rdkit.Numerics.rdAlignment module — The RDKit 2025.09.6 documentation

# rdkit.Numerics.rdAlignment module

Module containing functions to align pairs of points in 3D

rdkit.Numerics.rdAlignment.GetAlignmentTransform((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)refPoints, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)probePoints[, (rdkit.Chem.rdMolDescriptors.AtomPairsParameters)weights=[][, (bool)reflect=False[, (int)maxIterations=50]]]) → object :

  Compute the optimal alignment (minimum RMSD) between two set of points using the quaternion algorithm

  > ARGUMENTS:

  > > - refPointsreference points specified as a N by 3 Numeric array or

  > >     sequence of 3-sequences or sequence of Point3Ds

  > > - probePointsprobe points to align to reference points - same format

  > >     restrictions as reference points apply here

  > > - weights : optional numeric vector or list of weights to associate to each pair of points

  > > - reflect : reflect the probe points before attempting alignment

  > > - maxIteration : maximum number of iterations for the eigen solver

  > RETURNS:

  > > a 2-tuple:

  > >   - SSD value for the alignment

  > >   - the 4x4 transform matrix, as a Numeric array

  C++ signature :

    _object* GetAlignmentTransform(boost::python::api::object,boost::python::api::object [,boost::python::api::object=[] [,bool=False [,unsigned int=50]]])