rdkit.Chem.Pharm2D.SigFactory.SigFactory

Package rdkit :: Package Chem :: Package Pharm2D :: Module SigFactory :: Class SigFactory |
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# Class SigFactory

source code

    object --+
             |
            SigFactory

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

Instance Methods | [hide private]
__init__(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True) x.__init__(...) initializes x; see help(type(x)) for signature | source code
SetBins(self, bins) bins should be a list of 2-tuples | source code
GetBins(self) | source code
GetNumBins(self) | source code
GetSignature(self) | source code
_GetBitSummaryData(self, bitIdx) | source code
GetBitDescriptionAsText(self, bitIdx, includeBins=0, fullPage=1) returns text with a description of the bit | source code
GetBitDescription(self, bitIdx) returns a text description of the bit | source code
GetFeatFamilies(self) | source code
GetMolFeats(self, mol) | source code
GetBitIdx(self, featIndices, dists, sortIndices=True) returns the index for a pharmacophore described using a set of feature indices and distances | source code
GetBitInfo(self, idx) returns information about the given bit | source code
Init(self) Initializes internal parameters. | source code
GetSigSize(self) | source code
_findBinIdx(self, dists, bins, scaffolds) OBSOLETE: this has been rewritten in C++ Internal use only Returns the index of a bin defined by a set of distances. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

### __init__(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True) (Constructor) | source code
    x.__init__(...) initializes x; see help(type(x)) for signature
Overrides: object.__init__ (inherited documentation)

### GetBitDescriptionAsText(self, bitIdx, includeBins=0, fullPage=1) | source code
    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

### GetBitDescription(self, bitIdx) | source code
    returns a text description of the bit

    **Arguments**

      - bitIdx: an integer bit index

    **Returns**

      a string

### GetBitIdx(self, featIndices, dists, sortIndices=True) | source code
    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(self, idx) | source code
    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)

### Init(self) | source code
    Initializes internal parameters.  This **must** be called after
    making any changes to the signature parameters

### _findBinIdx(self, dists, bins, scaffolds) | source code
    OBSOLETE: this has been rewritten in C++
    Internal use only
     Returns the index of a bin defined by a set of distances.

    **Arguments**

      - dists: a sequence of distances (not binned)

      - bins: a sorted sequence of distance bins (2-tuples)

      - scaffolds: a list of possible scaffolds (bin combinations)

    **Returns**

      an integer bin index

    **Note**

      the value returned here is not an index in the overall
      signature.  It is, rather, an offset of a scaffold in the
      possible combinations of distance bins for a given
      proto-pharmacophore.