OMEGA Release 2.5.1.4 OpenEye Scientific Software, Inc.

CHAPTER
TEN
FILTER PREPROCESSING
Before the applying any of the molecular property filters a preprocessing step occurs that can alter the molecule
significantly to fit the criteria needed for most modeling applications. This filtering preprocessing step is a precisely
defined series of stages that occur on the molecule in the following order:
1. Metal Removal
2. Salt Removal
3. Canonicalization
4. pKa Normalization
5. Normalization
6. Reagent Selection
7. Type Checking
10.1 Metal Removal
Metal removal is the first stage of elemental based filtering. This stage will remove specified metal complexes from
the molecule. It will not reject a molecule for having a metal complex. This allows the filter to treat atoms in the
counter-ion portion of a molecule separately from the atoms in the primary portion of the molecular record.
For instance, this allows organic molecules that are complexed with silver to be eliminated based on their metal chelate
even though they themselves are acceptable while at the same time eliminating a sulphate counter-ion from another
molecule before it leads to elimination of the acceptable cationic molecule.
See Also:
Elemental Filters
10.2 Salt Removal
This step deletes all atoms that are not part of the largest connected component of a compound. This effectively
eliminates all non-covalently bound portions of the compound.
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