rdkit.Chem.Descriptors3D module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Descriptors3D module

Descriptors derived from a molecule’s 3D structure

rdkit.Chem.Descriptors3D.Asphericity(*x, **y)

  molecular asphericity

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics https://doi.org/10.1002/9783527618279.ch37

  > Definition:

  >   0.5 * ((pm3-pm2)**2 + (pm3-pm1)**2 + (pm2-pm1)**2)/(pm1**2+pm2**2+pm3**2)

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.CalcMolDescriptors3D(mol, confId=-1)

  Compute all 3D descriptors of a molecule

  Arguments: - mol: the molecule to work with - confId: conformer ID to work with. If not specified the default (-1) is used

  Return:

  dict

    A dictionary with decriptor names as keys and the descriptor values as values

  raises a ValueError

    If the molecule does not have conformers

rdkit.Chem.Descriptors3D.Eccentricity(*x, **y)

  molecular eccentricity

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics https://doi.org/10.1002/9783527618279.ch37

  > Definition:

  >   sqrt(pm3**2 -pm1**2) / pm3

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.InertialShapeFactor(*x, **y)

  Inertial shape factor

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics https://doi.org/10.1002/9783527618279.ch37

  > Definition:

  >   pm2 / (pm1*pm3)

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.NPR1(*x, **y)

  Normalized principal moments ratio 1 (=I1/I3)

  > from Sauer and Schwarz JCIM 43:987-1003 (2003) https://doi.org/10.1021/ci025599w

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.NPR2(*x, **y)

  Normalized principal moments ratio 2 (=I2/I3)

  > from Sauer and Schwarz JCIM 43:987-1003 (2003) https://doi.org/10.1021/ci025599w

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.PBF(*x, **y)
  Plane of best fit

    from: https://doi.org/10.1021/ci300293f

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

rdkit.Chem.Descriptors3D.PMI1(*x, **y)

  First (smallest) principal moment of inertia

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.PMI2(*x, **y)

  Second principal moment of inertia

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.PMI3(*x, **y)

  Third (largest) principal moment of inertia

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.RadiusOfGyration(*x, **y)

  Radius of gyration

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics https://doi.org/10.1002/9783527618279.ch37

  > Definition:

  >   for planar molecules: sqrt( sqrt(pm3*pm2)/MW ) for nonplanar molecules: sqrt( 2*pi*pow(pm3*pm2*pm1,1/3)/MW )

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use

  > - useAtomicMasses: (optional) toggles use of atomic masses in the calculation. Defaults to True

rdkit.Chem.Descriptors3D.SpherocityIndex(*x, **y)

  Molecular spherocityIndex

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics https://doi.org/10.1002/9783527618279.ch37

  > Definition:

  >   3 * pm1 / (pm1+pm2+pm3) where the moments are calculated without weights

  Arguments

  > - inMol: a molecule

  > - confId: (optional) the conformation ID to use