Standardizer, canonicalization and chemical business rules for structure database handling: US UGM 2008

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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 …

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:

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  • 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