OECXSMILESToMol

bool OECXSMILESToMol(OEMolBase &mol, const std::string &str)

Converts a CXSMILES string into a molecule. After constructing the molecule the following properties are perceived:

• Rings are perceived by calling the OEFindRingAtomsAndBonds function.

• The aromaticity is assigned by calling the OEAssignAromaticFlags function using the OEChem_OEAroModelOpenEye aromaticity model.

• The chirality is perceived by calling the OEPerceiveChiral function.

Note that since CXSMILES is a superset of the SMILES syntax, it is safe to use this function for either format. Using SMILES readers for known CXSMILES is discouraged since any appendix information will become a static addition to the molecule title and cannot be recovered.

The molecule object is cleared before parsing so the resulting molecule object only contains atoms and bonds from the CXSMILES. If one wishes to add atoms and bonds to an existing molecule, one can use the lower-level OEParseSmiles function (with an option argument that enables CXSMILES parsing), which preserves any existing atoms and bonds in the molecule.

See also

• OEMolToCXSMILES function

• OEMolToSmiles function

• Unique Representation section