Isosmiles function

If any structures contain stereochemical atomic centers, consider using the isosmiles function instead of the cansmiles function. The isosmiles function and isomeric SMILES are discussed in a later section of this chapter. 

The cansmiles function will not preserve any stereochemical information in the input SMILES. This is done so that the canonical SMILES for all stereoisomers is the same. It may be preferable to keep each isomer as a unique entry in a database. The isosmiles function preserves the stereochemical information while also reordering the atoms in the same way as the canonical SMILES. 

The next statement defines a t r igger function that will be used whenever data is inserted or updated in this table. This function performs three important functions. First, it modifies the SMILES to be inserted into the smi column so that it contains the result of the isosmiles function. The isosmiles function is similar to the cansmiles function, except that it retains any stereochemistry that might be contained within the SMILES. If two stereoisomers are entered into this table, each will have a unique isosmiles value, but the same cansmiles value. In this way, they can be kept distinct, but their identical canonical SMILES shows them to be stereoisomers. The trigger function also computes the fingerprint and inserts it into the table when the SMILES is inserted or updated. 

The following code will define the core functions described in Chapter 7 of this book. The isosmiles function is not included here because of limitation of PerlMol. These functions apply only to the PostgreSQL RDBMS. 

The use of the exception clause traps errors in any of the isosmiles, cansmiles, or fp functions. The creation of the error log table is shown above to contain these errors for later inspection and correction. 

The use of the group by clause causes all identical values of isosmiles to be grouped together and processed by the aggregate function count. For duplicate values of isosmiles, the count will be greater than 1. The above SQL statement will select these isosmiles. 

FROWNS python modules are used to show a second way in which the core functions might be implemented. The following plpythonu code extends PostgreSQL with most of the core functions described in Chapter 7. The isosmiles and keksmiles functions are not included here because of limitations of FROWNS. 

Create Or Replace Function openbabel.isosmiles(smi Text) Returns Text As EOPY import openbabel obc = openbabel.OBConversion() mol = openbabel.OBMol() obc.SetlnAndOutFormats("smi", "can") if obc.Readstring(mol, smi) mol.SetTitle("") return obc.WriteString(mol,1) else ... 

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