3D Coordinates


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

Input Ports

  1. Type: Data Table containing molecular structures.

Output Ports

  1. Type: Data As input table but with 3D coordinates added.

Find here

Community Nodes > CDK > 3D

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