rdkit.Chem.Pharm2D package — The RDKit 2025.09.6 documentation

# rdkit.Chem.Pharm2D package

## Submodules

- rdkit.Chem.Pharm2D.Generate module
  - `Gen2DFingerprint()`
- rdkit.Chem.Pharm2D.Gobbi_Pharm2D module
- rdkit.Chem.Pharm2D.Matcher module
  - `GetAtomsMatchingBit()`
  - `MatchError`
- rdkit.Chem.Pharm2D.SigFactory module
  - `SigFactory`
    - `SigFactory.GetBins()`
    - `SigFactory.GetBitDescription()`
    - `SigFactory.GetBitDescriptionAsText()`
    - `SigFactory.GetBitIdx()`
    - `SigFactory.GetBitInfo()`
    - `SigFactory.GetFeatFamilies()`
    - `SigFactory.GetMolFeats()`
    - `SigFactory.GetNumBins()`
    - `SigFactory.GetSigSize()`
    - `SigFactory.GetSignature()`
    - `SigFactory.Init()`
    - `SigFactory.SetBins()`
- rdkit.Chem.Pharm2D.Utils module
  - `BinsTriangleInequality()`
  - `CountUpTo()`
  - `GetAllCombinations()`
  - `GetIndexCombinations()`
  - `GetPossibleScaffolds()`
  - `GetTriangles()`
  - `GetUniqueCombinations()`
  - `GetUniqueCombinations_new()`
  - `NumCombinations()`
  - `OrderTriangle()`
  - `ScaffoldPasses()`
  - `UniquifyCombinations()`

## Module contents

module with functionality for 2D pharmacophores

rdkit.Chem.Pharm2D.DefaultSigFactory(fdefFile=None, minPointCount=2, maxPointCount=3, bins=[(2, 3), (3, 4), (4, 5), (5, 6), (6, 7), (7, 8), (8, 100)])