3D Alignment

The 3D Alignment Plugin overlays molecules onto each other by translating and rotating them in the space. The input can be two or more molecules in 2D or in 3D. If 2D molecules are given, their 3D structure is automatically generated.The molecules can be treated rigid (then the original conformation is preserved), or flexible (then dihedral degrees of freedom are added to the molecule).

Options

Alignment types
  • Align by extended atom types: extended atom types are assigned to each atom to enable chemically relevant atomic overlay. During the alignment process the overlap of the atoms of the same type is maximized. Types differentiate atomic number, hybridization state and aromaticity, e.g. aromatic nitrogen atom is not matched against a tertiary amine. These extended atom types correspond to the ones used in Dreiding force field.
  • Align by common scaffold (MCS): the atom-atom pairing is obtained from the 2D maximum common substructure of the molecules. Alignment by extended atom types is applied on the non-MCS atoms.
Initial conformation count
The number of diverse conformations to generate as an input for the alignment.
Accuracy
Determines the alignment accuracy. Normal, fast and accurate accuracy options are defined.
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 3D flexible alignment structure.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.5

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v250300
On NodePit since: 2025-07-04
Last update: 2025-07-13
KNIME versions: v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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