Parameter object for controlling embedding. More...

#include <Embedder.h>

Public Attributes
unsigned int	maxIterations {0}
int	numThreads {1}
int	randomSeed {-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}
double	pruneRmsThresh {-1.0}
bool	onlyHeavyAtomsForRMS {true}
unsigned int	ETversion {2}
boost::shared_ptr< const DistGeom::BoundsMatrix >	boundsMat {nullptr}
bool	embedFragmentsSeparately {true}
bool	useSmallRingTorsions {false}
bool	useMacrocycleTorsions {false}
bool	useMacrocycle14config {false}
unsigned int	timeout {0}
bool	useLegacyImplementation {true}
InitialEmbeddingMode	initialEmbeddingMode {InitialEmbeddingMode::DG_EMBEDDING}
std::shared_ptr< std::map< std::pair< unsigned int, unsigned int >, double > >	CPCI
void(*	callback )(unsigned int)
bool	forceTransAmides {true}
bool	useSymmetryForPruning {true}
double	boundsMatForceScaling {1.0}
bool	onlyInitialEmbedding {false}
bool	trackFailures {false}
std::vector< unsigned int >	failures {}
bool	enableSequentialRandomSeeds {false}
bool	symmetrizeConjugatedTerminalGroupsForPruning {true}
EmbedFF	embedForceField {EmbedFF::UFF}

Detailed Description

Parameter object for controlling embedding.

numConfs Number of conformations to be generated numThreads Sets the number of threads to use (more than one thread will only be used if the RDKit was build with multithread support) If set to zero, the max supported by the system will be used. maxIterations Max. number of times the embedding will be tried if coordinates are not obtained successfully. The default value is 10x the number of atoms. randomSeed provides a seed for the random number generator (so that the same coordinates can be obtained for a molecule on multiple runs) If -1, the RNG will not be seeded. clearConfs Clear all existing conformations on the molecule useRandomCoords Start the embedding from random coordinates instead of using eigenvalues of the distance matrix. boxSizeMult Determines the size of the box that is used for random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times boxSizeMult. If this is a negative number, the side length will equal -boxSizeMult (i.e. independent of the elements of the distance matrix). randNegEig Picks coordinates at random when a embedding process produces negative eigenvalues numZeroFail Fail embedding if we find this many or more zero eigenvalues (within a tolerance) pruneRmsThresh Retain only the conformations out of 'numConfs' after embedding that are at least this far apart from each other. RMSD is computed on the heavy atoms. Prunining is greedy; i.e. the first embedded conformation is retained and from then on only those that are at least pruneRmsThresh away from already retained conformations are kept. The pruning is done after embedding and bounds violation minimization. No pruning by default. coordMap a map of int to Point3D, between atom IDs and their locations their locations. If this container is provided, the coordinates are used to set distance constraints on the embedding. The resulting conformer(s) should have distances between the specified atoms that reproduce those between the points in coordMap. Because the embedding produces a molecule in an arbitrary reference frame, an alignment step is required to actually reproduce the provided coordinates. optimizerForceTol set the tolerance on forces in the DGeom optimizer (this shouldn't normally be altered in client code). ignoreSmoothingFailures try to embed the molecule even if triangle bounds smoothing fails enforceChirality enforce the correct chirality if chiral centers are present useExpTorsionAnglePrefs impose experimental torsion-angle preferences useBasicKnowledge impose "basic knowledge" terms such as flat aromatic rings, ketones, etc. ETversion version of the experimental torsion-angle preferences verbose print output of experimental torsion-angle preferences basinThresh set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code). onlyHeavyAtomsForRMS only use the heavy atoms when doing RMS filtering boundsMat custom bound matrix to specify upper and lower bounds of atom pairs embedFragmentsSeparately embed each fragment of molecule in turn useSmallRingTorsions optional torsions to improve small ring conformer sampling useMacrocycleTorsions optional torsions to improve macrocycle conformer sampling useMacrocycle14config This forces amides and esters to be trans in macrocycles. This does not affect chain amides / esters! timeout time out in seconds CPCI custom columbic interactions between atom pairs callback void pointer to a function for reporting progress, will be called with the current iteration number. forceTransAmides This forces chain amides and esters to be trans. This does not affect amides / esters in macrocycles!

useSymmetryForPruning use molecule symmetry when doing the RMSD pruning. NOTE that for reasons of computational efficiency, setting this will also set onlyHeavyAtomsForRMS to true. trackFailures keep track of which checks during the embedding process fail failures if trackFailures is true, this is used to track the number of times each embedding check fails enableSequentialRandomSeeds handle the random number seeds so that conformer generation can be restarted embedFF Force Field to use to determine ideal 1-2 and 1-3 distances.

Definition at line 151 of file Embedder.h.

Member Data Documentation

◆ basinThresh

double RDKit::DGeomHelpers::EmbedParameters::basinThresh {5.0}

Definition at line 167 of file Embedder.h.

◆ boundsMat

boost::shared_ptr<const DistGeom::BoundsMatrix> RDKit::DGeomHelpers::EmbedParameters::boundsMat {nullptr}

Definition at line 171 of file Embedder.h.

◆ boundsMatForceScaling

double RDKit::DGeomHelpers::EmbedParameters::boundsMatForceScaling {1.0}

Definition at line 184 of file Embedder.h.

◆ boxSizeMult

double RDKit::DGeomHelpers::EmbedParameters::boxSizeMult {2.0}

Definition at line 157 of file Embedder.h.

◆ callback

void(* RDKit::DGeomHelpers::EmbedParameters::callback) (unsigned int)

inline

Definition at line 181 of file Embedder.h.

◆ clearConfs

bool RDKit::DGeomHelpers::EmbedParameters::clearConfs {true}

Definition at line 155 of file Embedder.h.

