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3D Coordinates

KNIME CDK Integration version 1.5.700.v201907251211 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

As a prerequisite for the calculation of 3D coordinates, all hydrogens are converted to explicit hydrogens for template recognition. The resulting molecular structures have 3D coordinates calculated for all atoms, including the explicit hydrogens. Molecular structures for which the calculations failed are returned as missing values.

Standing problems:

  • condensed ring systems which are unknown for the template class
  • vdWaals clashes
  • stereochemistry
  • chains running through ring systems

Options

Column Selection
Select the column containing the molecular structures.

Input Ports

Table containing molecular structures.

Output Ports

As input table but with 3D coordinates added.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME-CDK from the following update site:

KNIME 4.1
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