Package rdkit :: Package Chem :: Module Descriptors3D
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Module Descriptors3D

source code

Descriptors derived from a molecule's 3D structure

Functions [hide private]
 
PMI1(*x, **y)
First (smallest) principal moment of inertia
source code
 
PMI2(*x, **y)
Second principal moment of inertia
source code
 
PMI3(*x, **y)
Third (largest) principal moment of inertia
source code
 
NPR1(*x, **y)
Normalized principal moments ratio 1 (=I1/I3)
source code
 
NPR2(*x, **y)
Normalized principal moments ratio 2 (=I2/I3)
source code
 
RadiusOfGyration(*x, **y)
Radius of gyration
source code
 
InertialShapeFactor(*x, **y)
Inertial shape factor
source code
 
Eccentricity(*x, **y)
molecular eccentricity
source code
 
Asphericity(*x, **y)
molecular asphericity
source code
 
SpherocityIndex(*x, **y)
Molecular spherocityIndex
source code
Variables [hide private]
  __package__ = 'rdkit.Chem'

Imports: rdMolDescriptors


Function Details [hide private]

PMI1(*x, **y)

source code 
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

PMI2(*x, **y)

source code 
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

PMI3(*x, **y)

source code 
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

NPR1(*x, **y)

source code 
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

NPR2(*x, **y)

source code 
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

RadiusOfGyration(*x, **y)

source code 
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

InertialShapeFactor(*x, **y)

source code 
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

Eccentricity(*x, **y)

source code 
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

Asphericity(*x, **y)

source code 
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

SpherocityIndex(*x, **y)

source code 
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