rdkit.Chem.Descriptors3D

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