OpenBabel molfile

Insert Into vla4.structure (id, name, cansmiles, coords, atoms) Select id, (openbabel.molfile mol(molfile)). from vla4.sdf ... 

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... 

Finally, any properties contained in the molfile will be stored in a separate table containing the text value copied from the file as well as a numeric value for the property, if that is appropriate for the property. There will be a one-to-many relationship between the structure and property table, allowing any number of properties to be stored for each structure. The function openbabel.molfile properties is shown in the Appendix. It expects a molfile and returns a composite data type, defined as follows. 

The following SQL is used to parse the molfile column from the vla4.structure table using the openbabel.molfile properties function. The name and value fields of the composite data type are inserted into the vla4. property table, along with the appropriate id selected from the vla4.structure table along with the molfile column. 

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 ... 

Create Or Replace Function openbabel.molfile properties(molfil Text) Returns Setof openbabel.named property As EOPY import pybel... 

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. 

Fig. 1.31 Conversion of a molfile of curcumin molecule to pdb file format in OpenBabel GUI...

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