rdkit.Chem.Subshape.SubshapeAligner module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Subshape.SubshapeAligner module

rdkit.Chem.Subshape.SubshapeAligner.ClusterAlignments(mol, alignments, builder, neighborTol=0.1, distMetric=1, tempConfId=1001)

  clusters a set of alignments and returns the cluster centroid

rdkit.Chem.Subshape.SubshapeAligner.GetShapeShapeDistance(s1, s2, distMetric)

  returns the distance between two shapes according to the provided metric

class rdkit.Chem.Subshape.SubshapeAligner.SubshapeAligner

  Bases: `object`

  GetSubshapeAlignments(targetMol, target, queryMol, query, builder, tgtConf=-1, queryConf=-1, pruneStats=None)
  GetTriangleMatches(target, query)

    this is a generator function returning the possible triangle matches between the two shapes

  PruneMatchesUsingDirection(target, query, alignments, pruneStats=None)
  PruneMatchesUsingFeatures(target, query, alignments, pruneStats=None)
  PruneMatchesUsingShape(targetMol, target, queryMol, query, builder, alignments, tgtConf=-1, queryConf=-1, pruneStats=None)
  coarseGridToleranceMult = 1.0
  dirThresh = 2.6
  distMetric = 1
  edgeTol = 6.0
  medGridToleranceMult = 1.0
  numFeatThresh = 3
  shapeDistTol = 0.2
  triangleRMSTol = 1.0

class rdkit.Chem.Subshape.SubshapeAligner.SubshapeAlignment

  Bases: `object`

  alignedConfId = -1
  dirMatch = 0.0
  queryTri = None
  shapeDist = 0.0
  targetTri = None
  transform = None
  triangleSSD = None

class rdkit.Chem.Subshape.SubshapeAligner.SubshapeDistanceMetric

  Bases: `object`

  PROTRUDE = 1
  TANIMOTO = 0

rdkit.Chem.Subshape.SubshapeAligner.TransformMol(mol, tform, confId=-1, newConfId=100)

  Applies the transformation to a molecule and sets it up with a single conformer