Code Structure of OpenBabel

From Open Babel
Jump to: navigation, search

Since version 2.0 OpenBabel has had a modular structure. Version 2.1 will probably have version the shown in the diagram, which is a bit more subdivided. Particularly for the use of OpenBabel as a chemical file format converter, it aims to:

  • separate the chemistry, the conversion process and the user interfaces, reducing, as far as possible, the dependency of one on another.
  • put all the code for each chemical format in one place (usually a single cpp file) and make the addition of new formats simple.
  • allow the format conversion of not just molecules, but also any other chemical objects, such as reactions.


Structure of OpenBabel


The separate parts of the OpenBabel program are:

  • The Chemical core, which contains OBMol etc. and has all the chemical structure description and manipulation. This bit is the heart of the application and its API can be used as a chemical toolbox. It has no input/output capabilities.
  • The Formats, which read and write to files of different types. These classes are derived from a common base class, OBFormat, which is in the Conversion Control module. They also make use of the chemical routines in the Chemical Core module. Each format file contains a global object of the format class. When the format is loaded the class constructor registers the presence of the class with OBConversion. This means the formats are plugins - new formats can be added without changing any framework code.
  • Common Formats include OBMoleculeFormats and XMLBaseFormat from which most other formats (like Format A and Format B in the diagram) are derived. Independent formats like Format C are also possible.
  • The Conversion control, which also keeps track of the available formats, the conversion options and the input and output streams. It can be compiled without reference to any other parts of the program. In particular, it knows nothing of the Chemical core: mol.h is not included.
  • The User interface, which may be a command line (in main.cpp), a Graphical User Interface(GUI), especially suited to Windows users and novices, or may be part of another program which uses OpenBabel's input and output facilities. This depends only on the Conversion control module (obconversion.h is included), but not on the Chemical core or on any of the Formats.
  • The Fingerprint API, as well as being usable in external programs, is employed by the fastsearch and fingerprint formats.
  • The Fingerprints, which are bit arrays which describe an object and which facilitate fast searching. They are also built as plugins, registering themselves with their base class OBFingerprint which is in the Fingerprint API.
  • The Error handling can be used throughout the program to log and display errors and warnings.

It is possible to build each box in the diagram as a separate DLL or shared library and the restricted dependencies helps to limit the amount of recompilation. For the formats or the fingerprints built in this way it may be possible to use only those whose DLL or so files are present when the program starts. Several formats or fingerprints may be present in a single dynamic library.

Alternatively, and most commonly, the same source code can be built into a single executable. The restricted dependencies still provide easier progam maintainance.

This segregation means that a module can directly call code only in other modules connected to it by forward arrows. So some discipline is needed when adding new code, and sometimes non-obvious work-arounds are necessary. For instance, since the user interface doesn't know about the Chemical Core, if it were necessary to set any parameters in it, then this would have to be done through a pseudo format OBAPIInterface. (In version 2.0 this was also necessary for altering the warning level in the Error handling code.)

Sometimes one format needs to use code from another format, for example, rxnformat needs to read mol files with code from mdlformat. The calling format should not use the code directly but should do it through a OBConversion object configured with the appropriate helper format.

The objects passed between the modules in the diagram above are polymorphic OBBase pointers. This means that the conversion framework can be used by any object derived from OBBase (which essentially means anything - chemical or not). Most commonly these refer to OBMol objects, less commonly to OBReaction objects, but could be extended to anything else without needing to change any existing code.