std::string &key) const
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
void	clearProp (const std::string &key) const
	clears the value of a property
void	clearComputedProps () const
	clears all of our computed properties
void	updateProps (const RDProps &source, bool preserveExisting=false)
	update the properties from another

Protected Member Functions
void	setOwningMol (ROMol *mol)
	Set owning molecule.
void	setOwningMol (ROMol &mol)
	Set owning molecule.

Friends
class	ROMol

Additional Inherited Members
Protected Attributes inherited from RDKit::RDProps
Dict	d_props

Detailed Description

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)

Definition at line 46 of file Conformer.h.

Constructor & Destructor Documentation

Conformer() [1/4]

RDKit::Conformer::Conformer ( )

default

Constructor.

Referenced by Conformer(), Conformer(), operator=(), and operator=().

Conformer() [2/4]

RDKit::Conformer::Conformer ( unsigned int numAtoms )

inline

Constructor with number of atoms specified ID specification.

Definition at line 54 of file Conformer.h.

Conformer() [3/4]

RDKit::Conformer::Conformer ( const Conformer & other )

default

Copy Constructor: initialize from a second conformation.

References Conformer().

Conformer() [4/4]

RDKit::Conformer::Conformer ( Conformer && o )

inlinenoexcept

Definition at line 60 of file Conformer.h.

References Conformer(), and RDKit::RDProps::RDProps().

~Conformer()

RDKit::Conformer::~Conformer ( )

default

Destructor.

Member Function Documentation

getAtomPos() [1/4]

template<class U>

RDGeom::Point3D & RDKit::Conformer::getAtomPos ( U atomId )

inline

overload

Definition at line 114 of file Conformer.h.

References getAtomPos(), and rdcast.

getAtomPos() [2/4]

template<class U>

const RDGeom::Point3D & RDKit::Conformer::getAtomPos ( U atomId ) const

inline

overload

Definition at line 106 of file Conformer.h.

References getAtomPos(), and rdcast.

getAtomPos() [3/4]

RDGeom::Point3D & RDKit::Conformer::getAtomPos

(

unsigned int

atomId

)

Get the position of the specified atom.

getAtomPos() [4/4]

const RDGeom::Point3D & RDKit::Conformer::getAtomPos

(

unsigned int

atomId

)

const

Get the position of the specified atom.

Referenced by getAtomPos(), and getAtomPos().

getId()

unsigned int RDKit::Conformer::getId ( ) const

inline

get the ID of this conformer

Definition at line 134 of file Conformer.h.

getNumAtoms()

unsigned int RDKit::Conformer::getNumAtoms ( ) const

inline

Get the number of atoms.

Definition at line 140 of file Conformer.h.

References rdcast.

getOwningMol()

ROMol & RDKit::Conformer::getOwningMol ( ) const

inline

Get the molecule that owns this instance.

Definition at line 91 of file Conformer.h.

References PRECONDITION, and ROMol.

getPositions() [1/2]

RDGeom::POINT3D_VECT & RDKit::Conformer::getPositions

(

)

Get a reference to the atom positions.

getPositions() [2/2]

const RDGeom::POINT3D_VECT & RDKit::Conformer::getPositions

(

)

const

Get a const reference to the vector of atom positions.

Referenced by RDKit::hasNonZeroZCoords().

hasOwningMol()

bool RDKit::Conformer::hasOwningMol ( ) const

inline

returns whether or not this instance belongs to a molecule

Definition at line 88 of file Conformer.h.

is3D()

bool RDKit::Conformer::is3D ( ) const

inline

Definition at line 143 of file Conformer.h.

operator=() [1/2]

Conformer & RDKit::Conformer::operator= ( Conformer && o )

inlinenoexcept

Definition at line 66 of file Conformer.h.

References Conformer(), and RDKit::RDProps::operator=().

operator=() [2/2]

Conformer & RDKit::Conformer::operator= ( const Conformer & other )

default

References Conformer().

reserve()

void RDKit::Conformer::reserve ( unsigned int size )

inline

Reserve more space for atom position.

Definition at line 85 of file Conformer.h.

resize()

void RDKit::Conformer::resize ( unsigned int size )

inline

Resize the conformer so that more atoms location can be added. Useful, for e.g., when adding hydrogens

Definition at line 82 of file Conformer.h.

set3D()

void RDKit::Conformer::set3D ( bool v )

inline

Definition at line 144 of file Conformer.h.

setAtomPos() [1/2]

template<class U>

void RDKit::Conformer::setAtomPos ( U atomId, const RDGeom::Point3D & position )

inline

overload

Definition at line 130 of file Conformer.h.

References rdcast, and setAtomPos().

setAtomPos() [2/2]

void RDKit::Conformer::setAtomPos ( unsigned int atomId, const RDGeom::Point3D & position )

inline

Set the position of the specified atom.

Definition at line 119 of file Conformer.h.

Referenced by setAtomPos().

setId()

void RDKit::Conformer::setId ( unsigned int id )

inline

set the ID of this conformer

Definition at line 137 of file Conformer.h.

setOwningMol() [1/2]

void RDKit::Conformer::setOwningMol ( ROMol & mol )

protected

Set owning molecule.

References ROMol.

setOwningMol() [2/2]

void RDKit::Conformer::setOwningMol ( ROMol * mol )

protected

Set owning molecule.

References ROMol.

Friends And Related Symbol Documentation

ROMol

friend class ROMol

friend

Definition at line 48 of file Conformer.h.

References ROMol.

Referenced by getOwningMol(), ROMol, setOwningMol(), and setOwningMol().

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The documentation for this class was generated from the following file:

• Conformer.h