RDKit Open3D Align

CATEGORY

Molecular Screening

SOURCE

RDKit

DESCRIPTION

Performs 3D alignment of molecules using Open3DAlign

INPUTS

  1. input: a dataset of molecules to be aligned
  2. queryMol: a data containing the query 3D structure

OUTPUTS

A dataset of molecules

OPTIONS

Query mol indexThe index of the structure in the queryMol dataset. Default is the first.
O3DAlign score thresholdAlignment score threshold determining which structures are output. If not specified then all are output.
Number of conformersNumber of conformers to generate (leave empty if input already contains 3D structures)

ADDITIONAL INFO

Open3DAlign can be used to perform a rigid alignment of 3D structures. Details can be found here. It has been incorporated into RDKit, which is how it is used by this cell.

The input to the cell can either already contains 3D conformers or they can be generated by the cell. If you want them to be generated specify a positive value for the Number of conformers option.

The input to the cell can either already contains 3D conformers or they can be generated by the cell. If you want them to be generated specify a positive value for the Number of conformers option.

Note: the options for conformer generation are quite limited. If you want a wider range of options use the RDKit Conformers cell and send the output of that into this cell.

The output are the structures aligned to the query molecule. The target molecule is translated and rotated to optimise the alignment, but the internal geometry is unmodified.

The alignment scores that are generated are only valid for that particular query molecule. They are numbers, typically in the range of 50 - 150 (bigger scores mean better alignments). The “ideal” score can be determined by aligning the query to itself (let’s call this score Q). You can control which structures are output using the O3DAlign score threshold option (let’s call this T) which allows target structures that have an alignment score lower than Q - T to be excluded from the output. You may need to play with this option to get the desired output.