RDKit: Embedder.h File Reference

| RDKit Open-source cheminformatics and machine learning.

Loading...
Searching...
No Matches
Classes | Namespaces | Enumerations | Functions | Variables
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::EXCEEDED_TIMEOUT = 11 , RDKit::DGeomHelpers::END_OF_ENUM = 12 }

## Functions
RDKIT_DISTGEOMHELPERS_EXPORT void | RDKit::DGeomHelpers::updateEmbedParametersFromJSON (EmbedParameters &params, const std::string &json)
| update parameters from a JSON string
RDKIT_DISTGEOMHELPERS_EXPORT std::string | RDKit::DGeomHelpers::embedParametersToJSON (const EmbedParameters &params)
| export parameters to 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, unsigned int timeout=0)
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, unsigned int timeout=0)
| 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::ETDGv2
| Parameters corresponding to Sereina Riniker's ETDG approach - version 2.
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