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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. 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 & | operator= (const Conformer &other) |
~Conformer () | |
Destructor. More... | |
void | resize (unsigned int size) |
void | reserve (unsigned int size) |
Reserve more space for atom position. More... | |
bool | hasOwningMol () const |
returns whether or not this instance belongs to a molecule More... | |
ROMol & | getOwningMol () const |
Get the molecule that owns this instance. 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) |
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RDProps () | |
RDProps (const RDProps &rhs) | |
RDProps & | operator= (const RDProps &rhs) |
void | clear () |
const Dict & | getDict () const |
gets the underlying Dictionary More... | |
Dict & | getDict () |
STR_VECT | getPropList (bool includePrivate=true, bool includeComputed=true) const |
returns a list with the names of our properties More... | |
template<typename T > | |
void | setProp (const std::string &key, T val, bool computed=false) const |
sets a property value More... | |
template<typename T > | |
void | getProp (const std::string &key, T &res) const |
allows retrieval of a particular property value More... | |
template<typename T > | |
T | getProp (const std::string &key) const |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const std::string &key) const |
void | clearProp (const std::string &key) const |
clears the value of a property More... | |
void | clearComputedProps () const |
clears all of our computed properties More... | |
void | updateProps (const RDProps &source, bool preserveExisting=false) |
update the properties from another More... | |
Protected Member Functions | |
void | setOwningMol (ROMol *mol) |
Set owning moelcule. More... | |
void | setOwningMol (ROMol &mol) |
Set owning moelcule. More... | |
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 43 of file Conformer.h.
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Constructor.
Definition at line 48 of file Conformer.h.
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Constructor with number of atoms specified ID specification.
Definition at line 51 of file Conformer.h.
RDKit::Conformer::Conformer | ( | const Conformer & | other | ) |
Copy Constructor: initialize from a second conformation.
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inline |
Destructor.
Definition at line 65 of file Conformer.h.
const RDGeom::Point3D& RDKit::Conformer::getAtomPos | ( | unsigned int | atomId | ) | const |
Get the position of the specified atom.
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overload
Definition at line 93 of file Conformer.h.
RDGeom::Point3D& RDKit::Conformer::getAtomPos | ( | unsigned int | atomId | ) |
Get the position of the specified atom.
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overload
Definition at line 101 of file Conformer.h.
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get the ID of this conformer
Definition at line 119 of file Conformer.h.
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Get the number of atoms.
Definition at line 125 of file Conformer.h.
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Get the molecule that owns this instance.
Definition at line 78 of file Conformer.h.
References PRECONDITION.
const RDGeom::POINT3D_VECT& RDKit::Conformer::getPositions | ( | ) | const |
Get a const reference to the vector of atom positions.
Referenced by RDKit::hasNonZeroZCoords().
RDGeom::POINT3D_VECT& RDKit::Conformer::getPositions | ( | ) |
Get a reference to the atom positions.
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returns whether or not this instance belongs to a molecule
Definition at line 75 of file Conformer.h.
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Definition at line 128 of file Conformer.h.
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Reserve more space for atom position.
Definition at line 72 of file Conformer.h.
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Resize the conformer so that more atoms location can be added. Useful, for e.g., when adding hydrogens
Definition at line 69 of file Conformer.h.
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Definition at line 129 of file Conformer.h.
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Set the position of the specified atom.
Definition at line 106 of file Conformer.h.
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overload
Definition at line 115 of file Conformer.h.
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set the ID of this conformer
Definition at line 122 of file Conformer.h.
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Set owning moelcule.
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protected |
Set owning moelcule.
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Definition at line 45 of file Conformer.h.