OECreateIsoSmiString

void OECreateIsoSmiString(std::string &str, const OEMolBase &mol)

Creates an canonical isomeric SMILES string representing a given molecule.

This function is just a special case of the OECreateSmiString function, called with the flavor OESMILESFlag_ISOMERIC.

Note

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

See also

• OEMolToSmiles for a high-level way to create SMILES equivalent to what is written by OEWriteMolecule.

• OECreateAbsSmiString to create an arbitrary SMILES

• OECreateCanSmiString to create a canonical SMILES

• Example program uniqmol.py

Validation:

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.

Performance of OECreateIsoSmiString to generate canonical isomeric SMILES

Database	Size	Success Rate
Wombat	53K	100.0 %
Maybridge	64K	100.0 %
MDDR	111K	100.0 %
NCI	250K	100.0 %

Running the validation test on 24M unique molecules produces only 129 failure cases.