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.