rdkit.Chem.Pharm2D.SigFactory module

contains factory class for producing signatures

class rdkit.Chem.Pharm2D.SigFactory.SigFactory(featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True)

Bases: object

SigFactory’s are used by creating one, setting the relevant parameters, then calling the GetSignature() method each time a signature is required.

GetBins()

GetBitDescription(bitIdx)

returns a text description of the bit

Arguments

• bitIdx: an integer bit index

Returns

a string

GetBitDescriptionAsText(bitIdx, includeBins=0, fullPage=1)

returns text with a description of the bit

Arguments

• bitIdx: an integer bit index
• includeBins: (optional) if nonzero, information about the bins will be included as well
• fullPage: (optional) if nonzero, html headers and footers will be included (so as to make the output a complete page)

Returns

a string with the HTML

GetBitIdx(featIndices, dists, sortIndices=True)

returns the index for a pharmacophore described using a set of

feature indices and distances

Arguments*

• featIndices: a sequence of feature indices
• dists: a sequence of distance between the features, only the unique distances should be included, and they should be in the order defined in Utils.
• sortIndices : sort the indices

Returns

the integer bit index

GetBitInfo(idx)

returns information about the given bit

Arguments

• idx: the bit index to be considered

Returns

a 3-tuple:

1. the number of points in the pharmacophore
2. the proto-pharmacophore (tuple of pattern indices)
3. the scaffold (tuple of distance indices)

GetFeatFamilies()

GetMolFeats(mol)

GetNumBins()

GetSigSize()

GetSignature()

Init()

Initializes internal parameters. This must be called after making any changes to the signature parameters

SetBins(bins)

bins should be a list of 2-tuples