This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.
The OESubSearchScreen objects are typed bit-vectors. The type of a screen determines what kind of queries in mind the screen was designed.
In OEChem TK, a query molecule (OEQMolBase) can be constructed in three different ways.
query read from MDL query file
query built from molecule
query built from SMARTS pattern
The expression trees of the queries that are initialized from different sources
can be significantly different.
For example, the “language” of SMARTS is the most expressive one allowing
complex logical operations and recursive patterns.
A SMARTS such as
[NX3;H2,H1;!$(NC=O)] (primary or secondary amine that is not in amide)
defines a substructure that can not be expressed using MDL query features.
This also makes queries built from SMARTS the most complex ones.
The other major difference between SMARTS and MDL queries is the way how they
are expected to match aromaticity. For these reasons, OEChem TK provides three
different screen types especially designed for the three different ways that are
available to built query molecules using OEChem TK.
For performance reason, OEChem TK does not support screening-based fast substructure
search with explicit hydrogens.
OEMakeSubSearchTargetScreen function automatically suppresses explicit
hydrogens of the molecule prior to the screen generation.
OEMakeSubSearchQueryScreen function will return
false if the query
molecule has any explicit hydrogen expression.
The default screen type is
It is highly recommended to use the
OEExprOpts.DefaultBondsoptions when building the query molecule with the
BuildExpressions. When using other option combinations, the built query molecule might not be suitable for the
If the input molecule has any explicit hydrogens, the
OESuppressHydrogensfunction should be called prior to calling
In case of a query molecule of unknown source, the
OEIsComplementaryScreenType function can be used to check
whether the query molecule is suited for a specific screen type.