rdkit.Chem.Descriptors3D module — The RDKit 2016.09.1 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 http://dx.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.` `Eccentricity`(*x, **y)

  molecular eccentricity

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

  > Definition:
  >   sqrt(pm3**2 -pm1**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.` `InertialShapeFactor`(*x, **y)

  Inertial shape factor

  > from Todeschini and Consoni “Descriptors from Molecular Geometry” Handbook of Chemoinformatics http://dx.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://dx.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://dx.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.` `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 http://dx.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 http://dx.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