2.1 Introduction
Babel should not really need a theory manual. The relevant theory
is OEChem theory. However, a few points are worth noting.
- OEChem adheres to format specifications insofar as they are defined by
authoritative documentation.
- Format variants are generally handled by "flavors".
- In some cases de facto format variants exist by virtue of their
general usage, which OEChem may support when not in conflict with
the defined format (e.g. MOL2 files with absent hydrogens).
- Different formats not only differ in their encoding, but also
differ in the information represented, e.g., the molecular representation.
Where source information is absent, use of the term "conversion" is a
something of a stretch, as information must be inferred (e.g.,
bonds from PDB files). Thus, is not always possible to guarantee correct
output for all conversions, when correctness is defined by information
not strictly contained in the data source.
- OEChem is specifically designed to handle and interconvert the
different chemical models intrinsic to certain formats, for example,
the varying aromaticity models of Tripos, MDL, and Daylight.
