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| OEChem - C++ Theory Manual
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Reaction processing in OEChem is divided into two categories:
unimolecular reactions and library generation. Unimolecular reactions
are useful for (although not limited to) normalization reactions. The
OEUniMolecularRxn class in OEChem applies chemical
transformations to individual molecules. Reactions can also be used
to generate combinatorial libraries using OEChem. Both 'clipping' and
reaction based enumeration can be achieved using the
OELibraryGen class.
Reactions are represented in OEChem as query molecules
(OEQMolBase). Sets of chemical transform operations are
derived from reaction molecules by differences between the reactant
and product patterns and in the reaction molecule. For example, atoms
and bonds that appear in the reactant pattern, but are absent the in
the product pattern are 'destroyed'. Atoms and bonds that appear in
the product pattern but not in the reactant pattern are 'created'.
Atoms are tracked between reactants and products by means atom maps.
Atom maps are stored and retrieved using the
OEAtomBase::SetMapIdx and OEAtomBase::GetMapIdx methods.
Product atoms that have the same map index as reactant atoms originate
from their reactant counterpart. Reactions are completely defined by
a fields in a query molecule. Reaction molecules can be created from
virtually any reaction file format (SMIRKS, MDL RXN, etc.), and can
even be constructed programmatically.
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