Pattern matching in OEChem is always done using query molecules or
query graphs. Non-query molecules, i.e. those that are derived
directly from OEMolBase or OEMCMolBase, must be
converted into a query molecule. Conversion into a query molecule is
controlled using the values in the OEExprOpts namespace. Expression
options can either be specified in the constructor for an
OEQMol, or using the convenience constructors in pattern
matching classes (OESubSearch, OEMCSSearch, and
OECliqueSearch) which take expression options as as arguments.
For a full description of expression options and their use please
refer to the OEExprOpts namespace section in the OEChem namespaces of
the OEChem C++ API document.