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Principal Moment of Intertia (PMI)-Derived Properties

StreamableVernalis PMI-extension for KNIME Workbench version 1.28.2.v202101281353 by Vernalis (R&D), UK

This node calculates Principal Moment of Intertia (PMI)-Derived Properties

The properties are:

  • PMI 1 - First (smallest) Principal Moment of Inertia (also referred to as: I₁)
  • PMI 2 - Second Principal Moment of Inertia (also referred to as: I₂)
  • PMI 3 - Third (largest) Principal Moment of Inertia (also referred to as: I₃)
  • npr1 - First Normalised PMI (i.e. I₁ / I₃) (See: Sauer and Schwartz, J. Chem. Inf. Comput. Sci., 2003, 43, 987-1003)
  • npr2 - Second Normalised PMI (i.e. I₂ / I₃) (See: Sauer and Schwartz, J. Chem. Inf. Comput. Sci., 2003, 43, 987-1003)
  • Sigma npr - npr1 + npr2 (also referred to as: Flatsum, npr1+npr2, Σnpr) (See: )
  • Sphericity - npr1 + npr2 - 1 (also referred to as: S) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Rodlikeness - npr2 - npr1 (also referred to as: R, Rod-likeness) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Disklikeness - 2 - 2 × npr2 (also referred to as: D, Disc-likeness) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Asphericity - 0.5 × [(I₁ - I₂)² + (I₁ - I₃)² + (I₂ - I₃)²]/[I₁² + I₂² + I₃²]; 0 corresponds to a spherical top and 1 to a linear molecule. ~0.25 corresponds to prolate (cigar-shaped) molecules, and disc-shaped ~1 (also referred to as: ΩA) (See: Arteca, Reviews in Computational Chemistry, Vol 9 VCH, NY, 1991, 191-253)
  • Inertial Shape Factor - I₂ / (I₁ × I₃); Undefined for planar molecules (also referred to as: S<sub>I</sub>) (See: Lister et al., Internal Rotation and Inversion, Academic Press, London, 1978)
  • Molecule Eccentricity - √(I₁² - I₃²) / I₂; 0 corresponds to a spherical top, and 1 to a linear molecule (also referred to as: ε) (See: Arteca, Reviews in Computational Chemistry, Vol 9 VCH, NY, 1991, 191-253)
  • Gyradius - Radius of Gyration (also referred to as: RG, Radius of Gyration, Gyradius) (See: )
  • Gyradius 2D - Radius of Gyration (2D) = √(I₁ × I₂) / MWt (also referred to as: RG, Radius of Gyration, Gyradius) (See: Volkenstein 'Configurational Statistics of Polymeric chains' Wiley, NY, 1963)
  • Gyradius 3D - Radius of Gyration (3D) = ∛(I₁ × I₂ × I₃) / MWt (also referred to as: RG, Radius of Gyration, Gyradius) (See: Tanford 'Physical Chemistry of Macromolecules', Wiley, NY, 1961)
  • PRG 0 - 1st Principle Radius of Gyration (R0 = √(I₁ / MWt)) (also referred to as: R0) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • PRG 1 - 2nd Principle Radius of Gyration (R1 = √(I₂ / MWt)) (also referred to as: R1) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • PRG 2 - 3rd Principle Radius of Gyration (R2 = √(I₃ / MWt)) (also referred to as: R2) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • Gyradius Ratio 1 - 1st Gyradius Ratio (r1 = PRG1 / PRG0) (also referred to as: r1) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • Gyradius Ratio 2 - 2nd Gyradius Ratio (r2 = PRG2 / PRG0) (also referred to as: r2) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)

This node was developed by Vernalis Research. For feedback and more information, please contact knime@vernalis.com

Options

Molecule column
Select the input column

Calculated Properties

Principal Moment of Intertia (PMI)-Derived Properties
Select at least 1 property to calculate (see above for details)
Select All
Selects all properties
Clear
Deselects all properties, and selects only the 1st property in the list
Show All/Show 1st 15
Toggles the display of the options list between the first 15 options and all options

Input Ports

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Input table

Output Ports

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Input table with calculated properties appended

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Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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