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