void OECreateIsoSmiString(std::string &str, const OEMolBase &mol)
Creates an canonical isomeric SMILES string representing a given molecule.
This function produces SMILES that correspond what Daylight Chemical Information Systems term an ‘absolute‘ SMILES
Note that the canonical SMILES generated by this function remains dependent on the state of the molecule, especially its aromaticity state (see examples in Aromaticity Models in OEChem TK section). Thus, to generate a canonical smiles suitable for purposes such as a database key, the user must assure that the state of the molecule has been standardized. In particular, aromaticity should be perceived according to the preferred model.
In contrast, the high-level output function OEWriteMolecule (and OEMolToSmiles) , when writing the canonical SMILES format (OEFormat_ISM) does invoke OEFindRingAtomsAndBonds and OEAssignAromaticFlags.
Furthermore, whether OEWriteMolecule or OECreateIsoSmiString is used, the canonical SMILES generated depends on the current stereo specifications for the molecule. If the goal is a canonical isomeric SMILES which is unique for all representations of an equivalent stereoisomer, i.e., for use as a database key, it is the user’s responsibility to assure that the stereochemical state of the molecule has been rationalized and standardized, using methods such as:
- OEPerceiveChiral, OE3DToAtomStereo, OE3DToBondStereo
- OEAtomBase.IsChiral, OEAtomBase.SetStereo
- OEBondBase.IsChiral, OEBondBase.SetStereo
The OECreateIsoSmiString is rigorously tested to ensure that it generates unique string representations of molecules. This test involves randomly reordering the atoms and bonds of molecules and confirming that this has no effect on the SMILES generated by the OECreateIsoSmiString function.
Running the validation test on 24M unique molecules produces only 129 failure cases.