RDKit
Open-source cheminformatics and machine learning.
RDKit::DGeomHelpers::EmbedParameters Struct Reference

Parameter object for controlling embedding. More...

#include <Embedder.h>

Public Member Functions

 EmbedParameters ()
 
 EmbedParameters (unsigned int maxIterations, int numThreads, int randomSeed, bool clearConfs, bool useRandomCoords, double boxSizeMult, bool randNegEig, unsigned int numZeroFail, const std::map< int, RDGeom::Point3D > *coordMap, double optimizerForceTol, bool ignoreSmoothingFailures, bool enforceChirality, bool useExpTorsionAnglePrefs, bool useBasicKnowledge, bool verbose, double basinThresh, double pruneRmsThresh)
 

Public Attributes

unsigned int maxIterations
 
int numThreads
 
int randomSeed
 
bool clearConfs
 
bool useRandomCoords
 
double boxSizeMult
 
bool randNegEig
 
unsigned int numZeroFail
 
const std::map< int, RDGeom::Point3D > * coordMap
 
double optimizerForceTol
 
bool ignoreSmoothingFailures
 
bool enforceChirality
 
bool useExpTorsionAnglePrefs
 
bool useBasicKnowledge
 
bool verbose
 
double basinThresh
 
double pruneRmsThresh
 

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 negative, 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.

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).

Definition at line 298 of file Embedder.h.

Constructor & Destructor Documentation

RDKit::DGeomHelpers::EmbedParameters::EmbedParameters ( )
inline

Definition at line 316 of file Embedder.h.

RDKit::DGeomHelpers::EmbedParameters::EmbedParameters ( unsigned int  maxIterations,
int  numThreads,
int  randomSeed,
bool  clearConfs,
bool  useRandomCoords,
double  boxSizeMult,
bool  randNegEig,
unsigned int  numZeroFail,
const std::map< int, RDGeom::Point3D > *  coordMap,
double  optimizerForceTol,
bool  ignoreSmoothingFailures,
bool  enforceChirality,
bool  useExpTorsionAnglePrefs,
bool  useBasicKnowledge,
bool  verbose,
double  basinThresh,
double  pruneRmsThresh 
)
inline

Member Data Documentation

double RDKit::DGeomHelpers::EmbedParameters::basinThresh
double RDKit::DGeomHelpers::EmbedParameters::boxSizeMult
bool RDKit::DGeomHelpers::EmbedParameters::clearConfs
const std::map<int, RDGeom::Point3D>* RDKit::DGeomHelpers::EmbedParameters::coordMap
bool RDKit::DGeomHelpers::EmbedParameters::enforceChirality
bool RDKit::DGeomHelpers::EmbedParameters::ignoreSmoothingFailures
unsigned int RDKit::DGeomHelpers::EmbedParameters::maxIterations
int RDKit::DGeomHelpers::EmbedParameters::numThreads

Definition at line 300 of file Embedder.h.

Referenced by RDKit::DGeomHelpers::EmbedMultipleConfs().

unsigned int RDKit::DGeomHelpers::EmbedParameters::numZeroFail
double RDKit::DGeomHelpers::EmbedParameters::optimizerForceTol
double RDKit::DGeomHelpers::EmbedParameters::pruneRmsThresh

Definition at line 315 of file Embedder.h.

Referenced by RDKit::DGeomHelpers::EmbedMultipleConfs().

bool RDKit::DGeomHelpers::EmbedParameters::randNegEig
int RDKit::DGeomHelpers::EmbedParameters::randomSeed
bool RDKit::DGeomHelpers::EmbedParameters::useBasicKnowledge
bool RDKit::DGeomHelpers::EmbedParameters::useExpTorsionAnglePrefs
bool RDKit::DGeomHelpers::EmbedParameters::useRandomCoords
bool RDKit::DGeomHelpers::EmbedParameters::verbose

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