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Compounds that contain unspecified or ambiguous definitions of stereochemistry may be preprocessed before generating conformers to add explicitly specify stereochemistry. Input molecules that have three dimensional coordinates inherently have stereochemistry specified, but SMILES or two dimensional SD files may have atoms (R/S) or bonds (E/Z) for which the stereochemistry is unknown or unspecified. Omega will generate structures for compounds of unknown configuration, however, in virtual screening exercises it may be beneficial to simply enumerate possible stereoisomers and treat each stereoisomer as a separate compound.
Omega distributions contain a utility called flipper that enumerates
unspecified stereochemistry within user defined limits. For an
explanation of how to use flipper, consult Section 5.
Stereochemistry enumeration is an exponential task. For every atom or
bond (N) in a molecule that has two possible stereochemical 'states',
there are 
possible stereoisomers for the molecule. Enumerating
all possible stereiosomers for molecules may be unreasonable in terms
of CPU time or storage space. flipper has user defined limits to
regulate the enumeration process and keep it practical for routine
applications.
Enumerating stereoisomers provides an information gain that may aid in
operations downstream from conformer generation. flipper, or a
similar stereochemistry enumeration tool should be used prior to
generating conformers with Omega.
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