Computer Representations of Molecular Structures - Design and Use of Relational Databases in Chemistry - page 85

7.9 Useful SQL Extensions
Several new SQL functions have been introduced here. These functions
make it possible to store molecular structures in an RDBMS as text strings.
They also allow these strings to be manipulated and searched in a chemi-
cally meaningful way. This greatly expands the usefulness of an RDBMS
for chemical applications. Table 7.2 summarizes these functions using
SQL notation for deining functions. Much of the rest of this topic will
describe more useful functions and describe ways of using and extending
these ever further.
The Appendix of this topic shows three complete implementations of
these functions using PostgreSQL and PerlMol, FROWNS, and OpenBabel
modules. Each of these three modules is free and open source. Using these
functions is an excellent way to become familiar with the concepts in this
chapter. It is possible to extend these functions even further to take advan-
tage of other features of PerlMol, FROWNS, and OpenBabel to satisfy the
needs of many molecular modeling projects. However, each of these three
modules has limitations. Before embarking on a large complex database
project, a thorough examination of the limitations of PerlMol, FROWNS,
and OpenBabel should be done. One important distinction between these
three modules is how they generate canonical SMILES. Each one generates
valid canonical SMILES, but each produces different canonical SMILES.
This is simply due to differing algorithms for canonically ordering atoms.
As discussed earlier, there is no universal canonical SMILES.
Table 7.2 summarizes the core functions used throughout the rest of
this topic. There are several commercially available chemical extensions
to SQL. There may not be an exact correspondence of functions from these
vendors to functions in Table 7.2.

Table 7.2 Core Chemical SQL Extension Functions

Function Input type Output type Description of output

valid Text Boolean Tests whether SMILES is valid

cansmiles Text Text Canonical form of SMILES

isosmiles Text Text Isomeric form of SMILES

keksmiles Text Text Kekule form of SMILES

matches Text,text Boolean Tests whether SMILES (arg #1)

matches SMARTS

count_matches Text,text Integer Number of times SMARTS

matches SMILES (arg #1)

list_matches Text,text Integer

array

Atoms in SMILES (arg #1),
which match SMARTS

smiles_to_molfile Text Text Molfile formatted string

molfile_to_smiles Text Text SMILES