I'm looking into the current status of techniques that use RDKit to perform 3D alignments based on shape (e.g. not using AlignMol()) and struggling to find what the best tools are and the status of each.
The Open3D align tools are relatively straightforward to use, but in my hands do not seem to give good alignments. e.g with this reference mol: [image: image.png] I get this alignment: [image: image.png] I also stumbled across shape-it e.g. https://iwatobipen.wordpress.com/2021/03/17/comparison-between-native-implemented-shape-align-method-of-rdkit-and-rdkit-shape-it-chemoinformatics-rdkit-shape-based-align/ But I find this very slow and most alignments seem to fail in my hands. Are there any guides to what tools work well here? Tim
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