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