rdkit.Chem.rdDistGeom module¶

Module containing functions to compute atomic coordinates in 3D using distance geometry

class rdkit.Chem.rdDistGeom.EmbedFailureCauses(*values)¶

Bases: IntEnum

BAD_DOUBLE_BOND_STEREO = 9¶

CHECK_CHIRAL_CENTERS = 3¶

CHECK_CHIRAL_CENTERS2 = 10¶

CHECK_TETRAHEDRAL_CENTERS = 2¶

CLASH = 14¶

ETK_MINIMIZATION = 5¶

EXCEEDED_TIMEOUT = 11¶

FINAL_CENTER_IN_VOLUME = 7¶

FINAL_CHIRAL_BOUNDS = 6¶

FIRST_MINIMIZATION = 1¶

INITIAL_COORDS = 0¶

KTERM_VIOLATION = 13¶

LINEAR_DOUBLE_BOND = 8¶

MINIMIZATION = 12¶

MINIMIZE_FOURTH_DIMENSION = 4¶

class rdkit.Chem.rdDistGeom.EmbedParameters(self)¶

Bases: object

Parameters controlling embedding

property ETversion¶: version of the experimental torsion-angle preferences

GetFailureCounts(self) → tuple¶: returns the counts of each failure type

SetBoundsMat(self, boundsMatArg: numpy.ndarray[dtype=float64, shape=(*, *), order='C']) → None¶: set the distance-bounds matrix to be used (no triangle smoothing will be done on this) from a Numpy array

SetCPCI(self, CPCIdict: dict) → None¶: set the customised pairwise Columb-like interaction to atom pairs. used during structural minimisation stage

SetCoordMap(self, arg: dict, /) → None¶: sets the coordmap to be used

property basinThresh¶: set the basin threshold for the DGeom force field.

property boundsMatForceScaling¶: scale the weights of the atom pair distance restraints relative to the other types of restraints

property boxSizeMult¶: determines the size of the box used for random coordinates

property clearConfs¶: clear all existing conformations on the molecule

property embedFragmentsSeparately¶: split the molecule into fragments and embed them separately

property enableSequentialRandomSeeds¶: handle random number seeds so that conformer generation can be restarted

property enforceChirality¶: enforce correct chirilaty if chiral centers are present

property forceTransAmides¶: This forces chain amides and esters to be trans. This does not affect amides / esters in macrocycles!

property ignoreSmoothingFailures¶: try and embed the molecule if if triangle smoothing of the bounds matrix fails

property maxIterations¶: maximum number of embedding attempts to use for a single conformation

property numThreads¶: number of threads to use when embedding multiple conformations

property numZeroFail¶: fail embedding if we have at least this many zero eigenvalues

property onlyHeavyAtomsForRMS¶: Only consider heavy atoms when doing RMS filtering

property optimizerForceTol¶: the tolerance to be used during the distance-geometry force field minimization

property pruneRmsThresh¶

keep only conformations that are at least this far apart from each other

Type:: used to filter multiple conformations

property randNegEig¶: if the embedding yields a negative eigenvalue, pick coordinates that correspond to this component at random

property randomSeed¶: seed for the random number generator

property symmetrizeConjugatedTerminalGroupsForPruning¶: symmetrize terminal conjugated groups for RMSD pruning

property timeout¶: maximum time in seconds to generate a conformer for a single molecule fragment. If set to 0, no timeout is set

property trackFailures¶: keep track of which checks during the embedding process fail

property useBasicKnowledge¶: impose basic-knowledge constraints such as flat rings

property useExpTorsionAnglePrefs¶: impose experimental torsion angle preferences

property useLegacyImplementation¶: whether to use the combined minimization approach

property useMacrocycle14config¶: This forces amides and esters to be trans in macrocycles. This does not affect chain amides / esters!

property useMacrocycleTorsions¶: impose macrocycle torsion angle preferences

property useRandomCoords¶: start the embedding from random coordinates instead of using eigenvalues of the distance matrix

property useSmallRingTorsions¶: impose small ring torsion angle preferences

property useSymmetryForPruning¶: use molecule symmetry when doing the RMSD pruning. Note that this option automatically also sets onlyHeavyAtomsForRMS to true.

property verbose¶: be verbose about configuration