Standardizer is a popular component of compound registration systems providing customizable functions for the transformations of mesomers, tautomers, salts and solvents in the molecule files and databases. New actions help to convert molecule libraries and to restore the chemical information encoded in old compound databases. For latest details see here: http://www.chemaxon.com/product/standardizer.html

1. Standardizer
canonicalization, conversion and registration
•Solutions for Cheminformatics

2. Introduction to Standardization
• Standardization is the first step of chemical
canonicalization, the conversion of functional groups
and other structural elements of molecules to a
predefined representation.
• Standardizer is a tool for the standardization of
structures, and it provides other conversion functions
as well.
• Standardizer is available in the form of a integratable
class, as a stand alone application, and integrated
with ChemAxon’s databases as well.
• Standardizer is configurable by a list of actions to
accommodate corporate standards.

3. Aromatization
Aromatize – Basic Method
Converts bonds to aromatic type according to the current resonant
form of the molecule.

4. Aromatizations
Aromatize – General Method
Converts bonds of rings having aromatic character to aromatic type
.
Dearomatize
Converts aromatic bonds to alternating single/double bonds.

5. Hydrogen Actions
Add Explicit Hydrogens
Converts implicit hydrogens to explicit ones (adds hydrogen atoms
to the graph).

6. Hydrogen Actions
Remove Explicit Hydrogens
Converts explicit hydrogens to implicit ones (removes hydrogen
atoms from the graph). Special hydrogens (isotope, charged,
radical, mapped, lonely) can be handled optionally.

7. Stereo Actions
Absolute Stereo
Sets the chiral flag if a compound has tetrahedral stereo center.
Clear Stereo
Removes stereo features.

8. Stereo Actions
Convert Wedge Interpretation
Converts an wedge between two stereo centers into two separate
wedges.
Convert Double Bonds
Converts the crossed and wiggly representations of unknown
stereo double bond

9. Clean Actions
Clean2D
Calculates the atom coordinates for two-dimensional structure
representation.

10. Clean Actions
Clean3D
Calculates the lowest energy conformer of the molecule.

11. Clean Actions
Wedge Clean
Realigns wedge bond according to the IUPAC preferences.

12. Clean Actions
Template based Cleaning
Calculates the atom coordinates using templates. It is a useful
action for the alignment of combichem libraries to the scaffold.

13. Group Actions
Ungroup
Ungroups superatoms and multiple groups irreversibly.
Expand/Contract
The superatoms and multiple groups can be opened and collapsed
with these reversible actions (the group info remains in the
structure).

14. Group Actions
Alias to Group
Converts alias and pseudo atoms to superatom groups according
to their symbols.

15. Transform Actions
Transform
The transform action provides a general interface for user defined
conversion of structural elements. Transforms are useful for the
standardization of mesomers, tautomers, salts and for the removal
of specific counterions and solvents.

16. Salt Handling Actions
Remove Fragment
Provides various options to remove small fragments like
counterions.

17. Salt Handling Actions
Neutralize
Neutralizes ionic functional groups but keeps the formal charges of
mesomers and quaternary ammonium ions.

18. Reaction Mapping Actions
Map Reactions
Assignes map numbers to the corresponding atoms of a reaction
scheme.
Unmap
Removes map numbers from the atoms of a reaction scheme.

19. Other Actions
Remove Isotopes
Converts isotopic atoms to elemental atoms.

20. Standardizer Demo

21. Future Plans
Multiprocessor support
Some complex actions will be converted to more
smaller actions to improve readability of the
configuration.
Structure checker functionality (just check, report, but
do not convert).
New actions
• Group (autocreating superatoms)
• Convert to enhanced stereo
Graphical design improvements.

22. • Thank you for your attention!
• For more information please visit
www.chemaxon.com