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What stereochemistry options exist when converting from 1D/SMILES or 2D to 3-dimensional ligand-like structures?

LigPrep is Schrodinger's program to convert from 1D or 2D structures and generate 3D, ligand-like structures. Both SMILES strings and 2D sdf files have chirality indications ("specifications") that LigPrep recognizes. This leads to the following stereochemisty options that can be chosen during conversion.

Retain specified chiralities, and generate both for unspecified chiralities. This is the most popular option when converting from smiles or 2D structures because LigPrep maintains the intended chiralities.

Determine chiralities from 3D structure. This is the most popular option when the input to LigPrep is already 3-dimensional and the chiralities are determined.

Generate all combinations. This is the option to generate both stereo forms for each chiral center. Specifications are ignored. Use the "Generate at most" feature to limit total output.

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