A program that generates the canonical SMILES of the molecules in the input file. It has a number of options such as -from3d, which perceives stereo from the 3D coordinates, -isomeric, which produces the canonical isomeric SMILES, and -kekule, which produces the Kekulé SMILES form.
prompt> cansmi.py dbase.oeb.gz output.smi
prompt> cansmi.py -from3d true -i dbase.sdf -o output.smi
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See also