rdkit.Chem.Draw.SimilarityMaps module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Draw.SimilarityMaps module

rdkit.Chem.Draw.SimilarityMaps.GetAPFingerprint(mol, atomId=-1, fpType='normal', nBits=2048, minLength=1, maxLength=30, nBitsPerEntry=4, **kwargs)

  Calculates the atom pairs fingerprint with the torsions of atomId removed.

  Parameters:

    - interest (mol -- the molecule of)

    - for (atomId -- the atom to remove the pairs)

    - fingerprint (fpType -- the type of AP)

    - vector (nBits -- the size of the bit)

    - pair (nBitsPerEntry -- the number of bits available for each)

    - pair

    - pair

rdkit.Chem.Draw.SimilarityMaps.GetAtomicWeightsForFingerprint(refMol, probeMol, fpFunction, metric=<Boost.Python.function object>)

  Calculates the atomic weights for the probe molecule based on a fingerprint function and a metric.

  Parameters:

    - molecule (probeMol -- the probe)

    - molecule

    - function (fpFunction -- the fingerprint)

    - metric (metric -- the similarity)

  Note

  If fpFunction needs additional parameters, use a lambda construct

rdkit.Chem.Draw.SimilarityMaps.GetAtomicWeightsForFingerprintGenerator(refMol, probeMol, fpg, useCounts=False, metric=<Boost.Python.function object>)

  Calculates the atomic weights for the probe molecule based on a fingerprint function and a metric.

  Parameters:

    - molecule (probeMol -- the probe)

    - molecule

    - generator (fpg -- the fingerprint)

    - metric (metric -- the similarity)

rdkit.Chem.Draw.SimilarityMaps.GetAtomicWeightsForModel(probeMol, fpFunction, predictionFunction)

  Calculates the atomic weights for the probe molecule based on a fingerprint function and the prediction function of a ML model.

  Parameters:

    - molecule (probeMol -- the probe)

    - function (fpFunction -- the fingerprint)

    - model (predictionFunction -- the prediction function of the ML)

rdkit.Chem.Draw.SimilarityMaps.GetMorganFingerprint(mol, atomId=-1, radius=2, fpType='bv', nBits=2048, useFeatures=False, **kwargs)

  Calculates the Morgan fingerprint with the environments of atomId removed.

  Parameters:

    - interest (mol -- the molecule of)

    - radius (radius -- the maximum)

    - fingerprint (fpType -- the type of Morgan) – ‘count’ or ‘bv’

    - for (atomId -- the atom to remove the environments)

    - vector (nBits -- the size of the bit)

    - false (useFeatures -- if) – ConnectivityMorgan, if true: FeatureMorgan

  any additional keyword arguments will be passed to the fingerprinting function.

rdkit.Chem.Draw.SimilarityMaps.GetRDKFingerprint(mol, atomId=-1, fpType='bv', nBits=2048, minPath=1, maxPath=5, nBitsPerHash=2, **kwargs)

  Calculates the RDKit fingerprint with the paths of atomId removed.

  Parameters:

    - interest (mol -- the molecule of)

    - for (atomId -- the atom to remove the paths)

    - fingerprint (fpType -- the type of RDKit) – ‘bv’

    - vector (nBits -- the size of the bit)

    - length (maxPath -- maximum path)

    - length

    - path (nBitsPerHash -- number of to set per)

rdkit.Chem.Draw.SimilarityMaps.GetSimilarityMapForFingerprint(refMol, probeMol, fpFunction, draw2d, metric=<Boost.Python.function object>, **kwargs)

  Generates the similarity map for a given reference and probe molecule, fingerprint function and similarity metric.

  Parameters:

    - molecule (probeMol -- the probe)

    - molecule

    - function (fpFunction -- the fingerprint)

    - metric. (metric -- the similarity)

    - drawing (kwargs -- additional arguments for)

rdkit.Chem.Draw.SimilarityMaps.GetSimilarityMapForFingerprintGenerator(refMol, probeMol, fpg, draw2d, metric=<Boost.Python.function object>, useCounts=False, **kwargs)

  Generates the similarity map for a given reference and probe molecule, fingerprint function and similarity metric.

  Parameters:

    - molecule (probeMol -- the probe)

    - molecule

    - generator (fpg -- the fingerprint)

    - metric. (metric -- the similarity)

    - drawing (kwargs -- additional arguments for)

rdkit.Chem.Draw.SimilarityMaps.GetSimilarityMapForModel(probeMol, fpFunction, predictionFunction, draw2d, **kwargs)

  Generates the similarity map for a given ML model and probe molecule, and fingerprint function.

  Parameters:

    - molecule (probeMol -- the probe)

    - function (fpFunction -- the fingerprint)

    - model (predictionFunction -- the prediction function of the ML)

    - drawing (kwargs -- additional arguments for)

rdkit.Chem.Draw.SimilarityMaps.GetSimilarityMapFromWeights(mol, weights, draw2d, colorMap=None, scale=-1, size=(250, 250), sigma=None, coordScale=1.5, step=0.01, colors='k', contourLines=10, alpha=0.5, gridResolution=0.1, extraGridPadding=0.5, useFillThreshold=False, fillThreshold=0.01, fillThresholdIsFraction=True, **kwargs)

  Generates the similarity map for a molecule given the atomic weights.

  Parameters:

    - interest (mol -- the molecule of)

    - use (weights -- the weights to)

    - object (draw2d -- the RDKit drawing)

    - scheme (colorMap -- the matplotlib color map)

    - map (default is custom PiWG color)

    - scaling (scale -- the) – scale < 0 -> the absolute maximum weight is used as maximum scale scale = double -> this is the maximum scale

    - figure (size -- the size of the)

    - Gaussians (sigma -- the sigma for the)

    - coordinates (coordScale -- scaling factor for the)

    - calcAtomGaussian (step -- the step for)

    - lines (alpha -- the alpha blending value for the contour)

    - N (contourLines -- if integer number) – N contour lines are drawn if list(numbers): contour lines at these numbers are drawn

    - lines

    - grid (extraGridPadding -- the extra padding of the)

    - grid

    - filled (useFillThreshold -- use a magnitude threshold to determine if a grid box is)

    - boxes (fillThreshold -- the magnitude threshold for filling grid)

    - True (fillThresholdIsFraction -- if)

    - range (the fillThreshold is a fraction of the data)

    - drawing (kwargs -- additional arguments for)

rdkit.Chem.Draw.SimilarityMaps.GetStandardizedWeights(weights)

  Normalizes the weights, such that the absolute maximum weight equals 1.0.

  Parameters:

    weights (weights -- the list with the atomic)

rdkit.Chem.Draw.SimilarityMaps.GetTTFingerprint(mol, atomId=-1, fpType='normal', nBits=2048, targetSize=4, nBitsPerEntry=4, **kwargs)

  Calculates the topological torsion fingerprint with the pairs of atomId removed.

  Parameters:

    - interest (mol -- the molecule of)

    - for (atomId -- the atom to remove the torsions)

    - fingerprint (fpType -- the type of TT)

    - vector (nBits -- the size of the bit)

    - pair (maxLength -- the maxmimum path length for an atom)

    - pair

    - torsion (nBitsPerEntry -- the number of bits available for each)

  any additional keyword arguments will be passed to the fingerprinting function.