Embedder.h File Reference

#include <RDGeneral/export.h>
#include <map>
#include <utility>
#include <Geometry/point.h>
#include <GraphMol/ROMol.h>
#include <boost/shared_ptr.hpp>
#include <DistGeom/BoundsMatrix.h>

Go to the source code of this file.

Classes
struct	RDKit::DGeomHelpers::EmbedParameters
	Parameter object for controlling embedding. More...

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDKit::DGeomHelpers

Enumerations
enum	RDKit::DGeomHelpers::EmbedFailureCauses {   RDKit::DGeomHelpers::INITIAL_COORDS = 0 , RDKit::DGeomHelpers::FIRST_MINIMIZATION = 1 , RDKit::DGeomHelpers::CHECK_TETRAHEDRAL_CENTERS = 2 , RDKit::DGeomHelpers::CHECK_CHIRAL_CENTERS = 3 ,   RDKit::DGeomHelpers::MINIMIZE_FOURTH_DIMENSION = 4 , RDKit::DGeomHelpers::ETK_MINIMIZATION = 5 , RDKit::DGeomHelpers::FINAL_CHIRAL_BOUNDS = 6 , RDKit::DGeomHelpers::FINAL_CENTER_IN_VOLUME = 7 ,   RDKit::DGeomHelpers::LINEAR_DOUBLE_BOND = 8 , RDKit::DGeomHelpers::BAD_DOUBLE_BOND_STEREO = 9 , RDKit::DGeomHelpers::CHECK_CHIRAL_CENTERS2 = 10 , RDKit::DGeomHelpers::END_OF_ENUM = 11 }

Functions
RDKIT_DISTGEOMHELPERS_EXPORT void	RDKit::DGeomHelpers::updateEmbedParametersFromJSON (EmbedParameters &params, const std::string &json)
	update parameters from a JSON string
RDKIT_DISTGEOMHELPERS_EXPORT void	RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs, EmbedParameters &params)
	Embed multiple conformations for a molecule.
INT_VECT	RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, unsigned int numConfs, EmbedParameters &params)
int	RDKit::DGeomHelpers::EmbedMolecule (ROMol &mol, EmbedParameters &params)
int	RDKit::DGeomHelpers::EmbedMolecule (ROMol &mol, unsigned int maxIterations=0, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true)
void	RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs=10, int numThreads=1, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=true, bool useMacrocycle14config=true)
INT_VECT	RDKit::DGeomHelpers::EmbedMultipleConfs (ROMol &mol, unsigned int numConfs=10, unsigned int maxIterations=30, int seed=-1, bool clearConfs=true, bool useRandomCoords=false, double boxSizeMult=2.0, bool randNegEig=true, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0, const std::map< int, RDGeom::Point3D > *coordMap=nullptr, double optimizerForceTol=1e-3, bool ignoreSmoothingFailures=false, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0, bool onlyHeavyAtomsForRMS=false, unsigned int ETversion=2, bool useSmallRingTorsions=false, bool useMacrocycleTorsions=false, bool useMacrocycle14config=false)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Variables
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::KDG
	Parameters corresponding to Sereina Riniker's KDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::ETDG
	Parameters corresponding to Sereina Riniker's ETDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::ETKDG
	Parameters corresponding to Sereina Riniker's ETKDG approach.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::ETKDGv2
	Parameters corresponding to Sereina Riniker's ETKDG approach - version 2.
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::ETKDGv3
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters	RDKit::DGeomHelpers::srETKDGv3