Difference between revisions of "HowTo:Add A New File Format"

From Open Babel
Jump to: navigation, search
Line 2: Line 2:
  
 
# Create a file for your format in <code>src/formats/</code> or <code>src/formats/xml/</code> (for XML-based formats). Ideally, this file is self-contained, although several formats modules are compiled across multiple source code files.
 
# Create a file for your format in <code>src/formats/</code> or <code>src/formats/xml/</code> (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 <code>exampleformat.cpp</code>, which contains a heavily-annotated description of writing a new format.
+
# Take a look at other file format code, particularly <code>exampleformat.cpp</code>, which contains a heavily-annotated description of writing a new format. XML formats need to take a different approach; see the code in <code>xcmlformat.cpp</code> or <code>pubchemformat.cpp</code>.
 
# When reading in molecules (and thus performing a lot of molecular modifications) call <code>OBMol::BeginModify()</code> at the beginning and <code>OBMol::EndModify()</code> 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.
 
# When reading in molecules (and thus performing a lot of molecular modifications) call <code>OBMol::BeginModify()</code> at the beginning and <code>OBMol::EndModify()</code> 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 <code>OBMol::ConnectTheDots()</code> and <code>OBMol::PerceiveBondOrders()</code> after <code>OBMol::EndModify()</code> to ensure bonds are assigned.
 
# Currently, lazy perception does not include connectivity and bond order assignment. If your format does not include bonds, make sure to call <code>OBMol::ConnectTheDots()</code> and <code>OBMol::PerceiveBondOrders()</code> after <code>OBMol::EndModify()</code> to ensure bonds are assigned.

Revision as of 00:54, 6 December 2005

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.

  1. Create a file for your format in src/formats/ or src/formats/xml/ (for XML-based formats). Ideally, this file is self-contained, although several formats modules are compiled across multiple source code files.
  2. 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 xcmlformat.cpp or pubchemformat.cpp.
  3. 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.
  4. Currently, lazy perception does not include connectivity and bond order assignment. If your format does not include bonds, make sure to call OBMol::ConnectTheDots() and OBMol::PerceiveBondOrders() after OBMol::EndModify() to ensure bonds are assigned.
  5. 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):
    • -as Call only OBMol::ConnectTheDots() (single bonds only)
    • -ab No bond perception
  6. Make sure to use generic data classes like OBUnitCell and others as appropriate. If your format stores any sort of common data types, consider adding a subclass of OBGenericData for use by other formats and user code.
  7. 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.
  8. That's it! Contact the openbabel-discuss mailing list with any questions, comments, or to contribute your new format code.
Retrieved from "http:///en/w/index.php?title=HowTo:Add_A_New_File_Format&oldid=1372"