standardizer, canonicalization and chemical business rules for structure database handling: us ugm...

•Solutions for Cheminformatics

Standardizer

canonicalization, conversion and registration

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.

Aromatization

Aromatize – Basic MethodConverts bonds to aromatic type according to the current resonant form of the molecule.

Aromatizations

Aromatize – General MethodConverts bonds of rings having aromatic character to aromatic type .

DearomatizeConverts aromatic bonds to alternating single/double bonds.

Hydrogen Actions

Add Explicit HydrogensConverts implicit hydrogens to explicit ones (adds hydrogen atoms to the graph).

Hydrogen Actions

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

Stereo Actions

Absolute StereoSets the chiral flag if a compound has tetrahedral stereo center.

Clear StereoRemoves stereo features.

Stereo Actions

Convert Wedge InterpretationConverts an wedge between two stereo centers into two separate wedges.

Convert Double BondsConverts the crossed and wiggly representations of unknown stereo double bond

Clean Actions

Clean2DCalculates the atom coordinates for two-dimensional structure representation.

Clean Actions

Clean3DCalculates the lowest energy conformer of the molecule.

Clean Actions

Wedge CleanRealigns wedge bond according to the IUPAC preferences.

Clean Actions

Template based CleaningCalculates the atom coordinates using templates. It is a useful action for the alignment of combichem libraries to the scaffold.

Group Actions

UngroupUngroups superatoms and multiple groups irreversibly.

Expand/ContractThe superatoms and multiple groups can be opened and collapsed with these reversible actions (the group info remains in the structure).

Group Actions

Alias to GroupConverts alias and pseudo atoms to superatom groups according to their symbols.

Transform Actions

TransformThe 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.

Salt Handling Actions

Remove FragmentProvides various options to remove small fragments like counterions.

Salt Handling Actions

NeutralizeNeutralizes ionic functional groups but keeps the formal charges of mesomers and quaternary ammonium ions.

Reaction Mapping Actions

Map ReactionsAssignes map numbers to the corresponding atoms of a reaction scheme.

UnmapRemoves map numbers from the atoms of a reaction scheme.

Other Actions

Remove IsotopesConverts isotopic atoms to elemental atoms.

Standardizer Demo

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.

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