OpenBabel

OpenBabel Conversion of molecular file formats http //openbabel.sourceforge.net/... 

The Chemistry Development Kit (CDK) Application Programming Interface (API) (7), OpenBabel (8), or CORINA... 

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. 

Open Babel Open Babel, http // openbabel.sourceforge.net/ (accessed Mar 2005), 2005 Wide variety of primarily Cartesian molecular modeling formats Wide variety of primarily Cartesian molecular modeling formats... 

OpenBabel A cross-platform program and library designed to interconvert between many file formats used in chemical drawing and molecular modeling. http //sourceforge.net/mailarchive/ forum. php thread id= 8125020 forum id=3042... 

There is an open-source extension of PostgreSQL called pgchem.7 It uses C functions and OpenBabel. It implements some of the core functions described in Chapter 7. The names of the functions are not the same as the names used here. Using pgchem, it should be possible to perform most of the operations represented by the core functions described in this book. 

Open Babel The Open Source Chemistry Toolbox. 2008. http //openbabel. sourceforge.net/ (accessed April 18,2008). 

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. 

Create Type openbabel. mol As (name Text, cansmiles Text, coords Float [] [3], atoms Integer [] ) ... 

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. 

Create Type openbabel.named j roperty As (name Text, value Text) ... 

This composite type is created when the openbabel schema and its associated functions are created using the code contained in the Appendix. It is not necessary to issue this SQL command again during the processing of the data from the vla-4.sdf file. 

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. 

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. 

This Appendix contains structured query language (SQL) functions and tables too large or complex for the explanatory nature of the earlier chapters. These functions and tables are practical, rather than explanatory. They all follow PostgreSQL syntax. Some of them require the core functions described in Chapter 7 of this book, for example, match, cansmiles, and count matches. Those functions are available in the CHORD product from gNova, Inc. This Appendix also contains a PerlMol implementation, a FROWNS implementation, and an OpenBabel implementation of the core functions for PostgreSQL. 

Create Or Replace Function openbabel.valid(smi Text) Returns Boolean As EOPY import openbabel try ... 

Create Or Replace Function openbabel.cansmiles(smi Text) Returns Text As EOPY import openbabel obc = openbabel.OBConversion() mol = openbabel.OBMol() obc.SetlnAndOutFormats("smi", "can") if obc.Readstring(mol, smi) mol.SetTitle("")... 

---