RDKit
Open-source cheminformatics and machine learning.
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RDKit::Conformer Class Reference

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

#include <Conformer.h>

Public Member Functions

 Conformer ()
 Constructor. More...
 
 Conformer (unsigned int numAtoms)
 Constructor with number of atoms specified ID specification. More...
 
 Conformer (const Conformer &other)
 Copy Constructor: initialize from a second conformation. More...
 
 ~Conformer ()
 Destructor. More...
 
void resize (unsigned int size)
 
void reserve (unsigned int size)
 Reserve more space for atom position. More...
 
ROMol & getOwningMol () const
 Get the molecule that oqns this conformation. More...
 
const RDGeom::POINT3D_VECT & getPositions () const
 Get a const reference to the vector of atom positions. More...
 
RDGeom::POINT3D_VECT & getPositions ()
 Get a reference to the atom positions. More...
 
const RDGeom::Point3D & getAtomPos (unsigned int atomId) const
 Get the position of the specified atom. More...
 
template<class U >
const RDGeom::Point3D & getAtomPos (U atomId) const
 overload More...
 
RDGeom::Point3D & getAtomPos (unsigned int atomId)
 Get the position of the specified atom. More...
 
template<class U >
RDGeom::Point3D & getAtomPos (U atomId)
 overload More...
 
void setAtomPos (unsigned int atomId, const RDGeom::Point3D &position)
 Set the position of the specified atom. More...
 
template<class U >
void setAtomPos (U atomId, const RDGeom::Point3D &position)
 overload More...
 
unsigned int getId () const
 get the ID of this conformer More...
 
void setId (unsigned int id)
 set the ID of this conformer More...
 
unsigned int getNumAtoms () const
 Get the number of atoms. More...
 
bool is3D () const
 
void set3D (bool v)
 

Protected Member Functions

void setOwningMol (ROMol *mol)
 Set owning moelcule. More...
 
void setOwningMol (ROMol &mol)
 Set owning moelcule. More...
 

Friends

class ROMol
 

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 41 of file Conformer.h.

Constructor & Destructor Documentation

◆ Conformer() [1/3]

RDKit::Conformer::Conformer ( )
inline

Constructor.

Definition at line 46 of file Conformer.h.

◆ Conformer() [2/3]

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

Constructor with number of atoms specified ID specification.

Definition at line 49 of file Conformer.h.

◆ Conformer() [3/3]

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

Copy Constructor: initialize from a second conformation.

◆ ~Conformer()

RDKit::Conformer::~Conformer ( )
inline

Destructor.

Definition at line 62 of file Conformer.h.

Member Function Documentation

◆ getAtomPos() [1/4]

const RDGeom::Point3D& RDKit::Conformer::getAtomPos ( unsigned int  atomId) const

Get the position of the specified atom.

◆ getAtomPos() [2/4]

template<class U >
const RDGeom::Point3D& RDKit::Conformer::getAtomPos ( U  atomId) const
inline

overload

Definition at line 84 of file Conformer.h.

◆ getAtomPos() [3/4]

RDGeom::Point3D& RDKit::Conformer::getAtomPos ( unsigned int  atomId)

Get the position of the specified atom.

◆ getAtomPos() [4/4]

template<class U >
RDGeom::Point3D& RDKit::Conformer::getAtomPos ( U  atomId)
inline

overload

Definition at line 92 of file Conformer.h.

◆ getId()

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

get the ID of this conformer

Definition at line 110 of file Conformer.h.

◆ getNumAtoms()

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

Get the number of atoms.

Definition at line 116 of file Conformer.h.

◆ getOwningMol()

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

Get the molecule that oqns this conformation.

Definition at line 72 of file Conformer.h.

◆ getPositions() [1/2]

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

Get a const reference to the vector of atom positions.

Referenced by RDKit::Drawing::DrawMol().

◆ getPositions() [2/2]

RDGeom::POINT3D_VECT& RDKit::Conformer::getPositions ( )

Get a reference to the atom positions.

◆ is3D()

bool RDKit::Conformer::is3D ( ) const
inline

Definition at line 118 of file Conformer.h.

◆ reserve()

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

Reserve more space for atom position.

Definition at line 69 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 66 of file Conformer.h.

◆ set3D()

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

Definition at line 119 of file Conformer.h.

◆ setAtomPos() [1/2]

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

Set the position of the specified atom.

Definition at line 97 of file Conformer.h.

◆ setAtomPos() [2/2]

template<class U >
void RDKit::Conformer::setAtomPos ( U  atomId,
const RDGeom::Point3D &  position 
)
inline

overload

Definition at line 106 of file Conformer.h.

◆ setId()

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

set the ID of this conformer

Definition at line 113 of file Conformer.h.

◆ setOwningMol() [1/2]

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

Set owning moelcule.

◆ setOwningMol() [2/2]

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

Set owning moelcule.

Friends And Related Function Documentation

◆ ROMol

friend class ROMol
friend

Definition at line 43 of file Conformer.h.

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