rdkit.DistanceGeometry.DistGeom module

Module containing functions for basic distance geometry operations

rdkit.DistanceGeometry.DistGeom.DoTriangleSmoothing((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((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]]]]])