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:

mol – the molecule of interest atomId – the atom to remove the pairs for (if -1, no pair is removed) fpType – the type of AP fingerprint (‘normal’, ‘hashed’, ‘bv’) nBits – the size of the bit vector (only for fpType=’bv’) minLength – the minimum path length for an atom pair maxLength – the maxmimum path length for an atom pair nBitsPerEntry – the number of bits available for each 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:

refMol – the reference molecule probeMol – the probe molecule fpFunction – the fingerprint function metric – the similarity metric

Note:

If fpFunction needs additional parameters, use a lambda construct

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:

probeMol – the probe molecule fpFunction – the fingerprint function predictionFunction – the prediction function of the ML model

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:

mol – the molecule of interest radius – the maximum radius fpType – the type of Morgan fingerprint: ‘count’ or ‘bv’ atomId – the atom to remove the environments for (if -1, no environments is removed) nBits – the size of the bit vector (only for fpType = ‘bv’) useFeatures – if false: 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:

mol – the molecule of interest atomId – the atom to remove the paths for (if -1, no path is removed) fpType – the type of RDKit fingerprint: ‘bv’ nBits – the size of the bit vector minPath – minimum path length maxPath – maximum path length nBitsPerHash – number of to set per path

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

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

Parameters:

refMol – the reference molecule probeMol – the probe molecule fpFunction – the fingerprint function metric – the similarity metric. kwargs – additional arguments for drawing

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

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

Parameters:

probeMol – the probe molecule fpFunction – the fingerprint function predictionFunction – the prediction function of the ML model kwargs – additional arguments for drawing

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

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

Parameters:

mol – the molecule of interest colorMap – the matplotlib color map scheme, default is custom PiWG color map scale – the scaling: scale < 0 -> the absolute maximum weight is used as maximum scale

scale = double -> this is the maximum scale

size – the size of the figure sigma – the sigma for the Gaussians coordScale – scaling factor for the coordinates step – the step for calcAtomGaussian colors – color of the contour lines contourLines – if integer number N: N contour lines are drawn

if list(numbers): contour lines at these numbers are drawn

alpha – the alpha blending value for the contour lines kwargs – additional arguments for drawing

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

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

Parameters:

weights – the list with the atomic weights

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:

mol – the molecule of interest atomId – the atom to remove the torsions for (if -1, no torsion is removed) fpType – the type of TT fingerprint (‘normal’, ‘hashed’, ‘bv’) nBits – the size of the bit vector (only for fpType=’bv’) minLength – the minimum path length for an atom pair maxLength – the maxmimum path length for an atom pair nBitsPerEntry – the number of bits available for each torsion

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