Cansmiles function

The cansmiles function should also be used to insert each SMILES when a table is created. For example ... 

The cansmiles function can also be used to enforce an SQL constraint that the cansmi column must contain valid canonical SMILES. SQL constrains like this are commonly used to maintain data integrity. For example, the SQL clause check (cansmi = cansmiles (cansmi)) can be used in the initial creation of the table. One might also consider using an SQL trigger to handle an insert or update to a column that is required to contain canonical SMILES. 

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. 

When the table contains unique canonical smiles in an indexed column cansmi, and the cansmiles function provides the proper canonical SMILES for phenol, this lookup is extremely fast. 

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. 

Reaction SMILES can be used to store and search chemical reactions using the same functions described earlier for standard SMILES. For example, cansmiles CCC(=0)0.NC CC(=0)NC.0 ) returns... 

Suppose it is decided that the valence 5, noncharge-separated representation of the nitro group is to be used throughout the database. The SMIRKS [0 2]=[N+ 1][0- 3] [0 2]=[N+0 1]=[0+0 3], when applied to any charge-separated nitro group will transform it into the proper form. This is accomplished by creating another new SQL function, xform(smiles, smarts). As with the cansmiles and matches functions, this is an extension to standard SQL. Some form of this transformation function is... 

The CHORD6 chemical cartridge is a commercial product from gNova, Inc. It is written using C functions and the OEChem toolkit from OpenEye. It provides the core functions discussed in this book, such as cansmiles, matches, count matches, list matches, smiles to molfile, molfile to smiles, and xform. CHORD makes it possible to efficiently process RDBMS tables containing many millions of chemical structures. 

The column structure.id is a unique integer relating the structure, sdf and property tables. The sdf.molfile column contains the molfile for each structure as defined by the vendor. The structure.name and structure.cansmiles columns contain the name and canonical smiles parsed and computed from the molfile. The structure.coord column will contain an array of atomic coordinates. The structure, atom column will contain an array of atom numbers from the file in canonical order to correspond to the atom order in the canonical SMILES. The OpenBabel/plpythonu extension functions molfile mol and molfile properties will be used to parse the vendor SDF molfiles and populate these tables. The molfile column of the sdf table is first populated from the SDF file, using the following perl script. 

Notice that the individual elements of the composite data type value returned by the openbabel.molf ile mol function must be used. Lor example, (openbabel.molfile mol (molf ile)). cansmiles... 

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. 

This Appendix contains structured query language (SQL) functions and tables too large or complex for the explanatory nature of the earlier chapters. These functions and tables are practical, rather than explanatory. They all follow PostgreSQL syntax. Some of them require the core functions described in Chapter 7 of this book, for example, match, cansmiles, and count matches. Those functions are available in the CHORD product from gNova, Inc. This Appendix also contains a PerlMol implementation, a FROWNS implementation, and an OpenBabel implementation of the core functions for PostgreSQL. 

Create Or Replace Function cansmiles(text) Returns Text As EOPERL use Chemistry File auto ... 

Create Or Replace Function openbabel.cansmiles(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("")... 

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