rdkit.DistanceGeometry.DistGeom module — The RDKit 2025.09.6 documentation

# rdkit.DistanceGeometry.DistGeom module

Module containing functions for basic distance geometry operations

rdkit.DistanceGeometry.DistGeom.DoTriangleSmoothing((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)boundsMatrix[, (float)tol=0.0]) → bool :

  Do triangle smoothing on a bounds matrix

  > ARGUMENTS:

  > > - mat: a square Numeric array of doubles containing the bounds matrix, this matrix

  > >     is modified by the smoothing

  > RETURNS:

  > > a boolean indicating whether or not the smoothing worked.

  C++ signature :

    bool DoTriangleSmoothing(boost::python::api::object [,double=0.0])

rdkit.DistanceGeometry.DistGeom.EmbedBoundsMatrix((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)boundsMatrix[, (int)maxIters=10[, (bool)randomizeOnFailure=False[, (int)numZeroFail=2[, (list)weights=[][, (int)randomSeed=-1]]]]]) → object :

  Embed a bounds matrix and return the coordinates

  > ARGUMENTS:

  > > - boundsMatrix: a square Numeric array of doubles containing the bounds matrix, this matrix

  > >     should already be smoothed

  > > - maxIters: (optional) the maximum number of random distance matrices to try

  > > - randomizeOnFailure: (optional) toggles using random coords if a matrix fails to embed

  > > - numZeroFail: (optional) sets the number of zero eigenvalues to be considered a failure

  > > - weights: (optional) a sequence of 3 sequences (i,j,weight) indicating elements of

  > >     the bounds matrix whose weights should be adjusted

  > > - randomSeed: (optional) sets the random number seed used for embedding

  > RETURNS:

  > > a Numeric array of doubles with the coordinates

  C++ signature :

    _object* EmbedBoundsMatrix(boost::python::api::object [,int=10 [,bool=False [,int=2 [,boost::python::list=[] [,int=-1]]]]])