The OEMDLQueryOpts namespace encodes symbolic constants used as bit-masks to indicate how to interpret MDL query files or MDL reaction imported by OEReadMDLQueryFile and OEReadMDLReactionQueryFile functions, respectively.

This namespace contains the following constants:


Only constraints explicitly specified in the MDL file are added to the OEQMolBase query structure with the the OEMDLQueryOpts.Optimize option.


Controls how the explicit hydrogens of the query are matched to the explicit/implicit hydrogens of the target structures.

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Controls whether or not map an aliphatic query bond only to aliphatic bonds in the target structure during the substructure search.

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By default, a bond that is part of any ring system in the query structure can only be mapped to ring bonds in the target structure. The OEMDLQueryOpts.AddBondTopologyConstraint option controls whether or not map a chain query bond only to chain bonds in the target structure during the substructures search.

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By default, Rgroup atoms and *atoms (OEElemNo.Du) match like an “any”-atom - matching atoms of any type for both SMARTS and MDL queries. Adding this non-default option flag will force *atoms that are neither pseudoatoms nor Rgroup atoms to match only explicit *atoms in the target.

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By default, atom stereo information is not considered when building query molecules, allowing unconditional match between any atom configuration.

When the OEMDLQueryOpts.MatchAtomStereo option is turned on, an S/R atom stereo configuration in the query will match only to any S/R configuration in the target molecule, but not to a R/S (opposite) or an unspecified one. If an atom stereo configuration is undefined in the query, it can match to any atom regardless to its stereo configuration.

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By default, the isotopic information (i.e. lines starting with M ISO in the MDL query file) is ignored.

When the OEMDLQueryOpts.MatchIsotope option is turned on, a query isotope atoms can be match to a target atom only if it has the same atomic mass. If the query atom has no specified isotope number, it will still match to any target atom regardless of its atomic mass.

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When the OEMDLQueryOpts.Optimize option is turned on, the atom and bond expressions are optimized for substructure search.


MDL reaction files are interpreted differently from MDL query files. The usage of OEMDLQueryOpts.ReactionQuery option is necessary when a MDL reaction is imported with the OEReadMDLReactionQueryFile function.

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