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Compounds that contain unspecified or ambiguous definitions of stereochemistry will be preprocessed before conformational sampling to explicitly enumerate stereochemistry. Input molecules that have three dimensional coordinates inherently have stereochemistry specified, but SMILES or two dimensional SD files may have atoms (R/S) or bonds (E/Z) for which the stereochemistry is unknown or unspecified. In the case where the stereochemistry supplied is suspect, flynn provides an option that will completely enumerate all stereochemical centers.
The resulting ligands will be sorted based on their best fit to density regardless of the stereo-chemistry. That is, the best solutions will percolate to the top of the output. See 3.1.4 below for more details.
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