The
io module deals with input and output of
entities,
multiple sequence alignments and map data. Importers for common file formats such as
PDB, SDF, FASTA, CLUSTAL W,
DX and the CHARMM files are available.
Entities are loaded via
LoadEntity() "LoadEntity()", maps with
LoadImage() and
LoadAlignment() loads seqence alignments. For all these functions the file format is automatically deduced fron the file extension, by probing against all the
IO handlers known to the
IO manager. The
PDB importer, for example is used for files with extension
.pdb and
.ent. For files with other extensions, or files without extensions, the file format may be passed explicitly as the second parameter to one of these functions.
In addition to the generic load functions described above, PDB files can be loaded with LoadPDB() and LoadMultiPDB(). These functions offer a tighter control over the exact loading behaviour.
Some of the file formats for molecules do not explicitly define bonds. The IO handlers for these file formats make use of the conop module to infer connectivity information (see Builder).
The specific logic for loading and storing data is implemented in so-called IO handlers. For sequence alignments, the basic interface for the IO handler is defined by the
SequenceIOHandler class, wheras
EntityIOHandler is the base class for entity IO handlers. In addition, the module also defines an interface for density map
io (
MapIOHandler). The IO-handler concept allows for a modular architecture and makes it possible to add support for external IO Handlers with seamless integration into the import/export API.
Adding a new IO handler is fairly straight forward:
- Subclass the appropriate IO Handler (one of EntityIOHandler, MapIOHandler, SequenceIOHandler).
- Define a factory class for your io handler.
- Overload the import and/or export method.
- Register the IO handler by calling the appropriate RegisterFactory method on the IOManager singleton instance.
