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Are there tools or algorithms to detect organic molecules from 3D crystal structures?

Your question has a few parts, but multiple solutions. Let's start with "XYZ from molecular dynamics" ...
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An automated approach to visualize several xyz structures

If you want to use Python, you could Use ase to load the xyz file structure by structure, see here. Then use existing molecular visualization tools, such as the kind built into ase, see here. Or use ...
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Is LiNbO3 a perovskite or not?

LiNbO3 has quite a unique non-perovskite structure (under ambient conditions) and it's referred to as a structural type (LiNbO3-type structure) as a result (see here). This is largely due to Li+ being ...
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What is the structure of hydrated beryllium chloride

As others have already mentioned it's more of a $\ce{[Be(H2O)4]Cl2}$ if you want to write it like this. It becomes much more visible if we move to the solid state structure. I'm adding a picture of ...
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