Molfile mol function

The next step is to parse the molfile data into separate columns of the table. The molfile mol function expects a molfile and returns a composite data type named mol. This data type is defined as ... 

The following SQL distributes the data returned from the molfile mol function into the columns of vla4. structure. 

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... 

This insert statement is a bit more complex than the one that inserted rows into the vla4.structure table. In that table, only one row was returned from the mol file mol function. The mol file properties function returns multiple rows for each molfile, when there are multiple properties for each molfile. The second select statement above (the one in parentheses and identified with the name atmp) selects all the rows for each molfile. The first select statement selects all the columns from each returned row from molfile properties. These are then inserted into the vla4. property table. 

Create Or Replace Function frowns,molfile mol(molfile Text) Returns... 

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 ... 

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