rdkit.Chem.Subshape.SubshapeAligner module — The RDKit 2016.09.1 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