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