Problem:
When adding a molecule from the command line to a molecule set, and not defining basic, openad poles Pubchem for the molecule and overwrites any 3D defined smiles molecule with the Canonical Smiles equivalent in 2D. It appears Pubchem only stored 2D in canonical smiles, Unlike Chemspider that has the stereo chemistry Canonical Smiles.
Success:
the canonical smiles filed retains the User defined SMILES.
Problem: When adding a molecule from the command line to a molecule set, and not defining basic, openad poles Pubchem for the molecule and overwrites any 3D defined smiles molecule with the Canonical Smiles equivalent in 2D. It appears Pubchem only stored 2D in canonical smiles, Unlike Chemspider that has the stereo chemistry Canonical Smiles.
Success:
the canonical smiles filed retains the User defined SMILES.