3D RMSD

Creates a new columns containing the RMSD distances between different conformers (required 3D coordinates). The computations are based of the CDK toolkit. At the moment two types of RMSD calculations are possible. One based on the alignment using the Kabsch algorithm and the other based on the isomorphic alignment of the molecular structure and using the global geometry.

Options

Column with molecules

Select the column containing the molecular structure with 3D coordinates

Alignment algorithm

Select the type of alignment to be used for the RMSD calculation

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