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RDKit
Open-source cheminformatics and machine learning.
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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, bool onlyHeavyAtomsForRMS, unsigned int ETversion=1) | |
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 |
bool | onlyHeavyAtomsForRMS |
unsigned int | ETversion |
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
Definition at line 99 of file Embedder.h.
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inline |
Definition at line 119 of file Embedder.h.
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inline |
Definition at line 139 of file Embedder.h.
References RDKit::DGeomHelpers::EmbedMultipleConfs(), and RDKIT_DISTGEOMHELPERS_EXPORT.
double RDKit::DGeomHelpers::EmbedParameters::basinThresh |
Definition at line 115 of file Embedder.h.
double RDKit::DGeomHelpers::EmbedParameters::boxSizeMult |
Definition at line 105 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::clearConfs |
Definition at line 103 of file Embedder.h.
const std::map<int, RDGeom::Point3D>* RDKit::DGeomHelpers::EmbedParameters::coordMap |
Definition at line 108 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::enforceChirality |
Definition at line 111 of file Embedder.h.
unsigned int RDKit::DGeomHelpers::EmbedParameters::ETversion |
Definition at line 118 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::ignoreSmoothingFailures |
Definition at line 110 of file Embedder.h.
unsigned int RDKit::DGeomHelpers::EmbedParameters::maxIterations |
Definition at line 100 of file Embedder.h.
int RDKit::DGeomHelpers::EmbedParameters::numThreads |
Definition at line 101 of file Embedder.h.
unsigned int RDKit::DGeomHelpers::EmbedParameters::numZeroFail |
Definition at line 107 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::onlyHeavyAtomsForRMS |
Definition at line 117 of file Embedder.h.
double RDKit::DGeomHelpers::EmbedParameters::optimizerForceTol |
Definition at line 109 of file Embedder.h.
double RDKit::DGeomHelpers::EmbedParameters::pruneRmsThresh |
Definition at line 116 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::randNegEig |
Definition at line 106 of file Embedder.h.
int RDKit::DGeomHelpers::EmbedParameters::randomSeed |
Definition at line 102 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::useBasicKnowledge |
Definition at line 113 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::useExpTorsionAnglePrefs |
Definition at line 112 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::useRandomCoords |
Definition at line 104 of file Embedder.h.
bool RDKit::DGeomHelpers::EmbedParameters::verbose |
Definition at line 114 of file Embedder.h.