HowTo:Add A New File Format
From Open Babel
Revision as of 17:06, 7 February 2006 by Ghutchis (Added mention of valid and invalid format examples.)
Adding support for a new file format is a relatively easy process, particularly with Open Babel 2.0 and later. This guide outlines several important steps to remember when developing a format translator.
- Create a file for your format in
src/formats/xml/(for XML-based formats). Ideally, this file is self-contained, although several formats modules are compiled across multiple source code files.
- Take a look at other file format code, particularly
exampleformat.cpp, which contains a heavily-annotated description of writing a new format. XML formats need to take a different approach; see the code in
- When reading in molecules (and thus performing a lot of molecular modifications) call
OBMol::BeginModify()at the beginning and
OBMol::EndModify()at the end. This will ensure that perception routines do not run while you read in a molecule and are reset after your code finishes.
- Currently, lazy perception does not include connectivity and bond order assignment. If your format does not include bonds, make sure to call
OBMol::EndModify()to ensure bonds are assigned.
- Consider various input and output options that users can set from the command-line or GUI. For example, many quantum mechanics or other formats which do not recognize bonds, offer the following options (GUI programs often offer these as a sub-menu which appears when choosing the appropriate format):
OBMol::ConnectTheDots()(single bonds only)
-abNo bond perception
- Make sure to use generic data classes like
OBUnitCelland others as appropriate. If your format stores any sort of common data types, consider adding a subclass of
OBGenericDatafor use by other formats and user code.
- Please make sure to add several example files to the test set repository. Ideally, these should work several areas of your import code -- in the end, the more robust the test set, the more stable and useful Open Babel will be. The test files should include at least one example of a correct file and one example of an invalid file (i.e., something which will properly be ignored and not crash babel).
- That's it! Contact the openbabel-discuss mailing list with any questions, comments, or to contribute your new format code.