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Geometrical Descriptors

StreamableChemAxon/Infocom JChem Extensions version 4.3.0.v202000 by Infocom Corporation

The Geometrical Descriptors Plugin calculates 3D geometric descriptors for a molecule.

Options

Type
  • Dreiding energy: calculates the energy of the 3D structure (conformation) of the molecule using Dreiding force field.
  • MMFF94 energy: calculates the energy of the 3D structure (conformation) of the molecule using MMFF94 force field.
  • Steric hindrance: calculates steric hindrance of an atom calculated from the covalent radii values and geometrical distances.
  • Minimal projection area: calculates the minimum of projection areas of the conformer, based on the van der Waals radius (in Å2).
  • Maximal projection area: calculates the maximum of projection areas of the conformer, based on the van der Waals radius (in Å2).
  • Minimal projection radius: calculates the radius for the minimal projection area of the conformer (in Å).
  • Maximal projection radius: calculates the radius for the maximal projection area of the conformer (in Å).
  • Maximal distance perpendicular to the min projection: calculates the maximal extension of the conformer perpendicular to the minimal projection area (in Å).
  • Maximal distance perpendicular to the max projection: calculates the maximal extension of the conformer perpendicular to the maximal projection area (in Å).
  • van der Waals volume: calculates the van der Waals volume of the conformer (in Å3).
Energy unit
Unit of the calculated energy (kcal/mol or kJ/mol).
Set MMFF94 optimization
The structure is optimized before MMFF94 energy calculation.
Set projection optimization
The structure is optimized before projection area and projection radius calculation(s).
Calculate for lowest energy conformer
  • If molecule is in 2D: the lowest energy conformer is generated if the input molecule is in 2D; 3D input molecules are considered in the given conformation.
  • Never: the input molecule is used for calculation.
  • Always: the lowest energy conformer is generated (for 3D and 2D molecules as well).
Optimization limit
Sets the rigour of convergence for optimization. Stricter convergence means lower gradient limit to reach during optimization. The values can be:
  • Very loose
  • Normal
  • Strict
  • Very strict
Structure column
The structure column.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains geometry.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install ChemAxon/Infocom JChem Extensions Feature from the following update site:

KNIME 4.3

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