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RDKit Optimize Geometry

StreamableRDKit Nodes for Knime version 3.8.0.v201906261723 by NIBR

Optimizes the geometry for an input RDKit Mol column and calculates the molecule's energy in kcal/mol. If the passed in molecules have no conformation, it will be calculated. The optimization is based on a particular force field and a number of iterations. It is also possible to turn off optimization completely by iterating 0 times. Optionally already available coordinates can be removed in order to calculate new ones from scratch. The following force fields are supported:

  • UFF: Universal force field is an all atom potential containing parameters for every atom. The force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity. Published in: UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations by A.K. Rappe, C.J. Casewit, K.S. Colwell, W.A. Goddard III, W.M. Skiff, J.Am. Chem. Soc. 114 (1992) 10024–10035
  • MMFF94: Merck molecular force field. Published in: Basis, form, scope, parameterization, and performance of MMFF94, Thomas A. Halgren, J. Comp. Chem.; 1996; 490-519
  • MMFF94S: Static variant of MMFF94. MMFF94S incorporates altered out of plane bending parameters that yield planar (or nearly planar) energy-minimized geometries at unstrained delocalized trigonal nitrogen centers. Published in: MMFF VI. MMFF94s option for energy minimization studies, Thomas A. Halgren; 1999; J. Comput. Chem., 20: 720–729

Options

RDKit Mol column
The input column with RDKit Molecules.
Force field
The force field type that shall be used for optimization.
New column name for optimized molecule
The name of the new column, which will contain the optimized molecule.
Remove source column
Set to true to remove the specified source column from the result table.
New column name for converge information
The name of the new column, which will contain a flag to tell whether the optimized molecule is converged. If iterations were set to 0 (no optimization) this value will always be false.
New column name for energy information
The name of the new column, which will contain the energy value of the optimized molecule in kcal/mol.

Advanced

Iterations
Number of iterations to use for optimization. If the number is set too small, molecules will not be fully converged. Set it to 0 iterations to skip optimizing and only calculate the energy value.
Remove starting coordinates before optimizing the molecule
Set to true to remove coordinates before starting the optimization process. This may affect the results in a positive way.

Input Ports

The molecules to optimize the geometry for

Output Ports

Optimized molecules with converge and energy information (kcal/mol)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.0
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