Smiles to molfile function

Consider the extended SQL functions smiles to molfile and molfile to smiles. Having these functions available as SQL extensions allows one to export a molfile from a table containing SMILES. For example ... 

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. 

Create Or Replace Function molfile to smiles(text) Returns Text As EOPERL ... 

Create Or Replace Function frowns.molfile to smiles(molfile Text)... 

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

Another choice for the internal representation of molecular structure is a molfile. It would be possible to construct SQL functions like those described in this chapter that would operate on this type of data. One disadvantage of molfiles is their greater size compared with SMILES. One advantage is that it is possible to store atomic coordinates, which is not possible with SMILES. There are other molecular file formats, but these are substantially the same as a molfile, except perhaps for specific atom types that may be of use in some database applications. 

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. 

There are many programs available to parse the various molecular structure file format. OpenBabel is an open-source program that can read many file formats and produce a SMILES representation of molecular structure. There are many other commercial products that can do this as well. In the following examples, the OpenBabel/plpythonu implementation of molfile parsing will be used. This was introduced in Chapter 10. The code to define the necessary functions is shown in the Appendix. 

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. 

PerlMol is a module add-on to the perl language that facilitates working with molecular structures using SMILES, SMARTS, and molfiles, as well as other functionality. PerlMol is available from CPAN, the Comprehensive Perl Archive Network. In order to install PerlMol, it is recommended to use the command cpan -i PerlMol as superuser in order to install the modules into the system perl library. This will install all the necessary modules for the following functions, as well as other parts of PerlMol that may be useful. 

Create Or Replace Function frowns.smiles to molfile(smi Text, name Text, coords Numeric ] [] ) Returns Text As EOPY from frowns import Smiles... 

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