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

type SigFactory

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)

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

Method Details

[hide private]

init(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True)
(Constructor)

source code

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.

type SigFactory

__init__(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True) (Constructor)

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

GetBitDescription(self, bitIdx)

GetBitIdx(self, featIndices, dists, sortIndices=True)

GetBitInfo(self, idx)

Init(self)

_findBinIdx(self, dists, bins, scaffolds)

init(self, featFactory, useCounts=False, minPointCount=2, maxPointCount=3, shortestPathsOnly=True, includeBondOrder=False, skipFeats=None, trianglePruneBins=True)
(Constructor)