Package rdkit :: Package Chem :: Package AtomPairs :: Module Sheridan

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# Module Sheridan

source code

    Contains an implementation of Physicochemical property fingerprints, as
    described in:
    Kearsley, S. K. et al.
    "Chemical Similarity Using Physiochemical Property Descriptors."
    J. Chem.Inf. Model. 36, 118-127 (1996)

Functions | [hide private]

_readPattyDefs(fname=os.path.join(RDConfig.RDDataDir,'SmartsLib','patty_rules.txt')) | source code

AssignPattyTypes(mol, defns=None) | source code

GetBPFingerprint(mol, fpfn=GetAtomPairFingerprint) >>> from rdkit import Chem... | source code

GetBTFingerprint(mol, fpfn=GetTopologicalTorsionFingerprint) >>> from rdkit import Chem... | source code

_test() | source code

Variables | [hide private]

| numPathBits = `rdMolDescriptors.AtomPairsParameters.numPathBits`
| _maxPathLen = `1 << numPathBits-1`
| numFpBits = `numPathBits+ 2* rdMolDescriptors.AtomPairsParamete`...``
| fpLen = `1 << numFpBits`
| _pattyDefs = `None` hash(x)
| typMap = `dict(CAT= 1, ANI= 2, POL= 3, DON= 4, ACC= 5, HYD= 6, `...``

Imports: IntSparseIntVect, Chem, rdMolDescriptors, DataStructs, GetAtomPairFingerprint, GetTopologicalTorsionFingerprint, os, re, RDConfig

Function Details | [hide private]

### AssignPattyTypes(mol, defns=None)

source code

    >>> from rdkit import Chem
    >>> AssignPattyTypes(Chem.MolFromSmiles('OCC(=O)O'))
    ['POL', 'HYD', 'OTH', 'ANI', 'ANI']

### GetBPFingerprint(mol, fpfn=GetAtomPairFingerprint)

source code

    >>> from rdkit import Chem
    >>> fp = GetBPFingerprint(Chem.MolFromSmiles('OCC(=O)O'))
    >>> fp.GetTotalVal()
    10
    >>> nze=fp.GetNonzeroElements()
    >>> sorted([(k,v) for k,v in nze.items()])
    [(32834, 1), (49219, 2), (98370, 2), (98401, 1), (114753, 2), (114786, 1), (114881, 1)]

### GetBTFingerprint(mol, fpfn=GetTopologicalTorsionFingerprint)

source code

    >>> from rdkit import Chem
    >>> mol = Chem.MolFromSmiles('OCC(N)O')
    >>> AssignPattyTypes(mol)
    ['POL', 'HYD', 'HYD', 'CAT', 'POL']
    >>> fp = GetBTFingerprint(mol)
    >>> fp.GetTotalVal()
    2
    >>> nze=fp.GetNonzeroElements()
    >>> sorted([(k,v) for k,v in nze.items()])
    [(538446850L, 1), (538446852L, 1)]

Variables Details | [hide private]

### numFpBits

Value:

      numPathBits+ 2* rdMolDescriptors.AtomPairsParameters.codeSize

### typMap

Value:

      dict(CAT= 1, ANI= 2, POL= 3, DON= 4, ACC= 5, HYD= 6, OTH= 7)