Hello Ilya,
I make some test some times ago, normally it is ok:
// Transformation of 2D mol file to a 3D mol file, (with 3D conversion)
OBConversion conv;
conv.OpenInAndOutFiles("test2D.mol","test3D.mol");
conv.SetInAndOutFormats("mol","mol");
conv.AddOption("gen3D",conv.GENOPTIONS);
conv.Convert();
conv.CloseOutFile();
Best regards,
Marianne
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