◆ coordMap

const std::map<int, RDGeom::Point3D>* RDKit::DGeomHelpers::EmbedParameters::coordMap {nullptr}

Definition at line 160 of file Embedder.h.

◆ CPCI

std::shared_ptr<std::map<std::pair<unsigned int, unsigned int>, double> > RDKit::DGeomHelpers::EmbedParameters::CPCI

Initial value:

{

nullptr}

Definition at line 179 of file Embedder.h.

◆ embedForceField

EmbedFF RDKit::DGeomHelpers::EmbedParameters::embedForceField {EmbedFF::UFF}

Definition at line 190 of file Embedder.h.

◆ embedFragmentsSeparately

bool RDKit::DGeomHelpers::EmbedParameters::embedFragmentsSeparately {true}

Definition at line 172 of file Embedder.h.

◆ enableSequentialRandomSeeds

bool RDKit::DGeomHelpers::EmbedParameters::enableSequentialRandomSeeds {false}

Definition at line 188 of file Embedder.h.

◆ enforceChirality

bool RDKit::DGeomHelpers::EmbedParameters::enforceChirality {true}

Definition at line 163 of file Embedder.h.

◆ ETversion

unsigned int RDKit::DGeomHelpers::EmbedParameters::ETversion {2}

Definition at line 170 of file Embedder.h.

◆ failures

std::vector<unsigned int> RDKit::DGeomHelpers::EmbedParameters::failures {}

Definition at line 187 of file Embedder.h.

◆ forceTransAmides

bool RDKit::DGeomHelpers::EmbedParameters::forceTransAmides {true}

Definition at line 182 of file Embedder.h.

◆ ignoreSmoothingFailures

bool RDKit::DGeomHelpers::EmbedParameters::ignoreSmoothingFailures {false}

Definition at line 162 of file Embedder.h.

◆ initialEmbeddingMode

InitialEmbeddingMode RDKit::DGeomHelpers::EmbedParameters::initialEmbeddingMode {InitialEmbeddingMode::DG_EMBEDDING}

Definition at line 178 of file Embedder.h.

◆ maxIterations

unsigned int RDKit::DGeomHelpers::EmbedParameters::maxIterations {0}

Definition at line 152 of file Embedder.h.

◆ numThreads

int RDKit::DGeomHelpers::EmbedParameters::numThreads {1}

Definition at line 153 of file Embedder.h.

◆ numZeroFail

unsigned int RDKit::DGeomHelpers::EmbedParameters::numZeroFail {1}

Definition at line 159 of file Embedder.h.

◆ onlyHeavyAtomsForRMS

bool RDKit::DGeomHelpers::EmbedParameters::onlyHeavyAtomsForRMS {true}

Definition at line 169 of file Embedder.h.

◆ onlyInitialEmbedding

bool RDKit::DGeomHelpers::EmbedParameters::onlyInitialEmbedding {false}

Definition at line 185 of file Embedder.h.

◆ optimizerForceTol

double RDKit::DGeomHelpers::EmbedParameters::optimizerForceTol {1e-3}

Definition at line 161 of file Embedder.h.

◆ pruneRmsThresh

double RDKit::DGeomHelpers::EmbedParameters::pruneRmsThresh {-1.0}

Definition at line 168 of file Embedder.h.

◆ randNegEig

bool RDKit::DGeomHelpers::EmbedParameters::randNegEig {true}

Definition at line 158 of file Embedder.h.

◆ randomSeed

int RDKit::DGeomHelpers::EmbedParameters::randomSeed {-1}

Definition at line 154 of file Embedder.h.

◆ symmetrizeConjugatedTerminalGroupsForPruning

bool RDKit::DGeomHelpers::EmbedParameters::symmetrizeConjugatedTerminalGroupsForPruning {true}

Definition at line 189 of file Embedder.h.

◆ timeout

unsigned int RDKit::DGeomHelpers::EmbedParameters::timeout {0}

Definition at line 176 of file Embedder.h.

◆ trackFailures

bool RDKit::DGeomHelpers::EmbedParameters::trackFailures {false}

Definition at line 186 of file Embedder.h.

◆ useBasicKnowledge

bool RDKit::DGeomHelpers::EmbedParameters::useBasicKnowledge {false}

Definition at line 165 of file Embedder.h.

◆ useExpTorsionAnglePrefs

bool RDKit::DGeomHelpers::EmbedParameters::useExpTorsionAnglePrefs {false}

Definition at line 164 of file Embedder.h.

◆ useLegacyImplementation

bool RDKit::DGeomHelpers::EmbedParameters::useLegacyImplementation {true}

Definition at line 177 of file Embedder.h.

◆ useMacrocycle14config

bool RDKit::DGeomHelpers::EmbedParameters::useMacrocycle14config {false}

Definition at line 175 of file Embedder.h.

◆ useMacrocycleTorsions

bool RDKit::DGeomHelpers::EmbedParameters::useMacrocycleTorsions {false}

Definition at line 174 of file Embedder.h.

◆ useRandomCoords

bool RDKit::DGeomHelpers::EmbedParameters::useRandomCoords {false}

Definition at line 156 of file Embedder.h.

◆ useSmallRingTorsions

bool RDKit::DGeomHelpers::EmbedParameters::useSmallRingTorsions {false}

Definition at line 173 of file Embedder.h.

◆ useSymmetryForPruning

bool RDKit::DGeomHelpers::EmbedParameters::useSymmetryForPruning {true}

Definition at line 183 of file Embedder.h.

◆ verbose

bool RDKit::DGeomHelpers::EmbedParameters::verbose {false}

Definition at line 166 of file Embedder.h.

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

Embedder.h

Public Attributes