Standardizer



canonicalization, conversion and registration



                                       •Solutions for Che...
Introduction to Standardization
• Standardization is the first step of chemical
  canonicalization, the conversion of func...
Aromatization
Aromatize – Basic Method
Converts bonds to aromatic type according to the current resonant
form of the molec...
Aromatizations
Aromatize – General Method
Converts bonds of rings having aromatic character to aromatic type
.




Dearoma...
Hydrogen Actions
Add Explicit Hydrogens
Converts implicit hydrogens to explicit ones (adds hydrogen atoms
to the graph).
Hydrogen Actions
Remove Explicit Hydrogens
Converts explicit hydrogens to implicit ones (removes hydrogen
atoms from the g...
Stereo Actions
Absolute Stereo
Sets the chiral flag if a compound has tetrahedral stereo center.




Clear Stereo
Removes ...
Stereo Actions
Convert Wedge Interpretation
Converts an wedge between two stereo centers into two separate
wedges.




Con...
Clean Actions
Clean2D
Calculates the atom coordinates for two-dimensional structure
representation.
Clean Actions
Clean3D
Calculates the lowest energy conformer of the molecule.
Clean Actions
Wedge Clean
Realigns wedge bond according to the IUPAC preferences.
Clean Actions
Template based Cleaning
Calculates the atom coordinates using templates. It is a useful
action for the align...
Group Actions
Ungroup
Ungroups superatoms and multiple groups irreversibly.




Expand/Contract
The superatoms and multipl...
Group Actions
Alias to Group
Converts alias and pseudo atoms to superatom groups according
to their symbols.
Transform Actions
Transform
The transform action provides a general interface for user defined
conversion of structural el...
Salt Handling Actions
Remove Fragment
Provides various options to remove small fragments like
counterions.
Salt Handling Actions
Neutralize
Neutralizes ionic functional groups but keeps the formal charges of
mesomers and quaterna...
Reaction Mapping Actions
Map Reactions
Assignes map numbers to the corresponding atoms of a reaction
scheme.




Unmap
Rem...
Other Actions
Remove Isotopes
Converts isotopic atoms to elemental atoms.
Standardizer Demo
Future Plans
Multiprocessor support
Some complex actions will be converted to more
  smaller actions to improve readabilit...
• Thank you for your attention!
• For more information please visit
  www.chemaxon.com
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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 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

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

  1. 1. Standardizer canonicalization, conversion and registration •Solutions for Cheminformatics
  2. 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. 3. Aromatization Aromatize – Basic Method Converts bonds to aromatic type according to the current resonant form of the molecule.
  4. 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. 5. Hydrogen Actions Add Explicit Hydrogens Converts implicit hydrogens to explicit ones (adds hydrogen atoms to the graph).
  6. 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. 7. Stereo Actions Absolute Stereo Sets the chiral flag if a compound has tetrahedral stereo center. Clear Stereo Removes stereo features.
  8. 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. 9. Clean Actions Clean2D Calculates the atom coordinates for two-dimensional structure representation.
  10. 10. Clean Actions Clean3D Calculates the lowest energy conformer of the molecule.
  11. 11. Clean Actions Wedge Clean Realigns wedge bond according to the IUPAC preferences.
  12. 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. 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. 14. Group Actions Alias to Group Converts alias and pseudo atoms to superatom groups according to their symbols.
  15. 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. 16. Salt Handling Actions Remove Fragment Provides various options to remove small fragments like counterions.
  17. 17. Salt Handling Actions Neutralize Neutralizes ionic functional groups but keeps the formal charges of mesomers and quaternary ammonium ions.
  18. 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. 19. Other Actions Remove Isotopes Converts isotopic atoms to elemental atoms.
  20. 20. Standardizer Demo
  21. 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. 22. • Thank you for your attention! • For more information please visit www.chemaxon.com
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