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RDKit
Open-source cheminformatics and machine learning.
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The class for representing 2D or 3D conformation of a molecule. More...
#include <Conformer.h>
Public Member Functions | |
Conformer () | |
Constructor. | |
Conformer (unsigned int numAtoms) | |
Constructor with number of atoms specified ID specification. | |
Conformer (const Conformer &other) | |
Copy Constructor: initialize from a second conformation. | |
Conformer & | operator= (const Conformer &other) |
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) |
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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 | |
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Dict | d_props |
The class for representing 2D or 3D conformation of a molecule.
This class contains
Definition at line 45 of file Conformer.h.
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inline |
Constructor.
Definition at line 50 of file Conformer.h.
Constructor with number of atoms specified ID specification.
Definition at line 53 of file Conformer.h.
Copy Constructor: initialize from a second conformation.
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inlinenoexcept |
Definition at line 65 of file Conformer.h.
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default |
Destructor.
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inline |
overload
Definition at line 119 of file Conformer.h.
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inline |
overload
Definition at line 111 of file Conformer.h.
RDGeom::Point3D & RDKit::Conformer::getAtomPos | ( | unsigned int | atomId | ) |
Get the position of the specified atom.
const RDGeom::Point3D & RDKit::Conformer::getAtomPos | ( | unsigned int | atomId | ) | const |
Get the position of the specified atom.
get the ID of this conformer
Definition at line 139 of file Conformer.h.
Get the number of atoms.
Definition at line 145 of file Conformer.h.
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inline |
Get the molecule that owns this instance.
Definition at line 96 of file Conformer.h.
References PRECONDITION.
RDGeom::POINT3D_VECT & RDKit::Conformer::getPositions | ( | ) |
Get a reference to the atom positions.
const RDGeom::POINT3D_VECT & RDKit::Conformer::getPositions | ( | ) | const |
Get a const reference to the vector of atom positions.
Referenced by RDKit::hasNonZeroZCoords().
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inline |
returns whether or not this instance belongs to a molecule
Definition at line 93 of file Conformer.h.
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inline |
Definition at line 148 of file Conformer.h.
Definition at line 71 of file Conformer.h.
Reserve more space for atom position.
Definition at line 90 of file Conformer.h.
Resize the conformer so that more atoms location can be added. Useful, for e.g., when adding hydrogens
Definition at line 87 of file Conformer.h.
Definition at line 149 of file Conformer.h.
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inline |
overload
Definition at line 135 of file Conformer.h.
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inline |
Set the position of the specified atom.
Definition at line 124 of file Conformer.h.
set the ID of this conformer
Definition at line 142 of file Conformer.h.
Definition at line 47 of file Conformer.h.