Package Chem :: Package Pharm2D :: Module Signature :: Class Pharm2DSig

Class Pharm2DSig

object --+
         |
        Pharm2DSig



**Notes on Use**

  - After any changes, the Init() method should be called

**Important Attributes**

 - patterns: a list of SmartsPatterns used to determine the features
    patterns can be initialized directly from the list or from a list of SMARTS
    strings

 - bins: the list of distance bins to be used.

 - minCount/maxCount: the minimum/maximum number of points to be included
    in a pharmacophore

 - shortestPathsOnly: toggles limiting the path-discovery algorithms to
    only find the shortest paths between 2 features.

 - includeBondOrder: toggles inclusion of bond order in consideration of
    shortest paths.

**Limitations of Current Implementation**

 - All distances have the same numbers of bins

 - Only shortest-path matches are implemented

Instance Methods

[hide private]

__init__(self, patts=None, bins=None, labels=None, minCnt=2, maxCnt=4, shortestPathsOnly=1, includeBondOrder=0)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

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_initLocals(self)
Internal use only...

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__getstate__(self)
used by the pickling machinery...

source code

__setstate__(self, state)
used by the pickling machinery...

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__len__(self)

source code

__getitem__(self, idx)

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SetPatterns(self, patts)

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SetPatternsFromSmarts(self, smarts)

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GetPattern(self, which)

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GetNumPatterns(self)

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SetLabels(self, labels)

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GetLabel(self, which)

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SetBins(self, bins)
bins should be a list of 2-tuples

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GetBin(self, which)

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GetNumBins(self)

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GetMinDist(self)

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GetMaxDist(self)

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SetMinCount(self, min)

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GetMinCount(self)

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SetMaxCount(self, max)

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GetMaxCount(self)

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SetShortestPathsOnly(self, val)

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GetShortestPathsOnly(self)

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SetIncludeBondOrder(self, val)

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GetIncludeBondOrder(self)

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GetSize(self)

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Init(self, createBitVect=1)
Initializes internal parameters.

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GetBitIdx(self, patts, dists, checkPatts=1)
returns the index for a pharmacophore described using a set of patterns and distances **Arguments*** - patts: a sequence of pattern indices - dists: a sequence of distance between the patterns, only the unique distances should be included, and they should be in the order defined in Utils.

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SetBit(self, patts, dists, checkPatts=1)
sets the bit defined by a collection of patterns and distances **Arguments*** - patts: a sequence of pattern indices - dists: a sequence of distance between the patterns, only the unique distances should be included, and they should be in the order defined in Utils.

source code

GetBit(self, patts, dists, checkPatts=1)
returns the value of a **Arguments*** - patts: a sequence of pattern indices - dists: a sequence of distance between the patterns, only the unique distances should be included, and they should be in the order defined in Utils.

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GetOnBits(self)
returns our on bits ...

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GetBitInfo(self, idx)
returns information about the given bit...

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GetBitDescription(self, bitIdx, includeBins=0, fullPage=1)
returns HTML with a description of the bit...

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_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.

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, patts=None, bins=None, labels=None, minCnt=2, maxCnt=4, shortestPathsOnly=1, includeBondOrder=0)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

_initLocals(self)

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Internal use only

getstate(self)

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used by the pickling machinery

setstate(self, state)

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used by the pickling machinery

Init(self, createBitVect=1)

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

**Arguments**

  - createBitVect: (optional) if this is nonzero, the bit vector
    used to store the on bits will be allocated.  Otherwise the
    existing bit vect will be reused (it better be big enough)

GetBitIdx(self, patts, dists, checkPatts=1)

source code

returns the index for a pharmacophore described using a set of
  patterns and distances

**Arguments***

  - patts: a sequence of pattern indices

  - dists: a sequence of distance between the patterns, only the
    unique distances should be included, and they should be in the
    order defined in Utils.

  - checkPatts: (optional) if nonzero, the pattern vector is
    checked to ensure it is sorted


**Returns**

  the integer bit index

SetBit(self, patts, dists, checkPatts=1)

source code

sets the bit defined by a collection of patterns and distances

**Arguments***

  - patts: a sequence of pattern indices

  - dists: a sequence of distance between the patterns, only the
    unique distances should be included, and they should be in the
    order defined in Utils.

  - checkPatts: (optional) if nonzero, the pattern vector is
    checked to ensure it is sorted

**Returns**

  the original status of the bit (whether or not it was set)

GetBit(self, patts, dists, checkPatts=1)

source code

returns the value of a 

**Arguments***

  - patts: a sequence of pattern indices

  - dists: a sequence of distance between the patterns, only the
    unique distances should be included, and they should be in the
    order defined in Utils.

  - checkPatts: (optional) if nonzero, the pattern vector is
    checked to ensure it is sorted

**Returns**

   whether or not the bit is set

GetOnBits(self)

source code

returns our on bits

GetBitInfo(self, idx)

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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)

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

source code

returns HTML 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

_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.

Class Pharm2DSig

__init__(self, patts=None, bins=None, labels=None, minCnt=2, maxCnt=4, shortestPathsOnly=1, includeBondOrder=0) (Constructor)

_initLocals(self)

__getstate__(self)

__setstate__(self, state)

Init(self, createBitVect=1)

GetBitIdx(self, patts, dists, checkPatts=1)

SetBit(self, patts, dists, checkPatts=1)

GetBit(self, patts, dists, checkPatts=1)

GetOnBits(self)

GetBitInfo(self, idx)

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

_findBinIdx(self, dists, bins, scaffolds)

init(self, patts=None, bins=None, labels=None, minCnt=2, maxCnt=4, shortestPathsOnly=1, includeBondOrder=0)
(Constructor)

getstate(self)

setstate(self, state)