Molfile properties function

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. 

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. 

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. 

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 Type frowns. named j roperty As (name Text, value Text) Create Or Replace Function frowns.molfile properties(molfile Text) Returns Setof f rowns. named j roperty As EOPY from frowns import MDL import StringlO... 

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

---