OpenBabel SMILES

Create Or Replace Function openbabel.smiles to symbols(smi Text) Returns Text[] As EOPY import openbabel obc = openbabel.OBConversion() mol = openbabel.OBMol() obc.SetlnAndOutFormats("smi", "mol") if obc.Readstring(mol, smi) tbl = openbabel.OBElementTable()... 

Babel [http //openbabel.sourceforge.net/]), it is important to keep in mind the limitations of each format. For example, conversion from SMILES, which does not store atom coordinates, into Mobile would result either in the molecule having undefined geometry or the geometry being supplied by the conversion tool, which might be completely different from the real one. 

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. 

Every one of these utilities will first require that a file of structures be loaded into a table in the database. Two methods are shown here importing a SMILES file and a mol file. Other file types could be added as needed, extending the core functions described earlier using mol file mol or molf ile to smiles as a model. OpenBabel is a good choice because of its support of many file formats. 

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